Starting phenix.real_space_refine on Sat Aug 23 13:11:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dsa_27687/08_2025/8dsa_27687.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dsa_27687/08_2025/8dsa_27687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dsa_27687/08_2025/8dsa_27687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dsa_27687/08_2025/8dsa_27687.map" model { file = "/net/cci-nas-00/data/ceres_data/8dsa_27687/08_2025/8dsa_27687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dsa_27687/08_2025/8dsa_27687.cif" } resolution = 3.48 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= 0.041 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-2.0-5787/lib/python3.9/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: 78 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: 2.67, per 1000 atoms: 0.22 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: 0.63 Conformation dependent library (CDL) restraints added in 491.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.58 Time building geometry restraints manager: 0.90 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: 6964 34.75 - 69.50: 257 69.50 - 104.25: 13 104.25 - 139.00: 2 139.00 - 173.75: 2 Dihedral angle restraints: 7238 sinusoidal: 2971 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 7235 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: 4.470 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.170 Find NCS groups from input model: 0.130 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 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 : 17.316 173.749 4433 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.98 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 aren 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 covalent geometry : bond 0.00527 (12385) covalent geometry : angle 0.80545 (16773) SS BOND : bond 0.00319 ( 17) SS BOND : angle 1.25539 ( 34) hydrogen bonds : bond 0.13389 ( 806) hydrogen bonds : angle 6.19165 ( 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 357 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 350 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.8039 (mt) cc_final: 0.7502 (mm) REVERT: A 131 LEU cc_start: 0.8425 (tt) cc_final: 0.8174 (tt) REVERT: A 143 TRP cc_start: 0.6701 (p90) cc_final: 0.6444 (p90) REVERT: B 35 MET cc_start: 0.6908 (mtp) cc_final: 0.6584 (mtt) REVERT: C 125 PHE cc_start: 0.7655 (t80) cc_final: 0.7378 (t80) REVERT: C 171 ARG cc_start: 0.8139 (tmt-80) cc_final: 0.7893 (tmt-80) REVERT: E 110 ASP cc_start: 0.5993 (m-30) cc_final: 0.5372 (m-30) REVERT: F 96 MET cc_start: 0.5211 (mpp) cc_final: 0.4965 (mmm) outliers start: 7 outliers final: 3 residues processed: 354 average time/residue: 0.0973 time to fit residues: 48.9242 Evaluate side-chains 241 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 238 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN C 370 ASN C 406 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.216320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.176675 restraints weight = 18785.937| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 2.95 r_work: 0.4041 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.2732 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= 0.146 Angle : 0.601 8.263 16807 Z= 0.317 Chirality : 0.041 0.242 1846 Planarity : 0.004 0.054 1985 Dihedral : 9.762 178.340 1676 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.57 % Allowed : 21.69 % Favored : 73.74 % 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 aren not related in a simple way. whole: 1.07 (0.22), residues: 1382 helix: 1.39 (0.16), residues: 960 sheet: 0.41 (0.52), residues: 107 loop : -1.22 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 345 TYR 0.029 0.002 TYR F 262 PHE 0.023 0.002 PHE E 291 TRP 0.032 0.002 TRP A 23 HIS 0.005 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00329 (12385) covalent geometry : angle 0.59905 (16773) SS BOND : bond 0.00297 ( 17) SS BOND : angle 1.30380 ( 34) hydrogen bonds : bond 0.04241 ( 806) hydrogen bonds : angle 4.42111 ( 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 310 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 250 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TRP cc_start: 0.6198 (p90) cc_final: 0.5449 (p90) REVERT: B 35 MET cc_start: 0.6788 (mtp) cc_final: 0.6360 (mtt) REVERT: B 117 ARG cc_start: 0.7342 (tpt90) cc_final: 0.6594 (mmm160) REVERT: B 275 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.6037 (t80) REVERT: B 331 PHE cc_start: 0.6536 (OUTLIER) cc_final: 0.5937 (m-10) REVERT: B 337 MET cc_start: 0.7263 (tmm) cc_final: 0.6794 (tmm) REVERT: C 25 ASP cc_start: 0.8028 (m-30) cc_final: 0.7771 (m-30) REVERT: C 110 ASP cc_start: 0.7349 (m-30) cc_final: 0.7058 (m-30) REVERT: C 125 PHE cc_start: 0.7822 (t80) cc_final: 0.7584 (t80) REVERT: C 161 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.6813 (pp) REVERT: C 171 ARG cc_start: 0.8545 (tmt-80) cc_final: 0.8064 (tmt-80) REVERT: C 388 LYS cc_start: 0.7383 (ttpt) cc_final: 0.7172 (tmmt) REVERT: C 389 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.7045 (ttm170) REVERT: D 157 VAL cc_start: 0.8078 (t) cc_final: 0.7713 (p) REVERT: D 281 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.5667 (m-10) REVERT: D 338 TYR cc_start: 0.4180 (t80) cc_final: 0.3724 (t80) REVERT: D 364 ASP cc_start: 0.7150 (t0) cc_final: 0.6530 (t0) REVERT: E 291 PHE cc_start: 0.4214 (m-10) cc_final: 0.2984 (p90) REVERT: E 314 LEU cc_start: 0.6134 (OUTLIER) cc_final: 0.5911 (pp) REVERT: F 35 MET cc_start: 0.6436 (mmt) cc_final: 0.5509 (mmt) REVERT: F 96 MET cc_start: 0.4542 (mpp) cc_final: 0.4201 (mmt) outliers start: 60 outliers final: 24 residues processed: 292 average time/residue: 0.0972 time to fit residues: 40.9523 Evaluate side-chains 255 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 292 ASP 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: 0.8980 chunk 54 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 75 optimal weight: 0.0170 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 32 optimal weight: 0.0670 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 288 ASN C 239 GLN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.214415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.175406 restraints weight = 18729.507| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.63 r_work: 0.4031 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.3382 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= 0.133 Angle : 0.557 8.279 16807 Z= 0.296 Chirality : 0.040 0.194 1846 Planarity : 0.003 0.043 1985 Dihedral : 9.260 176.843 1673 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.79 % Allowed : 21.99 % Favored : 73.21 % 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 aren not related in a simple way. whole: 1.38 (0.22), residues: 1382 helix: 1.61 (0.16), residues: 962 sheet: 0.66 (0.51), residues: 107 loop : -1.12 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 345 TYR 0.033 0.001 TYR F 262 PHE 0.026 0.002 PHE E 291 TRP 0.029 0.002 TRP E 24 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00298 (12385) covalent geometry : angle 0.55330 (16773) SS BOND : bond 0.00323 ( 17) SS BOND : angle 1.44089 ( 34) hydrogen bonds : bond 0.03876 ( 806) hydrogen bonds : angle 4.23769 ( 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 309 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 MET cc_start: 0.6774 (mtp) cc_final: 0.6398 (mtt) REVERT: B 275 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.6023 (t80) REVERT: B 331 PHE cc_start: 0.6571 (OUTLIER) cc_final: 0.6225 (t80) REVERT: B 337 MET cc_start: 0.6895 (tmm) cc_final: 0.6615 (tmm) REVERT: C 104 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.6673 (t70) REVERT: C 110 ASP cc_start: 0.7272 (m-30) cc_final: 0.6916 (m-30) REVERT: C 125 PHE cc_start: 0.7935 (t80) cc_final: 0.7689 (t80) REVERT: C 162 LYS cc_start: 0.7402 (ptpt) cc_final: 0.7096 (pttm) REVERT: C 171 ARG cc_start: 0.8671 (tmt-80) cc_final: 0.8390 (tmt-80) REVERT: C 401 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8487 (mmtm) REVERT: D 37 MET cc_start: 0.6289 (tmm) cc_final: 0.5797 (tpt) REVERT: D 239 GLN cc_start: 0.7542 (pm20) cc_final: 0.7198 (pm20) REVERT: D 245 GLU cc_start: 0.7630 (tp30) cc_final: 0.7386 (tp30) REVERT: D 281 TYR cc_start: 0.6448 (OUTLIER) cc_final: 0.5659 (m-10) REVERT: D 396 GLU cc_start: 0.7582 (pm20) cc_final: 0.7146 (pt0) REVERT: E 291 PHE cc_start: 0.4683 (m-80) cc_final: 0.3255 (p90) REVERT: E 299 ILE cc_start: 0.3485 (OUTLIER) cc_final: 0.2614 (pt) REVERT: E 343 MET cc_start: 0.0626 (mtp) cc_final: -0.0674 (ptp) REVERT: F 96 MET cc_start: 0.4508 (mpp) cc_final: 0.3962 (mmm) REVERT: F 145 TRP cc_start: 0.5770 (t-100) cc_final: 0.5539 (t-100) REVERT: F 303 TYR cc_start: 0.6256 (m-80) cc_final: 0.5613 (m-80) REVERT: F 318 LYS cc_start: 0.8253 (mmmt) cc_final: 0.7876 (mmmt) outliers start: 63 outliers final: 31 residues processed: 292 average time/residue: 0.0904 time to fit residues: 38.5898 Evaluate side-chains 260 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 401 LYS Chi-restraints excluded: chain C residue 411 TRP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 123 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 ASN E 132 HIS F 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.208540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.168372 restraints weight = 18960.452| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 2.73 r_work: 0.3970 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12402 Z= 0.194 Angle : 0.609 8.828 16807 Z= 0.323 Chirality : 0.043 0.194 1846 Planarity : 0.004 0.047 1985 Dihedral : 9.294 172.329 1673 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.48 % Allowed : 23.06 % Favored : 71.46 % 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 aren not related in a simple way. whole: 1.32 (0.22), residues: 1382 helix: 1.59 (0.16), residues: 966 sheet: 0.78 (0.50), residues: 105 loop : -1.34 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 345 TYR 0.038 0.002 TYR F 330 PHE 0.028 0.002 PHE E 291 TRP 0.029 0.002 TRP A 24 HIS 0.006 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00447 (12385) covalent geometry : angle 0.60725 (16773) SS BOND : bond 0.00486 ( 17) SS BOND : angle 1.24601 ( 34) hydrogen bonds : bond 0.04142 ( 806) hydrogen bonds : angle 4.38634 ( 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 307 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 235 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.7449 (OUTLIER) cc_final: 0.6873 (t70) REVERT: B 35 MET cc_start: 0.6863 (mtp) cc_final: 0.6457 (mtt) REVERT: B 275 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.6136 (t80) REVERT: B 308 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.7030 (m-80) REVERT: B 331 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.6044 (t80) REVERT: B 337 MET cc_start: 0.6707 (tmm) cc_final: 0.6480 (tmm) REVERT: C 104 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.6878 (t70) REVERT: C 161 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7034 (pp) REVERT: C 241 LYS cc_start: 0.8183 (mttm) cc_final: 0.7974 (mmtt) REVERT: C 401 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8502 (mmtm) REVERT: D 157 VAL cc_start: 0.8420 (t) cc_final: 0.8083 (p) REVERT: D 239 GLN cc_start: 0.7846 (pm20) cc_final: 0.7560 (pm20) REVERT: E 52 MET cc_start: 0.5054 (ppp) cc_final: 0.3407 (ttp) REVERT: E 299 ILE cc_start: 0.3693 (OUTLIER) cc_final: 0.2025 (mm) REVERT: E 343 MET cc_start: 0.0632 (mtp) cc_final: -0.0319 (ptp) REVERT: F 51 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.5841 (pttp) REVERT: F 303 TYR cc_start: 0.6311 (m-80) cc_final: 0.5842 (m-80) REVERT: F 318 LYS cc_start: 0.8356 (mmmt) cc_final: 0.7746 (mmpt) REVERT: F 328 SER cc_start: 0.6088 (t) cc_final: 0.5726 (p) outliers start: 72 outliers final: 50 residues processed: 282 average time/residue: 0.1201 time to fit residues: 48.4905 Evaluate side-chains 275 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 216 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 341 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 134 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 401 LYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 17 PHE 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 101 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 330 TYR Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 5 optimal weight: 0.0870 chunk 8 optimal weight: 0.0770 chunk 104 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 105 optimal weight: 0.0970 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 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 = 0.4666 r_free = 0.4666 target = 0.212162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.173018 restraints weight = 18910.444| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 3.10 r_work: 0.4014 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.4243 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= 0.118 Angle : 0.538 7.724 16807 Z= 0.285 Chirality : 0.040 0.159 1846 Planarity : 0.003 0.041 1985 Dihedral : 8.466 159.535 1673 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.88 % Allowed : 24.51 % Favored : 71.61 % 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 aren not related in a simple way. whole: 1.63 (0.23), residues: 1382 helix: 1.82 (0.16), residues: 961 sheet: 0.99 (0.50), residues: 105 loop : -1.22 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 345 TYR 0.026 0.001 TYR F 262 PHE 0.014 0.001 PHE D 372 TRP 0.023 0.001 TRP A 24 HIS 0.004 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00258 (12385) covalent geometry : angle 0.53693 (16773) SS BOND : bond 0.00223 ( 17) SS BOND : angle 0.98720 ( 34) hydrogen bonds : bond 0.03631 ( 806) hydrogen bonds : angle 4.13116 ( 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 298 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 247 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.7034 (OUTLIER) cc_final: 0.6394 (t70) REVERT: A 144 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6650 (m-80) REVERT: B 35 MET cc_start: 0.6718 (mtp) cc_final: 0.5856 (mtt) REVERT: B 38 ILE cc_start: 0.6226 (OUTLIER) cc_final: 0.6003 (tt) REVERT: B 275 PHE cc_start: 0.6580 (OUTLIER) cc_final: 0.6084 (t80) REVERT: C 104 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.6655 (t70) REVERT: C 125 PHE cc_start: 0.7882 (t80) cc_final: 0.7641 (t80) REVERT: D 156 PHE cc_start: 0.7716 (t80) cc_final: 0.7410 (t80) REVERT: D 157 VAL cc_start: 0.8375 (t) cc_final: 0.7995 (p) REVERT: D 245 GLU cc_start: 0.7731 (tp30) cc_final: 0.7482 (tp30) REVERT: E 25 ASP cc_start: 0.7038 (m-30) cc_final: 0.6688 (m-30) REVERT: E 52 MET cc_start: 0.5130 (ppp) cc_final: 0.3481 (ttp) REVERT: E 136 PHE cc_start: 0.2854 (OUTLIER) cc_final: 0.2649 (m-80) REVERT: E 299 ILE cc_start: 0.3414 (OUTLIER) cc_final: 0.2196 (mm) REVERT: E 343 MET cc_start: 0.1224 (mtp) cc_final: 0.0808 (mtp) REVERT: F 96 MET cc_start: 0.3773 (ptp) cc_final: 0.3533 (ptp) REVERT: F 288 GLN cc_start: 0.7251 (mm-40) cc_final: 0.7023 (mm110) REVERT: F 303 TYR cc_start: 0.6208 (m-80) cc_final: 0.5763 (m-80) REVERT: F 318 LYS cc_start: 0.8303 (mmmt) cc_final: 0.7746 (mmpt) outliers start: 51 outliers final: 32 residues processed: 281 average time/residue: 0.1035 time to fit residues: 42.1780 Evaluate side-chains 268 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 229 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 17 PHE 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 273 PHE Chi-restraints excluded: chain F residue 330 TYR Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 42 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 377 HIS ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.210449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.169516 restraints weight = 18916.847| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.86 r_work: 0.3995 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12402 Z= 0.154 Angle : 0.575 9.910 16807 Z= 0.303 Chirality : 0.041 0.205 1846 Planarity : 0.003 0.041 1985 Dihedral : 8.168 140.419 1673 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.63 % Allowed : 24.51 % Favored : 69.86 % 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 aren not related in a simple way. whole: 1.59 (0.22), residues: 1382 helix: 1.78 (0.16), residues: 965 sheet: 1.04 (0.50), residues: 105 loop : -1.24 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 306 TYR 0.023 0.001 TYR B 325 PHE 0.026 0.002 PHE E 291 TRP 0.029 0.002 TRP A 24 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00357 (12385) covalent geometry : angle 0.57460 (16773) SS BOND : bond 0.00349 ( 17) SS BOND : angle 0.91633 ( 34) hydrogen bonds : bond 0.03708 ( 806) hydrogen bonds : angle 4.19188 ( 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 300 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 226 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7125 (t0) cc_final: 0.6906 (t0) REVERT: A 104 HIS cc_start: 0.7323 (OUTLIER) cc_final: 0.6734 (t70) REVERT: A 144 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.6728 (m-80) REVERT: A 262 ARG cc_start: 0.3631 (mmm160) cc_final: 0.3283 (mmm160) REVERT: B 35 MET cc_start: 0.6826 (mtp) cc_final: 0.6468 (mtt) REVERT: B 275 PHE cc_start: 0.6558 (OUTLIER) cc_final: 0.6088 (t80) REVERT: B 337 MET cc_start: 0.6896 (tmm) cc_final: 0.6495 (tmm) REVERT: C 104 HIS cc_start: 0.7492 (OUTLIER) cc_final: 0.6655 (t70) REVERT: C 161 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7001 (pp) REVERT: D 157 VAL cc_start: 0.8425 (t) cc_final: 0.8055 (p) REVERT: D 245 GLU cc_start: 0.7808 (tp30) cc_final: 0.7525 (tp30) REVERT: D 374 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.6193 (m-80) REVERT: E 25 ASP cc_start: 0.6971 (m-30) cc_final: 0.6714 (m-30) REVERT: E 52 MET cc_start: 0.5364 (ppp) cc_final: 0.3760 (ttp) REVERT: E 136 PHE cc_start: 0.2945 (OUTLIER) cc_final: 0.2718 (m-80) REVERT: E 299 ILE cc_start: 0.3273 (OUTLIER) cc_final: 0.2385 (pt) REVERT: E 314 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6592 (pt) REVERT: E 343 MET cc_start: 0.1166 (mtp) cc_final: 0.0760 (mtp) REVERT: F 96 MET cc_start: 0.3773 (ptp) cc_final: 0.3540 (ptp) REVERT: F 288 GLN cc_start: 0.7337 (mm-40) cc_final: 0.7067 (mm110) REVERT: F 303 TYR cc_start: 0.6408 (m-80) cc_final: 0.6175 (m-10) REVERT: F 318 LYS cc_start: 0.8243 (mmmt) cc_final: 0.7759 (mmpt) outliers start: 74 outliers final: 46 residues processed: 280 average time/residue: 0.0968 time to fit residues: 39.9613 Evaluate side-chains 266 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 211 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 134 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 19 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain E residue 24 TRP Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 136 PHE 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 F residue 17 PHE Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 330 TYR Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 42 optimal weight: 0.0370 chunk 71 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 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 = 0.4643 r_free = 0.4643 target = 0.209845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.169667 restraints weight = 18748.737| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 2.83 r_work: 0.3993 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12402 Z= 0.138 Angle : 0.576 9.042 16807 Z= 0.302 Chirality : 0.040 0.183 1846 Planarity : 0.003 0.040 1985 Dihedral : 7.577 103.903 1673 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.72 % Allowed : 24.89 % 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 aren not related in a simple way. whole: 1.70 (0.22), residues: 1382 helix: 1.86 (0.16), residues: 961 sheet: 1.12 (0.50), residues: 105 loop : -1.16 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 306 TYR 0.021 0.001 TYR E 325 PHE 0.015 0.001 PHE F 326 TRP 0.033 0.002 TRP A 24 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00314 (12385) covalent geometry : angle 0.57594 (16773) SS BOND : bond 0.00287 ( 17) SS BOND : angle 0.79893 ( 34) hydrogen bonds : bond 0.03582 ( 806) hydrogen bonds : angle 4.13240 ( 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 294 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 232 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.7228 (OUTLIER) cc_final: 0.6566 (t70) REVERT: A 144 PHE cc_start: 0.7003 (OUTLIER) cc_final: 0.6719 (m-80) REVERT: A 337 MET cc_start: 0.5347 (tpt) cc_final: 0.5083 (tpt) REVERT: B 35 MET cc_start: 0.6869 (mtp) cc_final: 0.6543 (mtt) REVERT: B 275 PHE cc_start: 0.6512 (OUTLIER) cc_final: 0.6060 (t80) REVERT: B 308 TYR cc_start: 0.7664 (OUTLIER) cc_final: 0.6929 (m-80) REVERT: B 337 MET cc_start: 0.6879 (tmm) cc_final: 0.6510 (tmm) REVERT: C 104 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.6639 (t70) REVERT: C 125 PHE cc_start: 0.7911 (t80) cc_final: 0.7682 (t80) REVERT: C 401 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8491 (mmtm) REVERT: D 157 VAL cc_start: 0.8398 (t) cc_final: 0.8049 (p) REVERT: D 245 GLU cc_start: 0.7812 (tp30) cc_final: 0.7563 (tp30) REVERT: D 274 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7473 (ttmm) REVERT: D 301 SER cc_start: 0.8479 (p) cc_final: 0.8235 (m) REVERT: D 374 PHE cc_start: 0.7071 (OUTLIER) cc_final: 0.6204 (m-80) REVERT: E 25 ASP cc_start: 0.6941 (m-30) cc_final: 0.6711 (m-30) REVERT: E 52 MET cc_start: 0.5369 (ppp) cc_final: 0.3676 (ttp) REVERT: E 136 PHE cc_start: 0.2680 (OUTLIER) cc_final: 0.2440 (m-80) REVERT: E 299 ILE cc_start: 0.3485 (OUTLIER) cc_final: 0.2221 (mm) REVERT: E 343 MET cc_start: 0.1519 (mtp) cc_final: 0.1148 (mtp) REVERT: F 51 LYS cc_start: 0.6477 (OUTLIER) cc_final: 0.5892 (pttp) REVERT: F 96 MET cc_start: 0.3774 (ptp) cc_final: 0.3544 (ptp) REVERT: F 288 GLN cc_start: 0.7349 (mm-40) cc_final: 0.7044 (mm110) REVERT: F 318 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7904 (mmmt) outliers start: 62 outliers final: 42 residues processed: 276 average time/residue: 0.0945 time to fit residues: 38.2542 Evaluate side-chains 264 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 211 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 134 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 308 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 401 LYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 268 THR 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 314 LEU Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain E residue 24 TRP Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 67 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN ** F 112 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 = 0.4657 r_free = 0.4657 target = 0.211111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.170293 restraints weight = 18765.894| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 3.01 r_work: 0.3994 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12402 Z= 0.140 Angle : 0.593 8.353 16807 Z= 0.311 Chirality : 0.040 0.233 1846 Planarity : 0.003 0.040 1985 Dihedral : 7.173 78.913 1673 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.18 % Allowed : 25.57 % Favored : 69.25 % 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 aren not related in a simple way. whole: 1.74 (0.22), residues: 1382 helix: 1.88 (0.16), residues: 958 sheet: 1.24 (0.51), residues: 105 loop : -1.13 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 345 TYR 0.031 0.001 TYR B 325 PHE 0.019 0.001 PHE A 27 TRP 0.032 0.002 TRP A 24 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00319 (12385) covalent geometry : angle 0.59118 (16773) SS BOND : bond 0.00366 ( 17) SS BOND : angle 1.06417 ( 34) hydrogen bonds : bond 0.03646 ( 806) hydrogen bonds : angle 4.16490 ( 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 292 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 224 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.6458 (ppp) cc_final: 0.6121 (ptt) REVERT: A 50 ASP cc_start: 0.6997 (t0) cc_final: 0.6722 (t0) REVERT: A 104 HIS cc_start: 0.7216 (OUTLIER) cc_final: 0.6625 (t70) REVERT: A 144 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6733 (m-80) REVERT: A 337 MET cc_start: 0.5363 (tpt) cc_final: 0.5144 (tpt) REVERT: B 35 MET cc_start: 0.6935 (mtp) cc_final: 0.6086 (mtt) REVERT: B 38 ILE cc_start: 0.6199 (OUTLIER) cc_final: 0.5919 (tt) REVERT: B 275 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.6136 (t80) REVERT: B 308 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.6845 (m-80) REVERT: B 337 MET cc_start: 0.6826 (tmm) cc_final: 0.6452 (tmm) REVERT: C 104 HIS cc_start: 0.7481 (OUTLIER) cc_final: 0.6636 (t70) REVERT: C 125 PHE cc_start: 0.7909 (t80) cc_final: 0.7681 (t80) REVERT: C 161 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7136 (pp) REVERT: C 306 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7027 (ttm-80) REVERT: C 401 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8496 (mmtm) REVERT: D 37 MET cc_start: 0.5991 (tmm) cc_final: 0.5585 (tpt) REVERT: D 156 PHE cc_start: 0.7753 (t80) cc_final: 0.7466 (t80) REVERT: D 157 VAL cc_start: 0.8424 (t) cc_final: 0.8076 (p) REVERT: D 245 GLU cc_start: 0.7808 (tp30) cc_final: 0.7562 (tp30) REVERT: D 252 THR cc_start: 0.8803 (m) cc_final: 0.8600 (p) REVERT: D 301 SER cc_start: 0.8494 (p) cc_final: 0.8234 (m) REVERT: D 374 PHE cc_start: 0.6779 (OUTLIER) cc_final: 0.5988 (m-80) REVERT: E 25 ASP cc_start: 0.6948 (m-30) cc_final: 0.6746 (m-30) REVERT: E 52 MET cc_start: 0.5162 (ppp) cc_final: 0.3643 (ttp) REVERT: E 299 ILE cc_start: 0.3349 (OUTLIER) cc_final: 0.2140 (mm) REVERT: E 343 MET cc_start: 0.1580 (mtp) cc_final: 0.0778 (mtp) REVERT: F 96 MET cc_start: 0.3695 (ptp) cc_final: 0.3450 (ptp) REVERT: F 288 GLN cc_start: 0.7341 (mm-40) cc_final: 0.7018 (mm110) REVERT: F 318 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7879 (mmmt) outliers start: 68 outliers final: 48 residues processed: 274 average time/residue: 0.0938 time to fit residues: 37.7738 Evaluate side-chains 275 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 217 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 134 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 308 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 401 LYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 268 THR 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 283 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain E residue 24 TRP Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.210798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.169705 restraints weight = 18728.960| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.84 r_work: 0.4001 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12402 Z= 0.144 Angle : 0.610 10.521 16807 Z= 0.317 Chirality : 0.040 0.239 1846 Planarity : 0.003 0.040 1985 Dihedral : 7.084 76.942 1673 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.87 % Allowed : 25.80 % Favored : 69.33 % 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 aren not related in a simple way. whole: 1.65 (0.22), residues: 1382 helix: 1.83 (0.16), residues: 962 sheet: 1.24 (0.51), residues: 105 loop : -1.31 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 117 TYR 0.024 0.001 TYR D 284 PHE 0.018 0.001 PHE A 27 TRP 0.034 0.002 TRP A 24 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00330 (12385) covalent geometry : angle 0.60910 (16773) SS BOND : bond 0.00329 ( 17) SS BOND : angle 1.06401 ( 34) hydrogen bonds : bond 0.03648 ( 806) hydrogen bonds : angle 4.18372 ( 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 285 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 221 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.6446 (ppp) cc_final: 0.6087 (ptt) REVERT: A 50 ASP cc_start: 0.7022 (t0) cc_final: 0.6736 (t0) REVERT: A 104 HIS cc_start: 0.7271 (OUTLIER) cc_final: 0.6698 (t70) REVERT: A 144 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6745 (m-80) REVERT: B 35 MET cc_start: 0.6951 (mtp) cc_final: 0.6137 (mtt) REVERT: B 38 ILE cc_start: 0.6189 (OUTLIER) cc_final: 0.5895 (tt) REVERT: B 275 PHE cc_start: 0.6558 (OUTLIER) cc_final: 0.6133 (t80) REVERT: B 308 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6852 (m-80) REVERT: B 337 MET cc_start: 0.6831 (tmm) cc_final: 0.6471 (tmm) REVERT: C 104 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.6641 (t70) REVERT: C 125 PHE cc_start: 0.7906 (t80) cc_final: 0.7678 (t80) REVERT: C 161 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7186 (pp) REVERT: C 401 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8510 (mmtm) REVERT: D 37 MET cc_start: 0.5834 (tmm) cc_final: 0.5450 (tpt) REVERT: D 156 PHE cc_start: 0.7733 (t80) cc_final: 0.7454 (t80) REVERT: D 157 VAL cc_start: 0.8335 (t) cc_final: 0.7823 (p) REVERT: D 245 GLU cc_start: 0.7812 (tp30) cc_final: 0.7569 (tp30) REVERT: D 252 THR cc_start: 0.8796 (m) cc_final: 0.8593 (p) REVERT: D 301 SER cc_start: 0.8551 (p) cc_final: 0.8296 (m) REVERT: D 374 PHE cc_start: 0.6803 (OUTLIER) cc_final: 0.6017 (m-80) REVERT: E 52 MET cc_start: 0.5238 (ppp) cc_final: 0.3810 (ttp) REVERT: E 299 ILE cc_start: 0.3355 (OUTLIER) cc_final: 0.2153 (mm) REVERT: E 343 MET cc_start: 0.2104 (mtp) cc_final: 0.1581 (mtp) REVERT: F 96 MET cc_start: 0.3466 (ptp) cc_final: 0.3259 (ptp) REVERT: F 288 GLN cc_start: 0.7378 (mm-40) cc_final: 0.7052 (mm110) REVERT: F 318 LYS cc_start: 0.8313 (mmmt) cc_final: 0.7952 (mmmt) outliers start: 64 outliers final: 46 residues processed: 264 average time/residue: 0.1007 time to fit residues: 38.9285 Evaluate side-chains 270 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 214 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 401 LYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 268 THR 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 283 VAL Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain E residue 24 TRP Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 9 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 107 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN F 106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.209691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.168214 restraints weight = 18818.832| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 2.80 r_work: 0.3988 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12402 Z= 0.159 Angle : 0.632 10.639 16807 Z= 0.330 Chirality : 0.041 0.228 1846 Planarity : 0.004 0.041 1985 Dihedral : 7.061 74.141 1673 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.49 % Allowed : 26.64 % Favored : 68.87 % 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 aren not related in a simple way. whole: 1.56 (0.22), residues: 1382 helix: 1.77 (0.16), residues: 962 sheet: 1.20 (0.51), residues: 105 loop : -1.35 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 117 TYR 0.038 0.002 TYR B 325 PHE 0.017 0.001 PHE A 27 TRP 0.036 0.002 TRP A 24 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00369 (12385) covalent geometry : angle 0.63052 (16773) SS BOND : bond 0.00342 ( 17) SS BOND : angle 1.04281 ( 34) hydrogen bonds : bond 0.03751 ( 806) hydrogen bonds : angle 4.26440 ( 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 277 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.6452 (ppp) cc_final: 0.6099 (ptt) REVERT: A 50 ASP cc_start: 0.7010 (t0) cc_final: 0.6712 (t0) REVERT: A 104 HIS cc_start: 0.7365 (OUTLIER) cc_final: 0.6753 (t70) REVERT: A 144 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6618 (m-80) REVERT: B 35 MET cc_start: 0.7047 (mtp) cc_final: 0.6275 (mtt) REVERT: B 38 ILE cc_start: 0.6300 (OUTLIER) cc_final: 0.6082 (tt) REVERT: B 275 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.6126 (t80) REVERT: B 308 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.6951 (m-80) REVERT: B 337 MET cc_start: 0.6858 (tmm) cc_final: 0.6498 (tmm) REVERT: C 104 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.6655 (t70) REVERT: C 110 ASP cc_start: 0.7526 (m-30) cc_final: 0.7272 (m-30) REVERT: C 125 PHE cc_start: 0.7928 (t80) cc_final: 0.7689 (t80) REVERT: C 161 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7208 (pp) REVERT: D 37 MET cc_start: 0.5946 (tmm) cc_final: 0.5555 (tpt) REVERT: D 156 PHE cc_start: 0.7738 (t80) cc_final: 0.7470 (t80) REVERT: D 245 GLU cc_start: 0.7818 (tp30) cc_final: 0.7587 (tp30) REVERT: D 252 THR cc_start: 0.8804 (m) cc_final: 0.8598 (p) REVERT: D 301 SER cc_start: 0.8642 (p) cc_final: 0.8374 (m) REVERT: D 374 PHE cc_start: 0.6793 (OUTLIER) cc_final: 0.6001 (m-80) REVERT: E 52 MET cc_start: 0.5377 (ppp) cc_final: 0.3723 (ttp) REVERT: E 299 ILE cc_start: 0.3549 (OUTLIER) cc_final: 0.2311 (mm) REVERT: E 309 ARG cc_start: 0.7726 (ttt180) cc_final: 0.7523 (tmm-80) REVERT: E 343 MET cc_start: 0.2067 (mtp) cc_final: 0.1560 (mtp) REVERT: F 288 GLN cc_start: 0.7351 (mm-40) cc_final: 0.7033 (mm110) REVERT: F 305 ASN cc_start: 0.5788 (t0) cc_final: 0.5522 (m-40) REVERT: F 318 LYS cc_start: 0.8314 (mmmt) cc_final: 0.7973 (mmmt) outliers start: 59 outliers final: 44 residues processed: 259 average time/residue: 0.1085 time to fit residues: 40.7317 Evaluate side-chains 265 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 212 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain E residue 24 TRP Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 273 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 40 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 58 optimal weight: 0.1980 chunk 103 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 8 optimal weight: 0.0270 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.211616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.170994 restraints weight = 18881.418| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.80 r_work: 0.4018 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12402 Z= 0.136 Angle : 0.621 10.791 16807 Z= 0.325 Chirality : 0.040 0.221 1846 Planarity : 0.003 0.039 1985 Dihedral : 6.818 74.138 1673 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.96 % Allowed : 26.94 % Favored : 69.10 % 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 aren not related in a simple way. whole: 1.58 (0.22), residues: 1382 helix: 1.78 (0.16), residues: 962 sheet: 1.14 (0.51), residues: 105 loop : -1.30 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 306 TYR 0.035 0.001 TYR B 325 PHE 0.018 0.001 PHE A 27 TRP 0.039 0.002 TRP A 24 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00309 (12385) covalent geometry : angle 0.61986 (16773) SS BOND : bond 0.00282 ( 17) SS BOND : angle 1.01518 ( 34) hydrogen bonds : bond 0.03683 ( 806) hydrogen bonds : angle 4.21187 ( 2379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2994.28 seconds wall clock time: 52 minutes 8.15 seconds (3128.15 seconds total)