Starting phenix.real_space_refine on Fri Jul 3 05:09:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dsa_27687/07_2026/8dsa_27687.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dsa_27687/07_2026/8dsa_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_27687/07_2026/8dsa_27687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dsa_27687/07_2026/8dsa_27687.map" model { file = "/net/cci-nas-00/data/ceres_data/8dsa_27687/07_2026/8dsa_27687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dsa_27687/07_2026/8dsa_27687.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dsa_27687/07_2026/8dsa_27687.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dsa_27687/07_2026/8dsa_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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12039 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1662 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 2 Chain: "B" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1662 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 2 Chain: "C" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2685 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 9, 'TRANS': 310} Chain breaks: 2 Chain: "D" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2646 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1662 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 2 Chain: "F" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1599 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 3, 'TRANS': 187} Chain breaks: 2 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.56, per 1000 atoms: 0.21 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: 0.81 Conformation dependent library (CDL) restraints added in 397.8 milliseconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 73.0% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 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: 1.75 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2565 1.33 - 1.46: 3178 1.46 - 1.58: 6500 1.58 - 1.70: 2 1.70 - 1.82: 140 Bond restraints: 12385 Sorted by residual: bond pdb=" C10 PEE C 902 " pdb=" O4 PEE C 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C10 PEE C 901 " pdb=" O4 PEE C 901 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" O4P PEE D 902 " pdb=" P PEE D 902 " ideal model delta sigma weight residual 1.653 1.777 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" O4P PEE D 901 " pdb=" P PEE D 901 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C10 PEE C 902 " pdb=" O2 PEE C 902 " ideal model delta sigma weight residual 1.332 1.215 0.117 2.00e-02 2.50e+03 3.41e+01 ... (remaining 12380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 16543 2.77 - 5.54: 189 5.54 - 8.31: 32 8.31 - 11.08: 5 11.08 - 13.85: 4 Bond angle restraints: 16773 Sorted by residual: angle pdb=" O1P PEE D 902 " pdb=" P PEE D 902 " pdb=" O2P PEE D 902 " ideal model delta sigma weight residual 119.43 133.28 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE D 901 " pdb=" P PEE D 901 " pdb=" O2P PEE D 901 " ideal model delta sigma weight residual 119.43 133.19 -13.76 3.00e+00 1.11e-01 2.10e+01 angle pdb=" C11 PEE C 901 " pdb=" C10 PEE C 901 " pdb=" O2 PEE C 901 " ideal model delta sigma weight residual 111.70 124.69 -12.99 3.00e+00 1.11e-01 1.87e+01 angle pdb=" C11 PEE C 902 " pdb=" C10 PEE C 902 " pdb=" O2 PEE C 902 " ideal model delta sigma weight residual 111.70 124.67 -12.97 3.00e+00 1.11e-01 1.87e+01 angle pdb=" CA GLU C 245 " pdb=" CB GLU C 245 " pdb=" CG GLU C 245 " ideal model delta sigma weight residual 114.10 121.71 -7.61 2.00e+00 2.50e-01 1.45e+01 ... (remaining 16768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.75: 6951 34.75 - 69.50: 251 69.50 - 104.25: 12 104.25 - 139.00: 2 139.00 - 173.75: 2 Dihedral angle restraints: 7218 sinusoidal: 2951 harmonic: 4267 Sorted by residual: dihedral pdb=" CB CYS D 113 " pdb=" SG CYS D 113 " pdb=" SG CYS D 295 " pdb=" CB CYS D 295 " ideal model delta sinusoidal sigma weight residual 93.00 37.93 55.07 1 1.00e+01 1.00e-02 4.10e+01 dihedral pdb=" CA GLU A 115 " pdb=" C GLU A 115 " pdb=" N ASN A 116 " pdb=" CA ASN A 116 " ideal model delta harmonic sigma weight residual -180.00 -156.01 -23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" N PEE D 902 " pdb=" C4 PEE D 902 " pdb=" C5 PEE D 902 " pdb=" O4P PEE D 902 " ideal model delta sinusoidal sigma weight residual -56.97 116.78 -173.75 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 7215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1724 0.085 - 0.171: 117 0.171 - 0.256: 3 0.256 - 0.341: 0 0.341 - 0.426: 2 Chirality restraints: 1846 Sorted by residual: chirality pdb=" C2 PEE D 902 " pdb=" C1 PEE D 902 " pdb=" C3 PEE D 902 " pdb=" O2 PEE D 902 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" C2 PEE D 901 " pdb=" C1 PEE D 901 " pdb=" C3 PEE D 901 " pdb=" O2 PEE D 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CB VAL F 263 " pdb=" CA VAL F 263 " pdb=" CG1 VAL F 263 " pdb=" CG2 VAL F 263 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1843 not shown) Planarity restraints: 1985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 23 " 0.019 2.00e-02 2.50e+03 2.17e-02 1.18e+01 pdb=" CG TRP A 23 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A 23 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 23 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 23 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 23 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 23 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 23 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 120 " 0.021 2.00e-02 2.50e+03 2.00e-02 9.99e+00 pdb=" CG TRP D 120 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP D 120 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP D 120 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 120 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 120 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 120 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 120 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 120 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 120 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 143 " -0.022 2.00e-02 2.50e+03 1.94e-02 9.44e+00 pdb=" CG TRP A 143 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 143 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 143 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 143 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 143 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 143 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 143 " 0.001 2.00e-02 2.50e+03 ... (remaining 1982 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 835 2.74 - 3.28: 12354 3.28 - 3.82: 20773 3.82 - 4.36: 23360 4.36 - 4.90: 40918 Nonbonded interactions: 98240 Sorted by model distance: nonbonded pdb=" OD2 ASP A 50 " pdb=" OH TYR A 114 " model vdw 2.201 3.040 nonbonded pdb=" O ILE C 356 " pdb=" OG SER C 360 " model vdw 2.206 3.040 nonbonded pdb=" O THR E 44 " pdb=" OG1 THR E 48 " model vdw 2.221 3.040 nonbonded pdb=" OD2 ASP E 110 " pdb=" NE2 GLN F 106 " model vdw 2.251 3.120 nonbonded pdb=" OG1 THR C 316 " pdb=" OE2 GLU D 115 " model vdw 2.265 3.040 ... (remaining 98235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 15 through 407 or resid 901 through 902)) selection = (chain 'D' and (resid 15 through 407 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O2 \ or name O4 )) or (resid 902 and (name C10 or name C11 or name C12 or name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name O2 \ or name O4 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 10.860 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.151 12402 Z= 0.266 Angle : 0.807 13.851 16807 Z= 0.440 Chirality : 0.047 0.426 1846 Planarity : 0.006 0.054 1985 Dihedral : 17.196 173.749 4413 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.98 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 are not related in a simple way. whole: 0.06 (0.22), residues: 1382 helix: 0.52 (0.16), residues: 962 sheet: 0.25 (0.54), residues: 102 loop : -1.23 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 345 TYR 0.031 0.002 TYR E 325 PHE 0.039 0.002 PHE C 390 TRP 0.058 0.002 TRP A 23 HIS 0.023 0.002 HIS E 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.27 (12385) covalent geometry : angle 0.80545 / 0.44 (16773) SS BOND : bond 0.00319 / 0.20 ( 17) SS BOND : angle 1.25539 / 0.81 ( 34) hydrogen bonds : bond 0.13389 / 9.07 ( 806) hydrogen bonds : angle 6.19165 / 4.41 ( 2379) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 350 time to evaluate : 0.490 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: 0.6443 (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: 0.5994 (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: 0.1003 time to fit residues: 50.5428 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 : 0.457 ------------------------------------------------------------------------------- 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... ** 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** F 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.216111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.176672 restraints weight = 18731.578| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 2.90 r_work: 0.4042 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.2778 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= 0.145 Angle : 0.596 8.326 16807 Z= 0.315 Chirality : 0.041 0.242 1846 Planarity : 0.004 0.053 1985 Dihedral : 8.876 154.326 1656 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.64 % Allowed : 21.39 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.22), residues: 1382 helix: 1.42 (0.16), residues: 960 sheet: 0.40 (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 0.027 0.002 TYR F 262 PHE 0.024 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/Z covalent geometry : bond 0.00323 / 0.15 (12385) covalent geometry : angle 0.59423 / 0.31 (16773) SS BOND : bond 0.00302 / 0.20 ( 17) SS BOND : angle 1.27542 / 0.94 ( 34) hydrogen bonds : bond 0.04219 / 2.81 ( 806) hydrogen bonds : angle 4.40325 / 3.13 ( 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 314 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 253 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TRP cc_start: 0.6221 (p90) cc_final: 0.5488 (p90) REVERT: B 35 MET cc_start: 0.6811 (mtp) cc_final: 0.6380 (mtt) REVERT: B 117 ARG cc_start: 0.7315 (tpt90) cc_final: 0.6563 (mmm160) REVERT: B 275 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.6110 (t80) REVERT: B 331 PHE cc_start: 0.6545 (OUTLIER) cc_final: 0.5947 (m-10) REVERT: B 337 MET cc_start: 0.7276 (tmm) cc_final: 0.6803 (tmm) REVERT: C 25 ASP cc_start: 0.8016 (m-30) cc_final: 0.7755 (m-30) REVERT: C 110 ASP cc_start: 0.7348 (m-30) cc_final: 0.7057 (m-30) REVERT: C 125 PHE cc_start: 0.7808 (t80) cc_final: 0.7578 (t80) REVERT: C 161 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6800 (pp) REVERT: C 171 ARG cc_start: 0.8547 (tmt-80) cc_final: 0.8072 (tmt-80) REVERT: C 388 LYS cc_start: 0.7396 (ttpt) cc_final: 0.7189 (tmmt) REVERT: C 389 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.7076 (ttm170) REVERT: D 157 VAL cc_start: 0.8088 (t) cc_final: 0.7723 (p) REVERT: D 281 TYR cc_start: 0.6460 (OUTLIER) cc_final: 0.5666 (m-10) REVERT: D 364 ASP cc_start: 0.7164 (t0) cc_final: 0.6590 (t0) REVERT: E 291 PHE cc_start: 0.4203 (m-10) cc_final: 0.2973 (p90) REVERT: E 314 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5923 (pp) REVERT: F 35 MET cc_start: 0.6428 (mmt) cc_final: 0.5509 (mmt) REVERT: F 96 MET cc_start: 0.4560 (mpp) cc_final: 0.4208 (mmt) outliers start: 61 outliers final: 26 residues processed: 296 average time/residue: 0.0884 time to fit residues: 38.3838 Evaluate side-chains 261 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 344 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 59 VAL 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: 0.9980 chunk 54 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 239 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.211306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.172014 restraints weight = 18830.538| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 2.49 r_work: 0.4020 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.3585 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= 0.174 Angle : 0.598 8.684 16807 Z= 0.317 Chirality : 0.042 0.202 1846 Planarity : 0.004 0.048 1985 Dihedral : 8.359 129.784 1653 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.10 % Allowed : 21.69 % 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 are not related in a simple way. whole: 1.26 (0.22), residues: 1382 helix: 1.53 (0.16), residues: 961 sheet: 0.63 (0.52), residues: 107 loop : -1.24 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 345 TYR 0.034 0.002 TYR F 262 PHE 0.031 0.002 PHE E 291 TRP 0.030 0.002 TRP E 24 HIS 0.006 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (12385) covalent geometry : angle 0.59575 / 0.32 (16773) SS BOND : bond 0.00437 / 0.29 ( 17) SS BOND : angle 1.35677 / 0.98 ( 34) hydrogen bonds : bond 0.04076 / 2.69 ( 806) hydrogen bonds : angle 4.35835 / 3.08 ( 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 311 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 244 time to evaluate : 0.382 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: 0.7536 (ptm) cc_final: 0.7328 (ptm) REVERT: B 35 MET cc_start: 0.6869 (mtp) cc_final: 0.6491 (mtt) REVERT: B 115 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6739 (pt0) REVERT: B 117 ARG cc_start: 0.7488 (tpt90) cc_final: 0.7249 (tpm170) REVERT: B 275 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.6150 (t80) REVERT: B 337 MET cc_start: 0.6882 (tmm) cc_final: 0.6632 (tmm) REVERT: C 104 HIS cc_start: 0.7688 (OUTLIER) cc_final: 0.6954 (t70) REVERT: C 110 ASP cc_start: 0.7506 (m-30) cc_final: 0.7149 (m-30) REVERT: C 171 ARG cc_start: 0.8733 (tmt-80) cc_final: 0.8453 (tmt-80) REVERT: C 401 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8528 (mmtm) REVERT: D 239 GLN cc_start: 0.7666 (pm20) cc_final: 0.7355 (pm20) REVERT: D 245 GLU cc_start: 0.7727 (tp30) cc_final: 0.7496 (tp30) REVERT: D 396 GLU cc_start: 0.7576 (pm20) cc_final: 0.7189 (pt0) REVERT: E 299 ILE cc_start: 0.4070 (OUTLIER) cc_final: 0.3142 (pt) REVERT: E 314 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.6180 (pp) REVERT: E 343 MET cc_start: 0.0526 (mtp) cc_final: -0.0454 (ptp) REVERT: F 96 MET cc_start: 0.4282 (mpp) cc_final: 0.3682 (mmm) REVERT: F 145 TRP cc_start: 0.5782 (t-100) cc_final: 0.5547 (t-100) REVERT: F 303 TYR cc_start: 0.6308 (m-80) cc_final: 0.5839 (m-80) REVERT: F 318 LYS cc_start: 0.8247 (mmmt) cc_final: 0.7630 (mmpt) outliers start: 67 outliers final: 38 residues processed: 289 average time/residue: 0.0923 time to fit residues: 38.2982 Evaluate side-chains 268 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 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 134 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 275 PHE 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 20 LEU 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 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 363 SER 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 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: 0.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 288 ASN C 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 ASN E 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.210279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.169504 restraints weight = 18838.295| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 2.89 r_work: 0.3982 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.4088 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= 0.158 Angle : 0.576 8.668 16807 Z= 0.304 Chirality : 0.041 0.204 1846 Planarity : 0.004 0.045 1985 Dihedral : 7.561 111.482 1653 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 5.33 % Allowed : 22.98 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.22), residues: 1382 helix: 1.65 (0.16), residues: 955 sheet: 0.84 (0.50), residues: 105 loop : -1.27 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 306 TYR 0.036 0.002 TYR F 330 PHE 0.019 0.002 PHE D 372 TRP 0.029 0.002 TRP A 24 HIS 0.006 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (12385) covalent geometry : angle 0.57458 / 0.30 (16773) SS BOND : bond 0.00342 / 0.22 ( 17) SS BOND : angle 1.12750 / 0.84 ( 34) hydrogen bonds : bond 0.03908 / 2.58 ( 806) hydrogen bonds : angle 4.28591 / 3.03 ( 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 300 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 230 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7584 (ptm) cc_final: 0.7381 (ptm) REVERT: A 104 HIS cc_start: 0.7242 (OUTLIER) cc_final: 0.6665 (t70) REVERT: B 35 MET cc_start: 0.6908 (mtp) cc_final: 0.6494 (mtt) REVERT: B 117 ARG cc_start: 0.7249 (tpt90) cc_final: 0.6995 (tpm170) REVERT: B 275 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.6163 (t80) REVERT: B 308 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: C 25 ASP cc_start: 0.7971 (m-30) cc_final: 0.7758 (m-30) REVERT: C 104 HIS cc_start: 0.7468 (OUTLIER) cc_final: 0.6730 (t70) REVERT: C 110 ASP cc_start: 0.7487 (m-30) cc_final: 0.7145 (m-30) REVERT: C 161 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7109 (pp) REVERT: C 171 ARG cc_start: 0.8749 (tmt-80) cc_final: 0.8331 (tmt-80) REVERT: C 241 LYS cc_start: 0.8184 (mttm) cc_final: 0.7977 (mmtt) REVERT: C 401 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8486 (mmtm) REVERT: D 157 VAL cc_start: 0.8394 (t) cc_final: 0.8052 (p) REVERT: D 239 GLN cc_start: 0.7806 (pm20) cc_final: 0.7527 (pm20) REVERT: D 245 GLU cc_start: 0.7700 (tp30) cc_final: 0.7462 (tp30) REVERT: E 52 MET cc_start: 0.5126 (ppp) cc_final: 0.3549 (ttp) REVERT: E 299 ILE cc_start: 0.3605 (OUTLIER) cc_final: 0.2833 (pt) REVERT: E 314 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6596 (pt) REVERT: E 343 MET cc_start: 0.0901 (mtp) cc_final: 0.0023 (ptp) REVERT: F 51 LYS cc_start: 0.6366 (OUTLIER) cc_final: 0.5798 (pttp) REVERT: F 303 TYR cc_start: 0.6396 (m-80) cc_final: 0.5838 (m-80) REVERT: F 318 LYS cc_start: 0.8361 (mmmt) cc_final: 0.7736 (mmpt) REVERT: F 328 SER cc_start: 0.6122 (t) cc_final: 0.5796 (p) outliers start: 70 outliers final: 44 residues processed: 278 average time/residue: 0.0953 time to fit residues: 38.4213 Evaluate side-chains 269 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 216 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS 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 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 308 TYR 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 368 VAL Chi-restraints excluded: chain C residue 401 LYS 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 314 LEU Chi-restraints excluded: chain D residue 329 VAL 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 E residue 314 LEU 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 106 GLN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 292 ASP 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: 1.9990 chunk 8 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 105 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN C 49 GLN D 105 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.210240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.169642 restraints weight = 19044.106| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 3.03 r_work: 0.3977 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12402 Z= 0.155 Angle : 0.571 7.680 16807 Z= 0.303 Chirality : 0.041 0.180 1846 Planarity : 0.003 0.044 1985 Dihedral : 7.132 76.861 1653 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.48 % Allowed : 23.36 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.22), residues: 1382 helix: 1.65 (0.16), residues: 965 sheet: 0.88 (0.50), residues: 105 loop : -1.40 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 306 TYR 0.032 0.002 TYR F 330 PHE 0.015 0.001 PHE E 291 TRP 0.029 0.002 TRP E 24 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (12385) covalent geometry : angle 0.57010 / 0.30 (16773) SS BOND : bond 0.00418 / 0.27 ( 17) SS BOND : angle 0.99027 / 0.70 ( 34) hydrogen bonds : bond 0.03817 / 2.52 ( 806) hydrogen bonds : angle 4.24320 / 3.01 ( 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 305 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 233 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8663 (mtm) cc_final: 0.8268 (mtm) REVERT: A 37 MET cc_start: 0.7758 (ptm) cc_final: 0.7536 (ptm) REVERT: A 104 HIS cc_start: 0.7283 (OUTLIER) cc_final: 0.6684 (t70) REVERT: A 144 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6742 (m-80) REVERT: B 35 MET cc_start: 0.6769 (mtp) cc_final: 0.6344 (mtt) REVERT: B 117 ARG cc_start: 0.7327 (tpt90) cc_final: 0.7014 (tpm170) REVERT: B 275 PHE cc_start: 0.6562 (OUTLIER) cc_final: 0.6116 (t80) REVERT: B 308 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.7183 (m-80) REVERT: C 25 ASP cc_start: 0.7974 (m-30) cc_final: 0.7737 (m-30) REVERT: C 104 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.6716 (t70) REVERT: C 161 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7046 (pp) REVERT: C 241 LYS cc_start: 0.8238 (mttm) cc_final: 0.8031 (mmtt) REVERT: C 306 ARG cc_start: 0.7323 (ptp-110) cc_final: 0.7045 (ttm-80) REVERT: C 401 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8442 (mmtm) REVERT: D 156 PHE cc_start: 0.7853 (t80) cc_final: 0.7553 (t80) REVERT: D 157 VAL cc_start: 0.8451 (t) cc_final: 0.8124 (p) REVERT: D 245 GLU cc_start: 0.7836 (tp30) cc_final: 0.7545 (tp30) REVERT: D 301 SER cc_start: 0.8500 (p) cc_final: 0.8240 (m) REVERT: E 52 MET cc_start: 0.5314 (ppp) cc_final: 0.3754 (ttp) REVERT: E 299 ILE cc_start: 0.3632 (OUTLIER) cc_final: 0.2740 (pt) REVERT: F 51 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.5909 (pttp) REVERT: F 96 MET cc_start: 0.4189 (ptp) cc_final: 0.3968 (ptp) REVERT: F 303 TYR cc_start: 0.6415 (m-80) cc_final: 0.6213 (m-10) REVERT: F 318 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7778 (mmpt) outliers start: 72 outliers final: 46 residues processed: 285 average time/residue: 0.0977 time to fit residues: 40.2938 Evaluate side-chains 279 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 224 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 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 51 LYS Chi-restraints excluded: chain F residue 55 LEU 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 343 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 115 optimal weight: 0.2980 chunk 110 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 33 optimal weight: 0.0030 chunk 30 optimal weight: 3.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.211148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.169243 restraints weight = 18732.178| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 3.10 r_work: 0.4000 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12402 Z= 0.124 Angle : 0.548 9.735 16807 Z= 0.287 Chirality : 0.040 0.163 1846 Planarity : 0.003 0.041 1985 Dihedral : 6.601 71.186 1653 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.49 % Allowed : 24.66 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.22), residues: 1382 helix: 1.85 (0.16), residues: 956 sheet: 1.05 (0.50), residues: 105 loop : -1.27 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 306 TYR 0.030 0.001 TYR F 330 PHE 0.020 0.001 PHE E 291 TRP 0.033 0.002 TRP E 24 HIS 0.005 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (12385) covalent geometry : angle 0.54695 / 0.29 (16773) SS BOND : bond 0.00319 / 0.20 ( 17) SS BOND : angle 0.83662 / 0.59 ( 34) hydrogen bonds : bond 0.03580 / 2.37 ( 806) hydrogen bonds : angle 4.09555 / 2.92 ( 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 294 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 235 time to evaluate : 0.378 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: 0.7589 (ptm) cc_final: 0.7370 (ptm) REVERT: A 50 ASP cc_start: 0.7022 (t0) cc_final: 0.6813 (t0) REVERT: A 104 HIS cc_start: 0.7039 (OUTLIER) cc_final: 0.6325 (t70) REVERT: A 144 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6824 (m-80) REVERT: A 262 ARG cc_start: 0.3613 (mmm160) cc_final: 0.3286 (mmm160) REVERT: B 35 MET cc_start: 0.6759 (mtp) cc_final: 0.5894 (mtt) REVERT: B 38 ILE cc_start: 0.6231 (OUTLIER) cc_final: 0.5958 (tt) REVERT: B 117 ARG cc_start: 0.7221 (tpt90) cc_final: 0.6905 (tpm170) REVERT: B 275 PHE cc_start: 0.6585 (OUTLIER) cc_final: 0.6148 (t80) REVERT: B 308 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.6857 (m-80) REVERT: B 337 MET cc_start: 0.6888 (tmm) cc_final: 0.6496 (tmm) REVERT: C 104 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.6690 (t70) REVERT: C 108 TYR cc_start: 0.7985 (t80) cc_final: 0.7732 (t80) REVERT: C 125 PHE cc_start: 0.7923 (t80) cc_final: 0.7675 (t80) REVERT: C 161 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7006 (pp) REVERT: C 265 MET cc_start: 0.5282 (tpt) cc_final: 0.5076 (tpt) REVERT: C 306 ARG cc_start: 0.7341 (ptp-110) cc_final: 0.7061 (ttm-80) REVERT: C 401 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8466 (mmtm) REVERT: D 37 MET cc_start: 0.5954 (tmm) cc_final: 0.5590 (tpt) REVERT: D 156 PHE cc_start: 0.7710 (t80) cc_final: 0.7372 (t80) REVERT: D 157 VAL cc_start: 0.8408 (t) cc_final: 0.8091 (p) REVERT: D 245 GLU cc_start: 0.7801 (tp30) cc_final: 0.7556 (tp30) REVERT: D 301 SER cc_start: 0.8473 (p) cc_final: 0.8238 (m) REVERT: E 52 MET cc_start: 0.5266 (ppp) cc_final: 0.3656 (ttp) REVERT: E 299 ILE cc_start: 0.3407 (OUTLIER) cc_final: 0.2173 (mm) REVERT: F 51 LYS cc_start: 0.6443 (OUTLIER) cc_final: 0.5866 (pttp) REVERT: F 96 MET cc_start: 0.4118 (ptp) cc_final: 0.3889 (ptp) REVERT: F 318 LYS cc_start: 0.8268 (mmmt) cc_final: 0.7794 (mmpt) outliers start: 59 outliers final: 41 residues processed: 281 average time/residue: 0.0998 time to fit residues: 40.4282 Evaluate side-chains 269 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 218 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 115 GLU 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 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 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 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 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 E residue 17 TYR 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 106 GLN Chi-restraints excluded: chain F residue 273 PHE 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: 1.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 55 optimal weight: 0.2980 chunk 33 optimal weight: 0.0570 chunk 44 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** F 113 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.210901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.168773 restraints weight = 18784.964| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 3.01 r_work: 0.4002 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12402 Z= 0.128 Angle : 0.554 9.977 16807 Z= 0.290 Chirality : 0.040 0.158 1846 Planarity : 0.003 0.040 1985 Dihedral : 6.522 71.963 1653 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.79 % Allowed : 25.11 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.22), residues: 1382 helix: 1.90 (0.16), residues: 956 sheet: 1.17 (0.51), residues: 105 loop : -1.23 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 306 TYR 0.032 0.001 TYR F 330 PHE 0.014 0.001 PHE F 326 TRP 0.031 0.001 TRP E 24 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (12385) covalent geometry : angle 0.55367 / 0.29 (16773) SS BOND : bond 0.00264 / 0.16 ( 17) SS BOND : angle 0.77520 / 0.55 ( 34) hydrogen bonds : bond 0.03534 / 2.35 ( 806) hydrogen bonds : angle 4.06506 / 2.90 ( 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 297 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 234 time to evaluate : 0.377 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: 0.7619 (ptm) cc_final: 0.7396 (ptm) REVERT: A 104 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.6377 (t70) REVERT: A 144 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: A 337 MET cc_start: 0.5346 (tpt) cc_final: 0.5090 (tpt) REVERT: B 35 MET cc_start: 0.6847 (mtp) cc_final: 0.6007 (mtt) REVERT: B 38 ILE cc_start: 0.6254 (OUTLIER) cc_final: 0.5952 (tt) REVERT: B 117 ARG cc_start: 0.7174 (tpt90) cc_final: 0.6865 (tpm170) REVERT: B 275 PHE cc_start: 0.6581 (OUTLIER) cc_final: 0.6108 (t80) REVERT: B 308 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.6909 (m-80) REVERT: B 337 MET cc_start: 0.6810 (tmm) cc_final: 0.6423 (tmm) REVERT: C 104 HIS cc_start: 0.7502 (OUTLIER) cc_final: 0.6706 (t70) REVERT: C 108 TYR cc_start: 0.7980 (t80) cc_final: 0.7670 (t80) REVERT: C 125 PHE cc_start: 0.7931 (t80) cc_final: 0.7689 (t80) REVERT: C 161 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7091 (pp) REVERT: C 401 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8513 (mmtm) REVERT: D 37 MET cc_start: 0.6030 (tmm) cc_final: 0.5621 (tpt) REVERT: D 156 PHE cc_start: 0.7735 (t80) cc_final: 0.7448 (t80) REVERT: D 157 VAL cc_start: 0.8414 (t) cc_final: 0.8092 (p) REVERT: D 245 GLU cc_start: 0.7774 (tp30) cc_final: 0.7537 (tp30) REVERT: D 252 THR cc_start: 0.8792 (m) cc_final: 0.8579 (p) REVERT: D 301 SER cc_start: 0.8477 (p) cc_final: 0.8237 (m) REVERT: D 345 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.6333 (ptm160) REVERT: D 356 ILE cc_start: 0.4555 (OUTLIER) cc_final: 0.3919 (mt) REVERT: E 52 MET cc_start: 0.5315 (ppp) cc_final: 0.3737 (ttp) REVERT: E 299 ILE cc_start: 0.3280 (OUTLIER) cc_final: 0.2080 (mm) REVERT: F 55 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7321 (mt) REVERT: F 318 LYS cc_start: 0.8302 (mmmt) cc_final: 0.7810 (mmpt) outliers start: 63 outliers final: 44 residues processed: 285 average time/residue: 0.0914 time to fit residues: 38.0108 Evaluate side-chains 272 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 216 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 329 VAL Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 104 HIS 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 101 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 273 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 67 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 78 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.209643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.169147 restraints weight = 18719.385| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.98 r_work: 0.3994 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12402 Z= 0.145 Angle : 0.592 9.506 16807 Z= 0.311 Chirality : 0.041 0.218 1846 Planarity : 0.003 0.040 1985 Dihedral : 6.607 72.130 1653 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.87 % Allowed : 25.49 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.22), residues: 1382 helix: 1.80 (0.16), residues: 964 sheet: 1.11 (0.50), residues: 105 loop : -1.44 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 306 TYR 0.035 0.001 TYR B 325 PHE 0.017 0.001 PHE A 27 TRP 0.032 0.002 TRP E 24 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (12385) covalent geometry : angle 0.59066 / 0.31 (16773) SS BOND : bond 0.00333 / 0.22 ( 17) SS BOND : angle 1.07389 / 0.80 ( 34) hydrogen bonds : bond 0.03721 / 2.48 ( 806) hydrogen bonds : angle 4.18767 / 2.98 ( 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 291 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 227 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7634 (ptm) cc_final: 0.7400 (ptm) REVERT: A 50 ASP cc_start: 0.6942 (t0) cc_final: 0.6693 (t0) REVERT: A 104 HIS cc_start: 0.7222 (OUTLIER) cc_final: 0.6622 (t70) REVERT: A 144 PHE cc_start: 0.6959 (OUTLIER) cc_final: 0.6743 (m-80) REVERT: A 337 MET cc_start: 0.5351 (tpt) cc_final: 0.5136 (tpt) REVERT: B 35 MET cc_start: 0.6977 (mtp) cc_final: 0.6091 (mtt) REVERT: B 38 ILE cc_start: 0.6255 (OUTLIER) cc_final: 0.5955 (tt) REVERT: B 117 ARG cc_start: 0.7189 (tpt90) cc_final: 0.6876 (tpm170) REVERT: B 275 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.6142 (t80) REVERT: B 308 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.6967 (m-80) REVERT: B 337 MET cc_start: 0.6829 (tmm) cc_final: 0.6454 (tmm) REVERT: C 104 HIS cc_start: 0.7550 (OUTLIER) cc_final: 0.6691 (t70) REVERT: C 108 TYR cc_start: 0.8030 (t80) cc_final: 0.7654 (t80) REVERT: C 161 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7231 (pp) REVERT: C 401 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8520 (mmtm) REVERT: D 37 MET cc_start: 0.6046 (tmm) cc_final: 0.5656 (tpt) REVERT: D 156 PHE cc_start: 0.7776 (t80) cc_final: 0.7447 (t80) REVERT: D 157 VAL cc_start: 0.8474 (t) cc_final: 0.8100 (p) REVERT: D 245 GLU cc_start: 0.7783 (tp30) cc_final: 0.7548 (tp30) REVERT: D 252 THR cc_start: 0.8792 (m) cc_final: 0.8571 (p) REVERT: D 301 SER cc_start: 0.8499 (p) cc_final: 0.8263 (m) REVERT: D 345 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6552 (ptm160) REVERT: D 356 ILE cc_start: 0.4641 (OUTLIER) cc_final: 0.3965 (mt) REVERT: E 52 MET cc_start: 0.5305 (ppp) cc_final: 0.3832 (ttp) REVERT: E 299 ILE cc_start: 0.3358 (OUTLIER) cc_final: 0.2148 (mm) REVERT: E 343 MET cc_start: 0.1547 (mtp) cc_final: 0.0934 (ptp) REVERT: F 37 MET cc_start: 0.7456 (mpp) cc_final: 0.6954 (ptp) REVERT: F 55 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7324 (mt) REVERT: F 318 LYS cc_start: 0.8283 (mmmt) cc_final: 0.7949 (mmmt) outliers start: 64 outliers final: 44 residues processed: 280 average time/residue: 0.0872 time to fit residues: 35.7162 Evaluate side-chains 272 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 216 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 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 286 VAL Chi-restraints excluded: chain B residue 308 TYR 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 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 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 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 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 317 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 356 ILE 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 17 PHE Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 343 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: 1.9990 chunk 86 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 63 optimal weight: 0.0670 chunk 3 optimal weight: 0.7980 chunk 135 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 GLN C 49 GLN ** 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 288 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.210531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.169266 restraints weight = 18568.306| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 3.14 r_work: 0.3997 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12402 Z= 0.134 Angle : 0.590 7.789 16807 Z= 0.311 Chirality : 0.041 0.190 1846 Planarity : 0.003 0.040 1985 Dihedral : 6.569 72.588 1653 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.72 % Allowed : 25.80 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.22), residues: 1382 helix: 1.88 (0.16), residues: 963 sheet: 1.12 (0.50), residues: 105 loop : -1.42 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 306 TYR 0.033 0.001 TYR F 330 PHE 0.015 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/Z covalent geometry : bond 0.00305 / 0.13 (12385) covalent geometry : angle 0.58905 / 0.31 (16773) SS BOND : bond 0.00278 / 0.17 ( 17) SS BOND : angle 1.00359 / 0.75 ( 34) hydrogen bonds : bond 0.03601 / 2.39 ( 806) hydrogen bonds : angle 4.17102 / 2.96 ( 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 287 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 225 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7657 (ptm) cc_final: 0.7422 (ptm) REVERT: A 50 ASP cc_start: 0.6869 (t0) cc_final: 0.6573 (t0) REVERT: A 104 HIS cc_start: 0.7079 (OUTLIER) cc_final: 0.6445 (t70) REVERT: A 337 MET cc_start: 0.5380 (tpt) cc_final: 0.5158 (tpt) REVERT: B 35 MET cc_start: 0.6970 (mtp) cc_final: 0.6127 (mtt) REVERT: B 37 MET cc_start: 0.8780 (mtm) cc_final: 0.8541 (mtm) REVERT: B 38 ILE cc_start: 0.6242 (OUTLIER) cc_final: 0.5965 (tt) REVERT: B 117 ARG cc_start: 0.7180 (tpt90) cc_final: 0.6852 (tpm170) REVERT: B 275 PHE cc_start: 0.6561 (OUTLIER) cc_final: 0.6122 (t80) REVERT: B 308 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6860 (m-80) REVERT: B 337 MET cc_start: 0.6841 (tmm) cc_final: 0.6484 (tmm) REVERT: C 104 HIS cc_start: 0.7538 (OUTLIER) cc_final: 0.6678 (t70) REVERT: C 108 TYR cc_start: 0.7863 (t80) cc_final: 0.7552 (t80) REVERT: C 161 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7173 (pp) REVERT: C 401 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8536 (mmtm) REVERT: D 37 MET cc_start: 0.5966 (tmm) cc_final: 0.5678 (tpt) REVERT: D 156 PHE cc_start: 0.7740 (t80) cc_final: 0.7413 (t80) REVERT: D 157 VAL cc_start: 0.8457 (t) cc_final: 0.7995 (p) REVERT: D 161 LEU cc_start: 0.7654 (pp) cc_final: 0.7417 (tt) REVERT: D 245 GLU cc_start: 0.7844 (tp30) cc_final: 0.7610 (tp30) REVERT: D 252 THR cc_start: 0.8810 (m) cc_final: 0.8601 (p) REVERT: D 301 SER cc_start: 0.8505 (p) cc_final: 0.8269 (m) REVERT: D 345 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6587 (ptm160) REVERT: D 356 ILE cc_start: 0.4800 (OUTLIER) cc_final: 0.4194 (mt) REVERT: E 52 MET cc_start: 0.5401 (ppp) cc_final: 0.3985 (ttp) REVERT: E 299 ILE cc_start: 0.3282 (OUTLIER) cc_final: 0.2099 (mm) REVERT: E 343 MET cc_start: 0.1760 (mtp) cc_final: 0.1131 (ptp) REVERT: F 37 MET cc_start: 0.7472 (mpp) cc_final: 0.6979 (ptp) REVERT: F 55 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7328 (mt) REVERT: F 288 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6680 (tm-30) REVERT: F 318 LYS cc_start: 0.8267 (mmmt) cc_final: 0.7911 (mmmt) outliers start: 62 outliers final: 46 residues processed: 269 average time/residue: 0.0886 time to fit residues: 34.9942 Evaluate side-chains 274 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 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 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 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 134 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR 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 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP 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 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 317 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 104 HIS 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 55 LEU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 288 GLN 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: 0.9980 chunk 102 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 37 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 49 GLN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.208972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.169289 restraints weight = 18804.730| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 2.64 r_work: 0.4015 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.5352 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= 0.157 Angle : 0.621 9.756 16807 Z= 0.330 Chirality : 0.041 0.177 1846 Planarity : 0.004 0.041 1985 Dihedral : 6.738 72.729 1653 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.49 % Allowed : 26.41 % 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 are not related in a simple way. whole: 1.51 (0.22), residues: 1382 helix: 1.77 (0.16), residues: 963 sheet: 0.97 (0.51), residues: 107 loop : -1.48 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 306 TYR 0.038 0.002 TYR F 330 PHE 0.015 0.001 PHE A 27 TRP 0.037 0.002 TRP C 168 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (12385) covalent geometry : angle 0.62025 / 0.33 (16773) SS BOND : bond 0.00336 / 0.21 ( 17) SS BOND : angle 1.06252 / 0.80 ( 34) hydrogen bonds : bond 0.03742 / 2.49 ( 806) hydrogen bonds : angle 4.23317 / 3.00 ( 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 278 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 219 time to evaluate : 0.467 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: 0.7652 (ptm) cc_final: 0.7324 (ptt) REVERT: A 50 ASP cc_start: 0.6939 (t0) cc_final: 0.6586 (t0) REVERT: A 104 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.6822 (t70) REVERT: A 337 MET cc_start: 0.5454 (tpt) cc_final: 0.5244 (tpt) REVERT: B 35 MET cc_start: 0.7128 (mtp) cc_final: 0.6240 (mtt) REVERT: B 37 MET cc_start: 0.8880 (mtm) cc_final: 0.8621 (mtm) REVERT: B 38 ILE cc_start: 0.6397 (OUTLIER) cc_final: 0.6079 (tt) REVERT: B 117 ARG cc_start: 0.7354 (tpt90) cc_final: 0.7053 (tpm170) REVERT: B 275 PHE cc_start: 0.6696 (OUTLIER) cc_final: 0.6246 (t80) REVERT: B 308 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.7008 (m-80) REVERT: B 337 MET cc_start: 0.6861 (tmm) cc_final: 0.6502 (tmm) REVERT: C 104 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.6882 (t70) REVERT: C 108 TYR cc_start: 0.8009 (t80) cc_final: 0.7725 (t80) REVERT: C 161 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7240 (pp) REVERT: C 401 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8634 (mmtm) REVERT: D 37 MET cc_start: 0.6156 (tmm) cc_final: 0.5796 (tpt) REVERT: D 156 PHE cc_start: 0.7796 (t80) cc_final: 0.7494 (t80) REVERT: D 157 VAL cc_start: 0.8497 (t) cc_final: 0.8143 (p) REVERT: D 245 GLU cc_start: 0.7898 (tp30) cc_final: 0.7675 (tp30) REVERT: D 252 THR cc_start: 0.8804 (m) cc_final: 0.8590 (p) REVERT: D 279 ILE cc_start: 0.5517 (OUTLIER) cc_final: 0.5112 (mm) REVERT: D 301 SER cc_start: 0.8625 (p) cc_final: 0.8371 (m) REVERT: D 345 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6668 (ptm160) REVERT: D 356 ILE cc_start: 0.4786 (OUTLIER) cc_final: 0.4138 (mt) REVERT: E 52 MET cc_start: 0.5440 (ppp) cc_final: 0.3767 (ttp) REVERT: E 299 ILE cc_start: 0.3781 (OUTLIER) cc_final: 0.2457 (mm) REVERT: E 343 MET cc_start: 0.1814 (mtp) cc_final: 0.1177 (ptp) REVERT: F 37 MET cc_start: 0.7418 (mpp) cc_final: 0.6978 (ptp) REVERT: F 55 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7338 (mt) REVERT: F 288 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6580 (tm-30) REVERT: F 305 ASN cc_start: 0.5945 (t0) cc_final: 0.5652 (m-40) REVERT: F 318 LYS cc_start: 0.8314 (mmmt) cc_final: 0.7954 (mmmt) outliers start: 59 outliers final: 42 residues processed: 261 average time/residue: 0.0906 time to fit residues: 34.8953 Evaluate side-chains 268 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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 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 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 134 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR 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 275 PHE 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 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 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 317 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 356 ILE 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 55 LEU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 288 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 40 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 49 GLN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN F 288 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.208995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.169435 restraints weight = 18744.453| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 2.61 r_work: 0.4008 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.5430 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= 0.152 Angle : 0.627 11.507 16807 Z= 0.333 Chirality : 0.042 0.244 1846 Planarity : 0.004 0.041 1985 Dihedral : 6.843 73.371 1653 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.49 % Allowed : 26.33 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.22), residues: 1382 helix: 1.76 (0.16), residues: 963 sheet: 0.96 (0.51), residues: 107 loop : -1.49 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 306 TYR 0.035 0.001 TYR D 284 PHE 0.015 0.001 PHE C 250 TRP 0.043 0.002 TRP C 168 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (12385) covalent geometry : angle 0.62596 / 0.33 (16773) SS BOND : bond 0.00319 / 0.20 ( 17) SS BOND : angle 1.02175 / 0.77 ( 34) hydrogen bonds : bond 0.03732 / 2.47 ( 806) hydrogen bonds : angle 4.24707 / 3.01 ( 2379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2882.40 seconds wall clock time: 50 minutes 8.75 seconds (3008.75 seconds total)