Starting phenix.real_space_refine on Fri Jul 3 04:56:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ds9_27686/07_2026/8ds9_27686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ds9_27686/07_2026/8ds9_27686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ds9_27686/07_2026/8ds9_27686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ds9_27686/07_2026/8ds9_27686.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ds9_27686/07_2026/8ds9_27686.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ds9_27686/07_2026/8ds9_27686.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ds9_27686/07_2026/8ds9_27686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ds9_27686/07_2026/8ds9_27686.map" } resolution = 3.17 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= -0.001 sd= 0.064 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 97 5.16 5 C 8030 2.51 5 N 1877 2.21 5 O 2033 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12039 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1662 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 2 Chain: "B" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1662 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 2 Chain: "C" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2685 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 9, 'TRANS': 310} Chain breaks: 2 Chain: "D" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2646 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1662 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 2 Chain: "F" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1599 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 3, 'TRANS': 187} Chain breaks: 2 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.88, per 1000 atoms: 0.24 Number of scatterers: 12039 At special positions: 0 Unit cell: (105.848, 98.512, 137.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 97 16.00 P 2 15.00 O 2033 8.00 N 1877 7.00 C 8030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.02 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.02 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " 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 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 525.2 milliseconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 73.0% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 141 removed outlier: 3.538A pdb=" N LYS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 259 through 287 removed outlier: 4.844A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 345 Processing helix chain 'B' and resid 15 through 21 removed outlier: 4.205A pdb=" N ARG B 18 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 50 removed outlier: 3.793A pdb=" N ASP B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 119 through 141 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.781A pdb=" N LYS B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 286 removed outlier: 3.849A pdb=" N TYR B 285 " --> pdb=" O TYR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 345 removed outlier: 3.632A pdb=" N PHE B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.985A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 117 removed outlier: 3.519A pdb=" N ARG C 117 " --> pdb=" O CYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 141 Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.635A pdb=" N LYS C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 166 removed outlier: 3.928A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 175 removed outlier: 4.417A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 256 removed outlier: 4.104A pdb=" N GLU C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 315 through 346 removed outlier: 3.542A pdb=" N ALA C 322 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG C 346 " --> pdb=" O TRP C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 369 through 383 Processing helix chain 'C' and resid 383 through 395 removed outlier: 4.494A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 411 Processing helix chain 'D' and resid 17 through 21 Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.548A pdb=" N ASN D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 146 removed outlier: 3.547A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 4.828A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.149A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 175 removed outlier: 4.161A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 256 removed outlier: 4.063A pdb=" N GLU D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 287 removed outlier: 4.804A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 346 removed outlier: 3.905A pdb=" N ARG D 346 " --> pdb=" O TRP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 369 through 383 Processing helix chain 'D' and resid 383 through 391 removed outlier: 4.095A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 395 through 407 Processing helix chain 'E' and resid 22 through 50 removed outlier: 3.791A pdb=" N ASP E 50 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 124 through 141 Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.742A pdb=" N LYS E 145 " --> pdb=" O ASN E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 315 through 344 Processing helix chain 'F' and resid 22 through 48 removed outlier: 3.551A pdb=" N VAL F 26 " --> pdb=" O PRO F 22 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 Processing helix chain 'F' and resid 121 through 143 Proline residue: F 128 - end of helix removed outlier: 4.163A pdb=" N ASN F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 284 Processing helix chain 'F' and resid 285 through 287 No H-bonds generated for 'chain 'F' and resid 285 through 287' Processing helix chain 'F' and resid 312 through 344 removed outlier: 4.263A pdb=" N ARG F 344 " --> pdb=" O TRP F 340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.879A pdb=" N LEU A 55 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.701A pdb=" N LEU B 55 " --> pdb=" O ARG B 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'E' and resid 292 through 296 Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 56 806 hydrogen bonds defined for protein. 2379 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2565 1.33 - 1.46: 3178 1.46 - 1.58: 6500 1.58 - 1.70: 2 1.70 - 1.82: 140 Bond restraints: 12385 Sorted by residual: bond pdb=" C10 PEE C 902 " pdb=" O4 PEE C 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C10 PEE C 901 " pdb=" O4 PEE C 901 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" O4P PEE D 902 " pdb=" P PEE D 902 " ideal model delta sigma weight residual 1.653 1.777 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" O4P PEE D 901 " pdb=" P PEE D 901 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C10 PEE C 902 " pdb=" O2 PEE C 902 " ideal model delta sigma weight residual 1.332 1.215 0.117 2.00e-02 2.50e+03 3.41e+01 ... (remaining 12380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 16543 2.77 - 5.54: 189 5.54 - 8.31: 32 8.31 - 11.08: 5 11.08 - 13.85: 4 Bond angle restraints: 16773 Sorted by residual: angle pdb=" O1P PEE D 902 " pdb=" P PEE D 902 " pdb=" O2P PEE D 902 " ideal model delta sigma weight residual 119.43 133.28 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE D 901 " pdb=" P PEE D 901 " pdb=" O2P PEE D 901 " ideal model delta sigma weight residual 119.43 133.19 -13.76 3.00e+00 1.11e-01 2.10e+01 angle pdb=" C11 PEE C 901 " pdb=" C10 PEE C 901 " pdb=" O2 PEE C 901 " ideal model delta sigma weight residual 111.70 124.69 -12.99 3.00e+00 1.11e-01 1.87e+01 angle pdb=" C11 PEE C 902 " pdb=" C10 PEE C 902 " pdb=" O2 PEE C 902 " ideal model delta sigma weight residual 111.70 124.67 -12.97 3.00e+00 1.11e-01 1.87e+01 angle pdb=" CA GLU C 245 " pdb=" CB GLU C 245 " pdb=" CG GLU C 245 " ideal model delta sigma weight residual 114.10 121.71 -7.61 2.00e+00 2.50e-01 1.45e+01 ... (remaining 16768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.75: 6951 34.75 - 69.50: 251 69.50 - 104.25: 12 104.25 - 139.00: 2 139.00 - 173.75: 2 Dihedral angle restraints: 7218 sinusoidal: 2951 harmonic: 4267 Sorted by residual: dihedral pdb=" CB CYS D 113 " pdb=" SG CYS D 113 " pdb=" SG CYS D 295 " pdb=" CB CYS D 295 " ideal model delta sinusoidal sigma weight residual 93.00 37.93 55.07 1 1.00e+01 1.00e-02 4.10e+01 dihedral pdb=" CA GLU A 115 " pdb=" C GLU A 115 " pdb=" N ASN A 116 " pdb=" CA ASN A 116 " ideal model delta harmonic sigma weight residual -180.00 -156.01 -23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" N PEE D 902 " pdb=" C4 PEE D 902 " pdb=" C5 PEE D 902 " pdb=" O4P PEE D 902 " ideal model delta sinusoidal sigma weight residual -56.97 116.78 -173.75 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 7215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1724 0.085 - 0.171: 117 0.171 - 0.256: 3 0.256 - 0.341: 0 0.341 - 0.426: 2 Chirality restraints: 1846 Sorted by residual: chirality pdb=" C2 PEE D 902 " pdb=" C1 PEE D 902 " pdb=" C3 PEE D 902 " pdb=" O2 PEE D 902 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" C2 PEE D 901 " pdb=" C1 PEE D 901 " pdb=" C3 PEE D 901 " pdb=" O2 PEE D 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CB VAL F 263 " pdb=" CA VAL F 263 " pdb=" CG1 VAL F 263 " pdb=" CG2 VAL F 263 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1843 not shown) Planarity restraints: 1985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 23 " 0.019 2.00e-02 2.50e+03 2.17e-02 1.18e+01 pdb=" CG TRP A 23 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A 23 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 23 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 23 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 23 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 23 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 23 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 120 " 0.021 2.00e-02 2.50e+03 2.00e-02 9.99e+00 pdb=" CG TRP D 120 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP D 120 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP D 120 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 120 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 120 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 120 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 120 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 120 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 120 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 143 " -0.022 2.00e-02 2.50e+03 1.94e-02 9.44e+00 pdb=" CG TRP A 143 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 143 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 143 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 143 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 143 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 143 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 143 " 0.001 2.00e-02 2.50e+03 ... (remaining 1982 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 835 2.74 - 3.28: 12354 3.28 - 3.82: 20773 3.82 - 4.36: 23360 4.36 - 4.90: 40918 Nonbonded interactions: 98240 Sorted by model distance: nonbonded pdb=" OD2 ASP A 50 " pdb=" OH TYR A 114 " model vdw 2.201 3.040 nonbonded pdb=" O ILE C 356 " pdb=" OG SER C 360 " model vdw 2.206 3.040 nonbonded pdb=" O THR E 44 " pdb=" OG1 THR E 48 " model vdw 2.221 3.040 nonbonded pdb=" OD2 ASP E 110 " pdb=" NE2 GLN F 106 " model vdw 2.251 3.120 nonbonded pdb=" OG1 THR C 316 " pdb=" OE2 GLU D 115 " model vdw 2.265 3.040 ... (remaining 98235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 15 through 407 or resid 901 through 902)) selection = (chain 'D' and (resid 15 through 407 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O2 \ or name O4 )) or (resid 902 and (name C10 or name C11 or name C12 or name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name O2 \ or name O4 )))) } 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: 5.870 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.350 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 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 : 0.005 0.151 12402 Z= 0.266 Angle : 0.807 13.851 16807 Z= 0.440 Chirality : 0.047 0.426 1846 Planarity : 0.006 0.054 1985 Dihedral : 17.196 173.749 4413 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.53 % Allowed : 23.59 % Favored : 75.88 % 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: 0.06 (0.22), residues: 1382 helix: 0.52 (0.16), residues: 962 sheet: 0.25 (0.54), residues: 102 loop : -1.23 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 345 TYR 0.031 0.002 TYR E 325 PHE 0.039 0.002 PHE C 390 TRP 0.058 0.002 TRP A 23 HIS 0.023 0.002 HIS E 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.27 (12385) covalent geometry : angle 0.80545 / 0.44 (16773) SS BOND : bond 0.00319 / 0.20 ( 17) SS BOND : angle 1.25539 / 0.81 ( 34) hydrogen bonds : bond 0.13389 / 9.07 ( 806) hydrogen bonds : angle 6.19165 / 4.41 ( 2379) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 225 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 231 average time/residue: 0.1146 time to fit residues: 38.2980 Evaluate side-chains 211 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 206 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain C residue 253 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN C 404 GLN D 105 GLN ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.228197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.186451 restraints weight = 15759.667| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 2.87 r_work: 0.4125 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12402 Z= 0.138 Angle : 0.521 6.972 16807 Z= 0.282 Chirality : 0.040 0.171 1846 Planarity : 0.004 0.046 1985 Dihedral : 8.901 152.265 1660 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.41 % Allowed : 20.40 % Favored : 75.19 % 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: 1.11 (0.22), residues: 1382 helix: 1.45 (0.16), residues: 970 sheet: 0.42 (0.53), residues: 107 loop : -1.41 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 389 TYR 0.025 0.001 TYR D 284 PHE 0.022 0.002 PHE D 390 TRP 0.025 0.002 TRP A 23 HIS 0.009 0.001 HIS E 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (12385) covalent geometry : angle 0.51963 / 0.28 (16773) SS BOND : bond 0.00295 / 0.19 ( 17) SS BOND : angle 0.85593 / 0.55 ( 34) hydrogen bonds : bond 0.04103 / 2.72 ( 806) hydrogen bonds : angle 4.38114 / 3.14 ( 2379) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 233 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.3905 (mtmt) cc_final: 0.3287 (tppp) REVERT: B 46 GLN cc_start: 0.7358 (tm-30) cc_final: 0.7133 (tm-30) REVERT: B 98 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7896 (mmmt) REVERT: B 117 ARG cc_start: 0.7423 (mmm160) cc_final: 0.6741 (tpt90) REVERT: B 275 PHE cc_start: 0.6130 (OUTLIER) cc_final: 0.5462 (t80) REVERT: B 336 CYS cc_start: 0.6047 (m) cc_final: 0.5443 (t) REVERT: C 46 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7313 (tm-30) REVERT: C 47 VAL cc_start: 0.8800 (t) cc_final: 0.8342 (t) REVERT: C 49 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7911 (mm110) REVERT: C 108 TYR cc_start: 0.7269 (t80) cc_final: 0.6940 (t80) REVERT: C 275 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7463 (t80) REVERT: C 404 GLN cc_start: 0.7661 (tp-100) cc_final: 0.7450 (tp40) REVERT: D 305 TYR cc_start: 0.8502 (m-80) cc_final: 0.8017 (m-80) REVERT: D 324 PHE cc_start: 0.6721 (t80) cc_final: 0.6515 (t80) REVERT: D 390 PHE cc_start: 0.7491 (t80) cc_final: 0.7280 (t80) REVERT: E 299 ILE cc_start: 0.3626 (OUTLIER) cc_final: 0.2436 (pt) REVERT: E 314 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6447 (pp) REVERT: E 343 MET cc_start: 0.2274 (OUTLIER) cc_final: 0.2000 (mtt) REVERT: F 288 GLN cc_start: 0.7107 (mm110) cc_final: 0.6849 (mm110) outliers start: 58 outliers final: 29 residues processed: 276 average time/residue: 0.1059 time to fit residues: 43.1982 Evaluate side-chains 243 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 250 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 104 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.226537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.184906 restraints weight = 16027.443| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 2.90 r_work: 0.4116 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12402 Z= 0.140 Angle : 0.509 6.100 16807 Z= 0.276 Chirality : 0.040 0.144 1846 Planarity : 0.003 0.042 1985 Dihedral : 7.977 130.252 1656 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.79 % Allowed : 21.61 % Favored : 73.59 % 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: 1.34 (0.22), residues: 1382 helix: 1.67 (0.16), residues: 965 sheet: 0.46 (0.53), residues: 107 loop : -1.42 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 389 TYR 0.028 0.001 TYR D 284 PHE 0.023 0.002 PHE B 27 TRP 0.020 0.001 TRP B 23 HIS 0.007 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (12385) covalent geometry : angle 0.50770 / 0.28 (16773) SS BOND : bond 0.00349 / 0.23 ( 17) SS BOND : angle 0.91813 / 0.60 ( 34) hydrogen bonds : bond 0.03947 / 2.61 ( 806) hydrogen bonds : angle 4.26047 / 3.05 ( 2379) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 225 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 PHE cc_start: 0.5076 (OUTLIER) cc_final: 0.4768 (m-10) REVERT: A 319 LYS cc_start: 0.4002 (mtmt) cc_final: 0.3302 (tppp) REVERT: B 46 GLN cc_start: 0.7421 (tm-30) cc_final: 0.7146 (tm-30) REVERT: B 98 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7939 (mmmt) REVERT: B 130 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7090 (tp) REVERT: B 275 PHE cc_start: 0.6117 (OUTLIER) cc_final: 0.5412 (t80) REVERT: B 336 CYS cc_start: 0.6244 (m) cc_final: 0.5556 (t) REVERT: C 46 GLN cc_start: 0.7606 (tm-30) cc_final: 0.7317 (tm-30) REVERT: C 47 VAL cc_start: 0.8755 (t) cc_final: 0.8268 (t) REVERT: C 49 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7963 (mm110) REVERT: C 104 HIS cc_start: 0.7511 (OUTLIER) cc_final: 0.6702 (t70) REVERT: C 275 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7459 (t80) REVERT: D 305 TYR cc_start: 0.8547 (m-80) cc_final: 0.8096 (m-80) REVERT: E 314 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6376 (pp) REVERT: E 343 MET cc_start: 0.2840 (OUTLIER) cc_final: 0.2574 (mtt) REVERT: F 288 GLN cc_start: 0.7221 (mm110) cc_final: 0.6948 (mm110) outliers start: 63 outliers final: 36 residues processed: 274 average time/residue: 0.1030 time to fit residues: 42.1823 Evaluate side-chains 257 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 123 optimal weight: 0.0050 chunk 114 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 97 optimal weight: 0.0670 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.227478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.186229 restraints weight = 15628.002| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.40 r_work: 0.4156 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12402 Z= 0.114 Angle : 0.481 5.986 16807 Z= 0.262 Chirality : 0.038 0.133 1846 Planarity : 0.003 0.043 1985 Dihedral : 7.201 91.966 1656 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.49 % Allowed : 21.54 % Favored : 73.97 % 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: 1.63 (0.23), residues: 1382 helix: 1.88 (0.16), residues: 957 sheet: 0.46 (0.52), residues: 107 loop : -1.16 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 306 TYR 0.025 0.001 TYR D 284 PHE 0.024 0.001 PHE E 331 TRP 0.023 0.001 TRP B 23 HIS 0.003 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (12385) covalent geometry : angle 0.48027 / 0.26 (16773) SS BOND : bond 0.00224 / 0.15 ( 17) SS BOND : angle 0.75628 / 0.49 ( 34) hydrogen bonds : bond 0.03633 / 2.41 ( 806) hydrogen bonds : angle 4.09208 / 2.94 ( 2379) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.4098 (mtmt) cc_final: 0.3355 (tppp) REVERT: B 33 ILE cc_start: 0.7024 (mp) cc_final: 0.6711 (tp) REVERT: B 46 GLN cc_start: 0.7345 (tm-30) cc_final: 0.7123 (tm-30) REVERT: B 130 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7090 (tp) REVERT: B 275 PHE cc_start: 0.6098 (OUTLIER) cc_final: 0.5271 (t80) REVERT: B 336 CYS cc_start: 0.6304 (m) cc_final: 0.5570 (t) REVERT: C 46 GLN cc_start: 0.7577 (tm-30) cc_final: 0.7170 (tm-30) REVERT: C 49 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7844 (mm110) REVERT: C 104 HIS cc_start: 0.7437 (OUTLIER) cc_final: 0.6482 (t70) REVERT: C 127 TYR cc_start: 0.8508 (m-80) cc_final: 0.8191 (m-80) REVERT: C 145 LYS cc_start: 0.8553 (mmtp) cc_final: 0.8348 (mmtp) REVERT: C 275 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7453 (t80) REVERT: C 392 VAL cc_start: 0.8202 (p) cc_final: 0.7952 (m) REVERT: D 305 TYR cc_start: 0.8468 (m-80) cc_final: 0.8152 (m-80) REVERT: E 17 TYR cc_start: 0.4375 (OUTLIER) cc_final: 0.3700 (m-80) REVERT: E 299 ILE cc_start: 0.3556 (OUTLIER) cc_final: 0.2456 (pt) REVERT: E 314 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6223 (pp) REVERT: E 343 MET cc_start: 0.3766 (OUTLIER) cc_final: 0.3543 (mtt) REVERT: F 288 GLN cc_start: 0.7107 (mm110) cc_final: 0.6818 (mm110) outliers start: 59 outliers final: 40 residues processed: 271 average time/residue: 0.1015 time to fit residues: 41.0032 Evaluate side-chains 258 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 210 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 312 HIS D 105 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.223374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.180627 restraints weight = 15758.993| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.53 r_work: 0.4091 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12402 Z= 0.168 Angle : 0.543 6.177 16807 Z= 0.294 Chirality : 0.041 0.139 1846 Planarity : 0.004 0.040 1985 Dihedral : 6.816 72.442 1654 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.87 % Allowed : 22.68 % Favored : 72.45 % 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 (0.22), residues: 1382 helix: 1.69 (0.16), residues: 973 sheet: 0.40 (0.52), residues: 107 loop : -1.41 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 306 TYR 0.026 0.002 TYR D 284 PHE 0.024 0.002 PHE E 331 TRP 0.023 0.002 TRP D 120 HIS 0.004 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (12385) covalent geometry : angle 0.54072 / 0.29 (16773) SS BOND : bond 0.00467 / 0.31 ( 17) SS BOND : angle 1.30172 / 0.85 ( 34) hydrogen bonds : bond 0.03943 / 2.59 ( 806) hydrogen bonds : angle 4.22134 / 3.02 ( 2379) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 230 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.4441 (mtmt) cc_final: 0.3490 (tppp) REVERT: B 46 GLN cc_start: 0.7338 (tm-30) cc_final: 0.7057 (tm-30) REVERT: B 117 ARG cc_start: 0.7451 (mmm160) cc_final: 0.7192 (mmm160) REVERT: B 130 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7042 (tp) REVERT: B 275 PHE cc_start: 0.6136 (OUTLIER) cc_final: 0.5230 (t80) REVERT: C 47 VAL cc_start: 0.8831 (t) cc_final: 0.8619 (t) REVERT: C 49 GLN cc_start: 0.8324 (mm-40) cc_final: 0.7922 (mm110) REVERT: C 104 HIS cc_start: 0.7527 (OUTLIER) cc_final: 0.6644 (t70) REVERT: C 145 LYS cc_start: 0.8645 (mmtp) cc_final: 0.8439 (mmtp) REVERT: C 275 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7512 (t80) REVERT: D 305 TYR cc_start: 0.8566 (m-80) cc_final: 0.8254 (m-80) REVERT: E 17 TYR cc_start: 0.4483 (OUTLIER) cc_final: 0.3735 (m-80) REVERT: E 114 TYR cc_start: 0.7134 (t80) cc_final: 0.6928 (t80) REVERT: E 265 MET cc_start: 0.5747 (tpt) cc_final: 0.5330 (mmt) REVERT: E 290 LYS cc_start: 0.4496 (tptp) cc_final: 0.4226 (tptp) REVERT: E 299 ILE cc_start: 0.3603 (OUTLIER) cc_final: 0.2352 (pt) REVERT: E 314 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6342 (pp) REVERT: E 343 MET cc_start: 0.4153 (OUTLIER) cc_final: 0.3933 (mtt) REVERT: F 288 GLN cc_start: 0.7134 (mm110) cc_final: 0.6818 (mm110) outliers start: 64 outliers final: 44 residues processed: 280 average time/residue: 0.1010 time to fit residues: 42.3910 Evaluate side-chains 265 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 213 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 42 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.225653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.187766 restraints weight = 15935.172| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 2.51 r_work: 0.4168 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12402 Z= 0.158 Angle : 0.534 6.428 16807 Z= 0.290 Chirality : 0.040 0.154 1846 Planarity : 0.003 0.041 1985 Dihedral : 6.676 68.637 1654 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.10 % Allowed : 23.36 % Favored : 71.54 % 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 (0.22), residues: 1382 helix: 1.70 (0.16), residues: 972 sheet: 0.32 (0.51), residues: 107 loop : -1.46 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 306 TYR 0.024 0.001 TYR B 325 PHE 0.022 0.002 PHE B 27 TRP 0.027 0.001 TRP D 120 HIS 0.004 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (12385) covalent geometry : angle 0.53289 / 0.29 (16773) SS BOND : bond 0.00423 / 0.28 ( 17) SS BOND : angle 1.06159 / 0.69 ( 34) hydrogen bonds : bond 0.03875 / 2.56 ( 806) hydrogen bonds : angle 4.21944 / 3.01 ( 2379) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 218 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.4376 (mtmt) cc_final: 0.3522 (tppp) REVERT: B 27 PHE cc_start: 0.4446 (m-10) cc_final: 0.4190 (m-10) REVERT: B 117 ARG cc_start: 0.7420 (mmm160) cc_final: 0.7202 (mmm160) REVERT: B 130 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7044 (tp) REVERT: B 275 PHE cc_start: 0.6113 (OUTLIER) cc_final: 0.5140 (t80) REVERT: C 47 VAL cc_start: 0.8815 (t) cc_final: 0.8594 (t) REVERT: C 49 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7941 (mm110) REVERT: C 104 HIS cc_start: 0.7547 (OUTLIER) cc_final: 0.6547 (t70) REVERT: C 275 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7468 (t80) REVERT: C 337 MET cc_start: 0.6669 (tmm) cc_final: 0.6425 (tmm) REVERT: D 274 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7836 (tptm) REVERT: D 305 TYR cc_start: 0.8541 (m-80) cc_final: 0.8212 (m-80) REVERT: E 17 TYR cc_start: 0.4461 (OUTLIER) cc_final: 0.3725 (m-80) REVERT: E 265 MET cc_start: 0.5775 (tpt) cc_final: 0.5506 (mmt) REVERT: E 290 LYS cc_start: 0.4391 (tptp) cc_final: 0.4136 (tptp) REVERT: E 299 ILE cc_start: 0.3612 (OUTLIER) cc_final: 0.2552 (pt) REVERT: E 314 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6386 (pp) REVERT: E 343 MET cc_start: 0.4361 (OUTLIER) cc_final: 0.4152 (mtt) REVERT: F 288 GLN cc_start: 0.7021 (mm110) cc_final: 0.6706 (mm110) outliers start: 67 outliers final: 51 residues processed: 269 average time/residue: 0.1038 time to fit residues: 41.8599 Evaluate side-chains 272 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 212 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.225786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.185308 restraints weight = 15867.255| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 2.88 r_work: 0.4118 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12402 Z= 0.155 Angle : 0.536 6.391 16807 Z= 0.291 Chirality : 0.040 0.152 1846 Planarity : 0.003 0.041 1985 Dihedral : 6.611 66.167 1654 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.18 % Allowed : 23.44 % Favored : 71.39 % 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: 1.41 (0.22), residues: 1382 helix: 1.73 (0.16), residues: 972 sheet: 0.40 (0.52), residues: 107 loop : -1.46 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 389 TYR 0.031 0.001 TYR D 284 PHE 0.027 0.002 PHE E 331 TRP 0.030 0.001 TRP D 120 HIS 0.004 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (12385) covalent geometry : angle 0.53490 / 0.29 (16773) SS BOND : bond 0.00389 / 0.26 ( 17) SS BOND : angle 1.00051 / 0.65 ( 34) hydrogen bonds : bond 0.03803 / 2.51 ( 806) hydrogen bonds : angle 4.21102 / 3.00 ( 2379) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 214 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7469 (tt) REVERT: A 319 LYS cc_start: 0.4307 (mtmt) cc_final: 0.3393 (tppp) REVERT: B 117 ARG cc_start: 0.7498 (mmm160) cc_final: 0.7078 (mmm160) REVERT: B 130 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7091 (tp) REVERT: B 275 PHE cc_start: 0.6057 (OUTLIER) cc_final: 0.4993 (t80) REVERT: C 47 VAL cc_start: 0.8808 (t) cc_final: 0.8603 (t) REVERT: C 49 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7957 (mm110) REVERT: C 104 HIS cc_start: 0.7487 (OUTLIER) cc_final: 0.6474 (t70) REVERT: C 275 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7482 (t80) REVERT: D 274 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7810 (tptm) REVERT: D 305 TYR cc_start: 0.8566 (m-80) cc_final: 0.8249 (m-80) REVERT: D 389 ARG cc_start: 0.8733 (tpp80) cc_final: 0.8515 (tpp80) REVERT: E 17 TYR cc_start: 0.4461 (OUTLIER) cc_final: 0.3712 (m-80) REVERT: E 265 MET cc_start: 0.5647 (tpt) cc_final: 0.5404 (mmt) REVERT: E 290 LYS cc_start: 0.4398 (tptp) cc_final: 0.4123 (tptp) REVERT: E 299 ILE cc_start: 0.3653 (OUTLIER) cc_final: 0.2584 (pt) REVERT: E 314 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6271 (pp) REVERT: E 343 MET cc_start: 0.4323 (OUTLIER) cc_final: 0.4093 (mtt) outliers start: 68 outliers final: 50 residues processed: 266 average time/residue: 0.1019 time to fit residues: 40.4533 Evaluate side-chains 270 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 67 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.226750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.185644 restraints weight = 15848.488| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 3.05 r_work: 0.4117 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12402 Z= 0.139 Angle : 0.528 7.089 16807 Z= 0.287 Chirality : 0.040 0.148 1846 Planarity : 0.003 0.042 1985 Dihedral : 6.492 62.943 1654 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.72 % Allowed : 23.90 % Favored : 71.39 % 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: 1.48 (0.23), residues: 1382 helix: 1.79 (0.16), residues: 972 sheet: 0.35 (0.51), residues: 107 loop : -1.43 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 389 TYR 0.029 0.001 TYR D 284 PHE 0.035 0.001 PHE C 390 TRP 0.034 0.001 TRP D 120 HIS 0.011 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (12385) covalent geometry : angle 0.52693 / 0.29 (16773) SS BOND : bond 0.00342 / 0.22 ( 17) SS BOND : angle 0.98160 / 0.63 ( 34) hydrogen bonds : bond 0.03726 / 2.46 ( 806) hydrogen bonds : angle 4.16452 / 2.97 ( 2379) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 224 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.4299 (mtmt) cc_final: 0.3428 (tppp) REVERT: B 27 PHE cc_start: 0.4220 (m-10) cc_final: 0.3843 (m-10) REVERT: B 117 ARG cc_start: 0.7471 (mmm160) cc_final: 0.6982 (mmm160) REVERT: B 130 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7096 (tp) REVERT: B 275 PHE cc_start: 0.6004 (OUTLIER) cc_final: 0.4951 (t80) REVERT: C 46 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7161 (tm-30) REVERT: C 47 VAL cc_start: 0.8782 (t) cc_final: 0.8522 (t) REVERT: C 49 GLN cc_start: 0.8376 (mm-40) cc_final: 0.7958 (mm110) REVERT: C 104 HIS cc_start: 0.7509 (OUTLIER) cc_final: 0.6452 (t70) REVERT: C 275 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7479 (t80) REVERT: C 337 MET cc_start: 0.6537 (tmm) cc_final: 0.6309 (tmm) REVERT: C 371 ASP cc_start: 0.7516 (m-30) cc_final: 0.7249 (m-30) REVERT: D 274 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7809 (tptm) REVERT: D 305 TYR cc_start: 0.8546 (m-80) cc_final: 0.8206 (m-80) REVERT: D 389 ARG cc_start: 0.8705 (tpp80) cc_final: 0.8479 (tpp80) REVERT: E 17 TYR cc_start: 0.4446 (OUTLIER) cc_final: 0.3698 (m-80) REVERT: E 127 TYR cc_start: 0.5092 (m-10) cc_final: 0.4539 (m-10) REVERT: E 265 MET cc_start: 0.5514 (tpt) cc_final: 0.5309 (mmt) REVERT: E 290 LYS cc_start: 0.4356 (tptp) cc_final: 0.4087 (tptp) REVERT: E 299 ILE cc_start: 0.3716 (OUTLIER) cc_final: 0.2565 (pt) REVERT: E 314 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6150 (pp) REVERT: F 46 GLN cc_start: 0.6230 (mm-40) cc_final: 0.5686 (tm-30) REVERT: F 312 MET cc_start: 0.6542 (pmm) cc_final: 0.6311 (pmm) outliers start: 62 outliers final: 48 residues processed: 273 average time/residue: 0.0948 time to fit residues: 38.3063 Evaluate side-chains 272 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 216 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 86 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.224417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.182624 restraints weight = 15651.922| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 2.86 r_work: 0.4077 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12402 Z= 0.144 Angle : 0.546 8.263 16807 Z= 0.295 Chirality : 0.040 0.165 1846 Planarity : 0.003 0.042 1985 Dihedral : 6.372 58.112 1654 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.41 % Allowed : 24.66 % Favored : 70.93 % 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: 1.49 (0.23), residues: 1382 helix: 1.77 (0.16), residues: 974 sheet: 0.39 (0.52), residues: 107 loop : -1.39 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 389 TYR 0.031 0.001 TYR D 284 PHE 0.032 0.001 PHE C 390 TRP 0.037 0.001 TRP D 120 HIS 0.011 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (12385) covalent geometry : angle 0.54485 / 0.29 (16773) SS BOND : bond 0.00458 / 0.27 ( 17) SS BOND : angle 0.96438 / 0.62 ( 34) hydrogen bonds : bond 0.03731 / 2.47 ( 806) hydrogen bonds : angle 4.17318 / 2.98 ( 2379) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 215 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.4234 (mtmt) cc_final: 0.3203 (tppp) REVERT: B 27 PHE cc_start: 0.4375 (m-10) cc_final: 0.4001 (m-80) REVERT: B 117 ARG cc_start: 0.7415 (mmm160) cc_final: 0.6894 (mmm160) REVERT: B 275 PHE cc_start: 0.5923 (OUTLIER) cc_final: 0.4886 (t80) REVERT: C 25 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: C 46 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7105 (tm-30) REVERT: C 47 VAL cc_start: 0.8758 (t) cc_final: 0.8498 (t) REVERT: C 49 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7957 (mm110) REVERT: C 104 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.6481 (t70) REVERT: C 153 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7703 (mm) REVERT: C 253 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.6512 (p90) REVERT: C 275 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7461 (t80) REVERT: C 337 MET cc_start: 0.6496 (tmm) cc_final: 0.6242 (tmm) REVERT: D 30 TYR cc_start: 0.7066 (m-80) cc_final: 0.6630 (m-80) REVERT: D 274 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7810 (tptm) REVERT: D 305 TYR cc_start: 0.8583 (m-80) cc_final: 0.8234 (m-80) REVERT: D 389 ARG cc_start: 0.8687 (tpp80) cc_final: 0.8430 (tpp80) REVERT: E 17 TYR cc_start: 0.4459 (OUTLIER) cc_final: 0.3707 (m-80) REVERT: E 127 TYR cc_start: 0.4880 (m-10) cc_final: 0.4497 (m-10) REVERT: E 290 LYS cc_start: 0.4296 (tptp) cc_final: 0.4023 (tptp) REVERT: E 299 ILE cc_start: 0.3661 (OUTLIER) cc_final: 0.2519 (pt) REVERT: E 314 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.6118 (pp) REVERT: F 46 GLN cc_start: 0.6310 (mm-40) cc_final: 0.5765 (tm-30) REVERT: F 129 TYR cc_start: 0.6483 (m-80) cc_final: 0.5934 (t80) REVERT: F 312 MET cc_start: 0.6429 (pmm) cc_final: 0.6192 (pmm) outliers start: 58 outliers final: 44 residues processed: 258 average time/residue: 0.0975 time to fit residues: 37.5619 Evaluate side-chains 268 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 9 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 30 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.224718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.182984 restraints weight = 15709.523| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 3.10 r_work: 0.4070 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12402 Z= 0.140 Angle : 0.547 8.950 16807 Z= 0.296 Chirality : 0.040 0.153 1846 Planarity : 0.003 0.042 1985 Dihedral : 6.252 55.613 1654 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.26 % Allowed : 25.19 % Favored : 70.55 % 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: 1.52 (0.23), residues: 1382 helix: 1.80 (0.16), residues: 974 sheet: 0.37 (0.52), residues: 107 loop : -1.38 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 306 TYR 0.027 0.001 TYR F 339 PHE 0.031 0.001 PHE C 390 TRP 0.039 0.001 TRP D 120 HIS 0.010 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (12385) covalent geometry : angle 0.54564 / 0.30 (16773) SS BOND : bond 0.00353 / 0.22 ( 17) SS BOND : angle 0.96142 / 0.62 ( 34) hydrogen bonds : bond 0.03676 / 2.43 ( 806) hydrogen bonds : angle 4.15585 / 2.97 ( 2379) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 213 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.6778 (mt) cc_final: 0.6546 (mp) REVERT: A 319 LYS cc_start: 0.4341 (mtmt) cc_final: 0.3468 (tppt) REVERT: B 27 PHE cc_start: 0.4306 (m-10) cc_final: 0.3931 (m-10) REVERT: B 117 ARG cc_start: 0.7428 (mmm160) cc_final: 0.6909 (mmm160) REVERT: B 130 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7112 (tp) REVERT: B 265 MET cc_start: 0.1019 (mmm) cc_final: 0.0756 (tpp) REVERT: B 275 PHE cc_start: 0.5913 (OUTLIER) cc_final: 0.4890 (t80) REVERT: C 46 GLN cc_start: 0.7596 (tm-30) cc_final: 0.7097 (tm-30) REVERT: C 47 VAL cc_start: 0.8750 (t) cc_final: 0.8485 (t) REVERT: C 49 GLN cc_start: 0.8406 (mm-40) cc_final: 0.7948 (mm110) REVERT: C 104 HIS cc_start: 0.7564 (OUTLIER) cc_final: 0.6487 (t70) REVERT: C 145 LYS cc_start: 0.8581 (mttt) cc_final: 0.8341 (mmtp) REVERT: C 153 LEU cc_start: 0.7990 (mm) cc_final: 0.7618 (mm) REVERT: C 253 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.6658 (p90) REVERT: C 275 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7468 (t80) REVERT: C 293 VAL cc_start: 0.8723 (t) cc_final: 0.8450 (t) REVERT: D 30 TYR cc_start: 0.7055 (m-80) cc_final: 0.6613 (m-80) REVERT: D 305 TYR cc_start: 0.8577 (m-80) cc_final: 0.8227 (m-80) REVERT: D 389 ARG cc_start: 0.8725 (tpp80) cc_final: 0.8457 (tpp80) REVERT: E 17 TYR cc_start: 0.4459 (OUTLIER) cc_final: 0.3705 (m-80) REVERT: E 127 TYR cc_start: 0.4807 (m-10) cc_final: 0.4438 (m-10) REVERT: E 299 ILE cc_start: 0.3651 (OUTLIER) cc_final: 0.2507 (pt) REVERT: E 314 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.6025 (pp) REVERT: E 343 MET cc_start: 0.2954 (mtt) cc_final: 0.2057 (ttt) REVERT: F 46 GLN cc_start: 0.6177 (mm-40) cc_final: 0.5658 (tm-30) REVERT: F 96 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.6451 (mtt) REVERT: F 312 MET cc_start: 0.6442 (pmm) cc_final: 0.6208 (pmm) outliers start: 56 outliers final: 45 residues processed: 255 average time/residue: 0.0901 time to fit residues: 34.5897 Evaluate side-chains 265 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 211 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 40 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN C 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.223383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.181626 restraints weight = 15674.925| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 3.04 r_work: 0.4054 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12402 Z= 0.163 Angle : 0.570 9.208 16807 Z= 0.308 Chirality : 0.040 0.161 1846 Planarity : 0.004 0.041 1985 Dihedral : 6.195 53.588 1654 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.41 % Allowed : 25.19 % Favored : 70.40 % 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 (0.23), residues: 1382 helix: 1.73 (0.16), residues: 972 sheet: 0.27 (0.53), residues: 107 loop : -1.44 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 389 TYR 0.032 0.002 TYR D 284 PHE 0.029 0.002 PHE C 390 TRP 0.037 0.002 TRP D 120 HIS 0.011 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (12385) covalent geometry : angle 0.56901 / 0.31 (16773) SS BOND : bond 0.00382 / 0.25 ( 17) SS BOND : angle 0.99835 / 0.64 ( 34) hydrogen bonds : bond 0.03823 / 2.53 ( 806) hydrogen bonds : angle 4.22025 / 3.00 ( 2379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3209.43 seconds wall clock time: 55 minutes 55.54 seconds (3355.54 seconds total)