Starting phenix.real_space_refine on Wed Mar 4 00:32:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x17_21991/03_2026/6x17_21991.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x17_21991/03_2026/6x17_21991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x17_21991/03_2026/6x17_21991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x17_21991/03_2026/6x17_21991.map" model { file = "/net/cci-nas-00/data/ceres_data/6x17_21991/03_2026/6x17_21991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x17_21991/03_2026/6x17_21991.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 3 5.49 5 S 51 5.16 5 C 6195 2.51 5 N 1500 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9390 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3086 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 18, 'TRANS': 396} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 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} Restraints were copied for chains: B, C Time building chain proxies: 2.44, per 1000 atoms: 0.26 Number of scatterers: 9390 At special positions: 0 Unit cell: (109.472, 106.252, 82.6403, 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 51 16.00 P 3 15.00 O 1641 8.00 N 1500 7.00 C 6195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.78 Conformation dependent library (CDL) restraints added in 392.6 milliseconds 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 11 through 33 removed outlier: 3.533A pdb=" N LYS A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 removed outlier: 3.537A pdb=" N VAL A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.942A pdb=" N GLY A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.639A pdb=" N ILE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 107 removed outlier: 3.790A pdb=" N ARG A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 141 through 148 removed outlier: 4.169A pdb=" N ASN A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 169 Processing helix chain 'A' and resid 175 through 220 removed outlier: 3.573A pdb=" N ASP A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 227 through 254 removed outlier: 3.978A pdb=" N VAL A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 5.806A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 295 through 307 removed outlier: 3.558A pdb=" N TYR A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'A' and resid 337 through 352 removed outlier: 3.558A pdb=" N ILE A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 4.009A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 387 Processing helix chain 'A' and resid 389 through 416 removed outlier: 3.624A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 11 through 33 removed outlier: 3.532A pdb=" N LYS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 43 removed outlier: 3.536A pdb=" N VAL B 39 " --> pdb=" O TYR B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 57 removed outlier: 3.942A pdb=" N GLY B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 68 removed outlier: 3.639A pdb=" N ILE B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 107 removed outlier: 3.790A pdb=" N ARG B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 136 Processing helix chain 'B' and resid 141 through 148 removed outlier: 4.169A pdb=" N ASN B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 169 Processing helix chain 'B' and resid 175 through 220 removed outlier: 3.573A pdb=" N ASP B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Proline residue: B 206 - end of helix Processing helix chain 'B' and resid 227 through 254 removed outlier: 3.978A pdb=" N VAL B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 5.807A pdb=" N ASP B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ALA B 268 " --> pdb=" O HIS B 264 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.559A pdb=" N TYR B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE B 301 " --> pdb=" O GLY B 297 " (cutoff:3.500A) Proline residue: B 304 - end of helix Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 337 through 352 removed outlier: 3.557A pdb=" N ILE B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 371 removed outlier: 4.008A pdb=" N ILE B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 370 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 387 Processing helix chain 'B' and resid 389 through 416 removed outlier: 3.624A pdb=" N LEU B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 10 Processing helix chain 'C' and resid 11 through 33 removed outlier: 3.532A pdb=" N LYS C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.537A pdb=" N VAL C 39 " --> pdb=" O TYR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 57 removed outlier: 3.942A pdb=" N GLY C 47 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 68 removed outlier: 3.640A pdb=" N ILE C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 66 " --> pdb=" O VAL C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 107 removed outlier: 3.790A pdb=" N ARG C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 141 through 148 removed outlier: 4.169A pdb=" N ASN C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 169 Processing helix chain 'C' and resid 175 through 220 removed outlier: 3.572A pdb=" N ASP C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) Proline residue: C 206 - end of helix Processing helix chain 'C' and resid 227 through 254 removed outlier: 3.978A pdb=" N VAL C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 276 removed outlier: 5.807A pdb=" N ASP C 267 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA C 268 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 276 " --> pdb=" O ALA C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 295 through 307 removed outlier: 3.558A pdb=" N TYR C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE C 301 " --> pdb=" O GLY C 297 " (cutoff:3.500A) Proline residue: C 304 - end of helix Processing helix chain 'C' and resid 311 through 329 Processing helix chain 'C' and resid 337 through 352 removed outlier: 3.558A pdb=" N ILE C 341 " --> pdb=" O GLN C 337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 371 removed outlier: 4.009A pdb=" N ILE C 361 " --> pdb=" O GLY C 357 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 387 Processing helix chain 'C' and resid 389 through 416 removed outlier: 3.624A pdb=" N LEU C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) 706 hydrogen bonds defined for protein. 2118 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: 1.60 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1440 1.31 - 1.43: 2305 1.43 - 1.56: 5672 1.56 - 1.68: 51 1.68 - 1.80: 99 Bond restraints: 9567 Sorted by residual: bond pdb=" C16 6OU C 501 " pdb=" O18 6OU C 501 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C16 6OU A 501 " pdb=" O18 6OU A 501 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C16 6OU B 501 " pdb=" O18 6OU B 501 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" C31 6OU C 501 " pdb=" O30 6OU C 501 " ideal model delta sigma weight residual 1.331 1.407 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C31 6OU A 501 " pdb=" O30 6OU A 501 " ideal model delta sigma weight residual 1.331 1.406 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 9562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 12738 3.13 - 6.26: 222 6.26 - 9.39: 45 9.39 - 12.51: 6 12.51 - 15.64: 3 Bond angle restraints: 13014 Sorted by residual: angle pdb=" O22 6OU C 501 " pdb=" P23 6OU C 501 " pdb=" O26 6OU C 501 " ideal model delta sigma weight residual 93.95 109.59 -15.64 3.00e+00 1.11e-01 2.72e+01 angle pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " pdb=" O26 6OU A 501 " ideal model delta sigma weight residual 93.95 109.57 -15.62 3.00e+00 1.11e-01 2.71e+01 angle pdb=" O22 6OU B 501 " pdb=" P23 6OU B 501 " pdb=" O26 6OU B 501 " ideal model delta sigma weight residual 93.95 109.56 -15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" N ALA B 205 " pdb=" CA ALA B 205 " pdb=" C ALA B 205 " ideal model delta sigma weight residual 109.81 119.47 -9.66 2.21e+00 2.05e-01 1.91e+01 angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 119.45 -9.64 2.21e+00 2.05e-01 1.90e+01 ... (remaining 13009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.60: 5297 25.60 - 51.21: 331 51.21 - 76.81: 30 76.81 - 102.42: 0 102.42 - 128.02: 6 Dihedral angle restraints: 5664 sinusoidal: 2130 harmonic: 3534 Sorted by residual: dihedral pdb=" CA LEU C 333 " pdb=" C LEU C 333 " pdb=" N THR C 334 " pdb=" CA THR C 334 " ideal model delta harmonic sigma weight residual 180.00 141.62 38.38 0 5.00e+00 4.00e-02 5.89e+01 dihedral pdb=" CA LEU B 333 " pdb=" C LEU B 333 " pdb=" N THR B 334 " pdb=" CA THR B 334 " ideal model delta harmonic sigma weight residual 180.00 141.63 38.37 0 5.00e+00 4.00e-02 5.89e+01 dihedral pdb=" CA LEU A 333 " pdb=" C LEU A 333 " pdb=" N THR A 334 " pdb=" CA THR A 334 " ideal model delta harmonic sigma weight residual 180.00 141.67 38.33 0 5.00e+00 4.00e-02 5.88e+01 ... (remaining 5661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1028 0.040 - 0.080: 412 0.080 - 0.119: 111 0.119 - 0.159: 39 0.159 - 0.199: 24 Chirality restraints: 1614 Sorted by residual: chirality pdb=" CA SER C 74 " pdb=" N SER C 74 " pdb=" C SER C 74 " pdb=" CB SER C 74 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CA SER A 74 " pdb=" N SER A 74 " pdb=" C SER A 74 " pdb=" CB SER A 74 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CA SER B 74 " pdb=" N SER B 74 " pdb=" C SER B 74 " pdb=" CB SER B 74 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 1611 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 405 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" CG ASP A 405 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP A 405 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 405 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 405 " -0.014 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" CG ASP C 405 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP C 405 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP C 405 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 405 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.64e+00 pdb=" CG ASP B 405 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP B 405 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP B 405 " 0.018 2.00e-02 2.50e+03 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2620 2.81 - 3.33: 8925 3.33 - 3.85: 15445 3.85 - 4.38: 16959 4.38 - 4.90: 30388 Nonbonded interactions: 74337 Sorted by model distance: nonbonded pdb=" O SER C 65 " pdb=" OG SER C 300 " model vdw 2.284 3.040 nonbonded pdb=" O SER A 65 " pdb=" OG SER A 300 " model vdw 2.284 3.040 nonbonded pdb=" O SER B 65 " pdb=" OG SER B 300 " model vdw 2.284 3.040 nonbonded pdb=" O GLN A 337 " pdb=" OG1 THR A 340 " model vdw 2.295 3.040 nonbonded pdb=" O GLN C 337 " pdb=" OG1 THR C 340 " model vdw 2.295 3.040 ... (remaining 74332 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.770 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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: 13.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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 : 0.007 0.089 9567 Z= 0.347 Angle : 1.053 15.642 13014 Z= 0.533 Chirality : 0.051 0.199 1614 Planarity : 0.008 0.063 1593 Dihedral : 16.083 128.021 3426 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.74 (0.18), residues: 1239 helix: -2.09 (0.12), residues: 984 sheet: None (None), residues: 0 loop : -3.16 (0.30), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 397 TYR 0.018 0.002 TYR A 299 PHE 0.009 0.001 PHE A 301 HIS 0.002 0.000 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00739 ( 9567) covalent geometry : angle 1.05277 (13014) hydrogen bonds : bond 0.11679 ( 706) hydrogen bonds : angle 5.63341 ( 2118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.213 Fit side-chains REVERT: A 105 ARG cc_start: 0.8383 (mtp-110) cc_final: 0.8178 (mtm180) REVERT: A 115 LEU cc_start: 0.7992 (pp) cc_final: 0.7682 (pp) REVERT: A 203 GLN cc_start: 0.8482 (tp-100) cc_final: 0.8159 (tp-100) REVERT: A 362 MET cc_start: 0.8084 (mtp) cc_final: 0.7741 (mtp) REVERT: B 105 ARG cc_start: 0.8195 (mtp-110) cc_final: 0.7915 (mtm180) REVERT: B 120 GLN cc_start: 0.6800 (pp30) cc_final: 0.6566 (pp30) REVERT: B 401 ASN cc_start: 0.8126 (m-40) cc_final: 0.7725 (m-40) REVERT: C 312 ASP cc_start: 0.8933 (m-30) cc_final: 0.8468 (m-30) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.0817 time to fit residues: 31.7752 Evaluate side-chains 204 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 318 GLN A 327 ASN B 32 HIS B 223 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS C 318 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.114781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.097201 restraints weight = 12783.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.099708 restraints weight = 7520.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.101415 restraints weight = 5210.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.102601 restraints weight = 4072.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.103293 restraints weight = 3409.265| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9567 Z= 0.136 Angle : 0.607 8.803 13014 Z= 0.301 Chirality : 0.039 0.145 1614 Planarity : 0.005 0.049 1593 Dihedral : 10.326 91.877 1440 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.37 % Allowed : 16.26 % Favored : 81.38 % 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: -0.84 (0.22), residues: 1239 helix: 0.07 (0.15), residues: 987 sheet: None (None), residues: 0 loop : -2.78 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 80 TYR 0.013 0.001 TYR C 299 PHE 0.012 0.001 PHE B 323 HIS 0.008 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9567) covalent geometry : angle 0.60699 (13014) hydrogen bonds : bond 0.04444 ( 706) hydrogen bonds : angle 3.93351 ( 2118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.315 Fit side-chains REVERT: A 33 TYR cc_start: 0.7844 (m-10) cc_final: 0.7614 (m-10) REVERT: A 269 MET cc_start: 0.8450 (mtp) cc_final: 0.8099 (mtm) REVERT: A 286 MET cc_start: 0.9087 (mtp) cc_final: 0.8851 (mtm) REVERT: A 362 MET cc_start: 0.8184 (mtp) cc_final: 0.7910 (mtp) REVERT: B 18 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8591 (mp) REVERT: C 103 MET cc_start: 0.8813 (tpp) cc_final: 0.8601 (mmt) REVERT: C 136 ASP cc_start: 0.7542 (t0) cc_final: 0.7080 (t0) outliers start: 23 outliers final: 16 residues processed: 236 average time/residue: 0.0827 time to fit residues: 28.4286 Evaluate side-chains 232 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 332 HIS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 223 HIS B 14 GLN B 32 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS C 14 GLN C 337 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.114331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.096470 restraints weight = 12834.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.099010 restraints weight = 7535.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.100683 restraints weight = 5226.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.101871 restraints weight = 4095.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.102729 restraints weight = 3442.813| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9567 Z= 0.138 Angle : 0.595 8.884 13014 Z= 0.292 Chirality : 0.039 0.132 1614 Planarity : 0.004 0.046 1593 Dihedral : 9.729 76.962 1440 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.47 % Allowed : 20.16 % Favored : 77.37 % 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: 0.46 (0.23), residues: 1239 helix: 1.02 (0.16), residues: 990 sheet: None (None), residues: 0 loop : -2.53 (0.33), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.016 0.001 TYR C 299 PHE 0.009 0.001 PHE C 323 HIS 0.008 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9567) covalent geometry : angle 0.59472 (13014) hydrogen bonds : bond 0.04261 ( 706) hydrogen bonds : angle 3.73395 ( 2118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 0.339 Fit side-chains REVERT: A 269 MET cc_start: 0.8436 (mtp) cc_final: 0.8156 (mtm) REVERT: A 362 MET cc_start: 0.8078 (mtp) cc_final: 0.7863 (mtp) REVERT: B 340 THR cc_start: 0.9057 (p) cc_final: 0.8848 (p) REVERT: B 362 MET cc_start: 0.8090 (mtp) cc_final: 0.7638 (ttm) REVERT: C 103 MET cc_start: 0.8835 (tpp) cc_final: 0.8585 (mmt) REVERT: C 136 ASP cc_start: 0.7458 (t0) cc_final: 0.6930 (t0) outliers start: 24 outliers final: 20 residues processed: 229 average time/residue: 0.0853 time to fit residues: 28.3867 Evaluate side-chains 225 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 332 HIS Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 32 HIS B 223 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN C 318 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.113502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.095854 restraints weight = 12971.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.098202 restraints weight = 7715.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.099900 restraints weight = 5419.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.101159 restraints weight = 4224.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.101996 restraints weight = 3552.580| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9567 Z= 0.145 Angle : 0.594 8.057 13014 Z= 0.291 Chirality : 0.040 0.133 1614 Planarity : 0.004 0.044 1593 Dihedral : 9.400 67.541 1440 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.09 % Allowed : 20.68 % Favored : 76.23 % 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: 0.94 (0.24), residues: 1239 helix: 1.36 (0.16), residues: 990 sheet: None (None), residues: 0 loop : -2.39 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.014 0.001 TYR C 299 PHE 0.011 0.001 PHE B 323 HIS 0.008 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9567) covalent geometry : angle 0.59361 (13014) hydrogen bonds : bond 0.04221 ( 706) hydrogen bonds : angle 3.72846 ( 2118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.328 Fit side-chains REVERT: A 115 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7815 (pp) REVERT: A 194 MET cc_start: 0.8982 (mmt) cc_final: 0.8550 (mmt) REVERT: A 269 MET cc_start: 0.8452 (mtp) cc_final: 0.8182 (mtm) REVERT: B 136 ASP cc_start: 0.7430 (t0) cc_final: 0.6986 (t0) REVERT: B 340 THR cc_start: 0.9067 (p) cc_final: 0.8856 (p) REVERT: C 103 MET cc_start: 0.8759 (tpp) cc_final: 0.8532 (mmt) REVERT: C 136 ASP cc_start: 0.7398 (t0) cc_final: 0.6971 (t0) REVERT: C 286 MET cc_start: 0.8859 (mtm) cc_final: 0.8396 (mtp) outliers start: 30 outliers final: 23 residues processed: 222 average time/residue: 0.0862 time to fit residues: 27.3508 Evaluate side-chains 228 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 93 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 32 HIS B 223 HIS ** B 318 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 = 0.3087 r_free = 0.3087 target = 0.111192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.093539 restraints weight = 13214.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.096029 restraints weight = 7747.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.097745 restraints weight = 5397.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.098813 restraints weight = 4218.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.099489 restraints weight = 3587.885| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9567 Z= 0.179 Angle : 0.633 13.927 13014 Z= 0.309 Chirality : 0.041 0.159 1614 Planarity : 0.004 0.045 1593 Dihedral : 9.212 67.669 1440 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.42 % Allowed : 20.78 % Favored : 74.79 % 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: 1.05 (0.24), residues: 1239 helix: 1.43 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -2.38 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.016 0.001 TYR C 88 PHE 0.014 0.001 PHE C 323 HIS 0.008 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 9567) covalent geometry : angle 0.63335 (13014) hydrogen bonds : bond 0.04641 ( 706) hydrogen bonds : angle 3.86776 ( 2118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 0.364 Fit side-chains REVERT: A 269 MET cc_start: 0.8501 (mtp) cc_final: 0.8245 (mtm) REVERT: A 362 MET cc_start: 0.8019 (mtp) cc_final: 0.7537 (mtp) REVERT: B 136 ASP cc_start: 0.7488 (t0) cc_final: 0.7163 (t0) REVERT: C 136 ASP cc_start: 0.7401 (t0) cc_final: 0.7034 (t0) outliers start: 43 outliers final: 37 residues processed: 232 average time/residue: 0.0828 time to fit residues: 27.7112 Evaluate side-chains 237 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 332 HIS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 35 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 29 optimal weight: 0.0470 chunk 57 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 32 HIS ** B 318 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 = 0.3151 r_free = 0.3151 target = 0.115870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.098207 restraints weight = 12812.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.100743 restraints weight = 7658.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.102490 restraints weight = 5363.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.103670 restraints weight = 4180.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.104166 restraints weight = 3532.265| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9567 Z= 0.122 Angle : 0.589 11.392 13014 Z= 0.286 Chirality : 0.039 0.158 1614 Planarity : 0.004 0.044 1593 Dihedral : 8.871 70.500 1440 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.22 % Allowed : 21.40 % Favored : 74.38 % 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: 1.40 (0.24), residues: 1239 helix: 1.68 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -2.27 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.027 0.001 TYR B 88 PHE 0.010 0.001 PHE B 323 HIS 0.008 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9567) covalent geometry : angle 0.58911 (13014) hydrogen bonds : bond 0.03820 ( 706) hydrogen bonds : angle 3.63657 ( 2118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 0.314 Fit side-chains REVERT: A 269 MET cc_start: 0.8453 (mtp) cc_final: 0.8209 (mtm) REVERT: A 362 MET cc_start: 0.7797 (mtp) cc_final: 0.7343 (mtp) REVERT: B 136 ASP cc_start: 0.7415 (t0) cc_final: 0.7040 (t0) REVERT: B 242 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.7244 (tp40) REVERT: B 362 MET cc_start: 0.8114 (mtp) cc_final: 0.7889 (ttm) REVERT: C 136 ASP cc_start: 0.7241 (t0) cc_final: 0.6864 (t0) REVERT: C 286 MET cc_start: 0.8796 (mtm) cc_final: 0.8395 (mtp) outliers start: 41 outliers final: 32 residues processed: 244 average time/residue: 0.0825 time to fit residues: 29.0861 Evaluate side-chains 235 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 332 HIS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 32 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 74 optimal weight: 0.0050 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS B 223 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.116540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.098894 restraints weight = 12907.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.101329 restraints weight = 7674.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.103125 restraints weight = 5402.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.104360 restraints weight = 4215.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.104959 restraints weight = 3527.257| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9567 Z= 0.121 Angle : 0.601 16.260 13014 Z= 0.290 Chirality : 0.039 0.192 1614 Planarity : 0.004 0.043 1593 Dihedral : 8.429 74.633 1440 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.01 % Allowed : 23.56 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.24), residues: 1239 helix: 1.85 (0.16), residues: 990 sheet: None (None), residues: 0 loop : -2.17 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 276 TYR 0.021 0.001 TYR A 88 PHE 0.010 0.001 PHE B 323 HIS 0.008 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9567) covalent geometry : angle 0.60121 (13014) hydrogen bonds : bond 0.03738 ( 706) hydrogen bonds : angle 3.56698 ( 2118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.330 Fit side-chains REVERT: A 269 MET cc_start: 0.8431 (mtp) cc_final: 0.8193 (mtm) REVERT: A 362 MET cc_start: 0.7755 (mtp) cc_final: 0.7327 (mtp) REVERT: B 136 ASP cc_start: 0.7376 (t0) cc_final: 0.6999 (t0) REVERT: B 242 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.6939 (tp40) REVERT: B 340 THR cc_start: 0.8921 (p) cc_final: 0.8643 (p) REVERT: B 362 MET cc_start: 0.8113 (mtp) cc_final: 0.7791 (ttm) REVERT: C 136 ASP cc_start: 0.7273 (t0) cc_final: 0.6934 (t0) REVERT: C 286 MET cc_start: 0.8749 (mtm) cc_final: 0.8371 (mtp) outliers start: 39 outliers final: 30 residues processed: 236 average time/residue: 0.0843 time to fit residues: 28.8051 Evaluate side-chains 239 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 106 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 76 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 53 optimal weight: 0.0670 chunk 77 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 overall best weight: 0.4520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 32 HIS C 332 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.117856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.100113 restraints weight = 12848.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.102648 restraints weight = 7638.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.104376 restraints weight = 5326.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.105414 restraints weight = 4168.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.106310 restraints weight = 3534.151| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9567 Z= 0.116 Angle : 0.610 16.148 13014 Z= 0.290 Chirality : 0.039 0.180 1614 Planarity : 0.003 0.042 1593 Dihedral : 8.120 77.535 1440 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.81 % Allowed : 24.18 % Favored : 72.02 % 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: 1.81 (0.24), residues: 1239 helix: 1.96 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -2.07 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 276 TYR 0.017 0.001 TYR A 88 PHE 0.008 0.001 PHE A 323 HIS 0.008 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9567) covalent geometry : angle 0.60958 (13014) hydrogen bonds : bond 0.03556 ( 706) hydrogen bonds : angle 3.51667 ( 2118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 0.268 Fit side-chains REVERT: A 18 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8484 (mp) REVERT: A 30 LEU cc_start: 0.9041 (mt) cc_final: 0.8840 (mt) REVERT: A 269 MET cc_start: 0.8417 (mtp) cc_final: 0.8197 (mtm) REVERT: A 362 MET cc_start: 0.7684 (mtp) cc_final: 0.7283 (mtp) REVERT: B 136 ASP cc_start: 0.7503 (t0) cc_final: 0.7144 (t0) REVERT: B 169 MET cc_start: 0.8500 (mmm) cc_final: 0.7647 (mtt) REVERT: B 242 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.6658 (tp40) REVERT: B 362 MET cc_start: 0.8041 (mtp) cc_final: 0.7726 (ttm) REVERT: C 136 ASP cc_start: 0.7167 (t0) cc_final: 0.6855 (t0) REVERT: C 215 TYR cc_start: 0.8047 (t80) cc_final: 0.7823 (t80) outliers start: 37 outliers final: 29 residues processed: 245 average time/residue: 0.0813 time to fit residues: 29.0896 Evaluate side-chains 241 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 38 optimal weight: 0.7980 chunk 79 optimal weight: 0.2980 chunk 82 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS B 332 HIS C 332 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.117194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.099445 restraints weight = 12808.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.101973 restraints weight = 7625.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.103723 restraints weight = 5336.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.104778 restraints weight = 4189.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.105571 restraints weight = 3563.044| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9567 Z= 0.121 Angle : 0.610 17.149 13014 Z= 0.291 Chirality : 0.040 0.174 1614 Planarity : 0.003 0.041 1593 Dihedral : 7.992 76.847 1440 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.60 % Allowed : 24.38 % Favored : 72.02 % 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: 1.92 (0.24), residues: 1239 helix: 2.02 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -1.97 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 276 TYR 0.017 0.001 TYR A 88 PHE 0.009 0.001 PHE C 323 HIS 0.009 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9567) covalent geometry : angle 0.61038 (13014) hydrogen bonds : bond 0.03676 ( 706) hydrogen bonds : angle 3.53452 ( 2118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.355 Fit side-chains REVERT: A 18 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8499 (mp) REVERT: A 269 MET cc_start: 0.8440 (mtp) cc_final: 0.8219 (mtm) REVERT: A 362 MET cc_start: 0.7755 (mtp) cc_final: 0.7320 (mtp) REVERT: B 136 ASP cc_start: 0.7543 (t0) cc_final: 0.7192 (t0) REVERT: B 169 MET cc_start: 0.8561 (mmm) cc_final: 0.8153 (mtm) REVERT: B 217 MET cc_start: 0.9159 (tpp) cc_final: 0.8891 (mmt) REVERT: B 261 PHE cc_start: 0.8982 (t80) cc_final: 0.8720 (t80) REVERT: B 362 MET cc_start: 0.8096 (mtp) cc_final: 0.7698 (ttm) REVERT: C 13 LEU cc_start: 0.8291 (mt) cc_final: 0.8046 (mt) REVERT: C 136 ASP cc_start: 0.7234 (t0) cc_final: 0.6922 (t0) outliers start: 35 outliers final: 31 residues processed: 235 average time/residue: 0.0819 time to fit residues: 28.0526 Evaluate side-chains 238 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 45 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.0000 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 89 optimal weight: 0.0570 overall best weight: 0.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS B 223 HIS C 332 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.119157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.101213 restraints weight = 12825.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.103722 restraints weight = 7580.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.105594 restraints weight = 5315.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.106844 restraints weight = 4130.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.107676 restraints weight = 3459.681| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9567 Z= 0.115 Angle : 0.612 16.976 13014 Z= 0.290 Chirality : 0.039 0.176 1614 Planarity : 0.003 0.041 1593 Dihedral : 7.883 76.228 1440 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.60 % Allowed : 24.69 % Favored : 71.71 % 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: 2.04 (0.24), residues: 1239 helix: 2.08 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -1.87 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 276 TYR 0.015 0.001 TYR A 88 PHE 0.007 0.001 PHE A 323 HIS 0.009 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9567) covalent geometry : angle 0.61218 (13014) hydrogen bonds : bond 0.03471 ( 706) hydrogen bonds : angle 3.47841 ( 2118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 0.336 Fit side-chains REVERT: A 18 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8352 (mp) REVERT: A 269 MET cc_start: 0.8422 (mtp) cc_final: 0.8207 (mtm) REVERT: A 362 MET cc_start: 0.7666 (mtp) cc_final: 0.7262 (mtp) REVERT: B 136 ASP cc_start: 0.7724 (t0) cc_final: 0.7283 (t0) REVERT: B 169 MET cc_start: 0.8505 (mmm) cc_final: 0.8051 (mtt) REVERT: B 217 MET cc_start: 0.9167 (tpp) cc_final: 0.8924 (tpp) REVERT: B 242 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.6335 (tp40) REVERT: B 261 PHE cc_start: 0.8962 (t80) cc_final: 0.8709 (t80) REVERT: B 362 MET cc_start: 0.8038 (mtp) cc_final: 0.7710 (ttm) REVERT: C 136 ASP cc_start: 0.7248 (t0) cc_final: 0.6935 (t0) REVERT: C 286 MET cc_start: 0.8748 (mtm) cc_final: 0.8394 (mtp) outliers start: 35 outliers final: 31 residues processed: 240 average time/residue: 0.0856 time to fit residues: 30.0348 Evaluate side-chains 243 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 47 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.115330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.097707 restraints weight = 12941.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.100166 restraints weight = 7600.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.101982 restraints weight = 5319.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.103015 restraints weight = 4134.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.103944 restraints weight = 3506.636| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9567 Z= 0.139 Angle : 0.626 17.103 13014 Z= 0.298 Chirality : 0.040 0.165 1614 Planarity : 0.004 0.042 1593 Dihedral : 7.932 75.708 1440 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.19 % Allowed : 25.31 % Favored : 71.50 % 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: 1.96 (0.24), residues: 1239 helix: 2.05 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -1.94 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 276 TYR 0.015 0.001 TYR A 88 PHE 0.009 0.001 PHE A 323 HIS 0.008 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9567) covalent geometry : angle 0.62594 (13014) hydrogen bonds : bond 0.03931 ( 706) hydrogen bonds : angle 3.59835 ( 2118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1486.98 seconds wall clock time: 26 minutes 23.69 seconds (1583.69 seconds total)