Starting phenix.real_space_refine on Fri Sep 11 13:27:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x17_21991/09_2026/6x17_21991.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x17_21991/09_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_21991/09_2026/6x17_21991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x17_21991/09_2026/6x17_21991.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6x17_21991/09_2026/6x17_21991.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x17_21991/09_2026/6x17_21991.cif" model { file = "/net/cci-nas-00/data/ceres_data/6x17_21991/09_2026/6x17_21991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x17_21991/09_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-2.2.1-6174/lib/python3.11/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: 2.59, per 1000 atoms: 0.28 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: 0.95 Conformation dependent library (CDL) restraints added in 351.5 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: 0.25 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: 1.43 Time building geometry restraints manager: 1.23 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: 5288 25.60 - 51.21: 316 51.21 - 76.81: 24 76.81 - 102.42: 0 102.42 - 128.02: 3 Dihedral angle restraints: 5631 sinusoidal: 2097 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 5628 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: 0.02 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: 1.230 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: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.780 Find NCS groups from input model: 0.060 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 15.449 128.021 3393 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/Z covalent geometry : bond 0.00739 / 0.35 ( 9567) covalent geometry : angle 1.05277 / 0.53 (13014) hydrogen bonds : bond 0.11679 / 7.65 ( 706) hydrogen bonds : angle 5.63341 / 4.01 ( 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 : 0.331 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: 0.0791 time to fit residues: 30.9976 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 : 0.246 ------------------------------------------------------------------------------- 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... 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 = 0.3133 r_free = 0.3133 target = 0.114811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.097081 restraints weight = 12799.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.099491 restraints weight = 7520.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.101387 restraints weight = 5237.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.102479 restraints weight = 4051.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.103274 restraints weight = 3428.052| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1682 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 : 0.604 8.748 13014 Z= 0.300 Chirality : 0.039 0.138 1614 Planarity : 0.005 0.050 1593 Dihedral : 8.353 89.884 1407 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.37 % Allowed : 16.36 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.22), residues: 1239 helix: 0.05 (0.15), residues: 987 sheet: None (None), residues: 0 loop : -2.77 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 397 TYR 0.013 0.001 TYR C 299 PHE 0.012 0.001 PHE B 323 HIS 0.009 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 9567) covalent geometry : angle 0.60410 / 0.30 (13014) hydrogen bonds : bond 0.04482 / 3.05 ( 706) hydrogen bonds : angle 3.93905 / 2.80 ( 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 250 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.350 Fit side-chains REVERT: A 33 TYR cc_start: 0.7863 (m-10) cc_final: 0.7632 (m-10) REVERT: A 269 MET cc_start: 0.8449 (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: 0.8185 (mtp) cc_final: 0.7913 (mtp) REVERT: B 18 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8586 (mp) REVERT: C 103 MET cc_start: 0.8805 (tpp) cc_final: 0.8582 (mmt) REVERT: C 136 ASP cc_start: 0.7546 (t0) cc_final: 0.7085 (t0) outliers start: 23 outliers final: 16 residues processed: 237 average time/residue: 0.0802 time to fit residues: 27.8924 Evaluate side-chains 230 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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: 0.8980 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: 1.9990 chunk 86 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3132 r_free = 0.3132 target = 0.114726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.096970 restraints weight = 12848.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.099424 restraints weight = 7681.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.101053 restraints weight = 5368.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.102295 restraints weight = 4219.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.102848 restraints weight = 3554.738| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2111 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= 0.134 Angle : 0.591 9.021 13014 Z= 0.290 Chirality : 0.039 0.132 1614 Planarity : 0.004 0.046 1593 Dihedral : 7.899 70.458 1407 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.26 % Allowed : 20.16 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.23), residues: 1239 helix: 0.98 (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 0.003 0.000 ARG A 276 TYR 0.015 0.001 TYR C 299 PHE 0.008 0.001 PHE C 323 HIS 0.009 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9567) covalent geometry : angle 0.59108 / 0.29 (13014) hydrogen bonds : bond 0.04186 / 2.86 ( 706) hydrogen bonds : angle 3.73098 / 2.66 ( 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 246 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 224 time to evaluate : 0.274 Fit side-chains REVERT: A 269 MET cc_start: 0.8429 (mtp) cc_final: 0.8144 (mtm) REVERT: A 362 MET cc_start: 0.8079 (mtp) cc_final: 0.7867 (mtp) REVERT: B 340 THR cc_start: 0.9063 (p) cc_final: 0.8861 (p) REVERT: B 362 MET cc_start: 0.8048 (mtp) cc_final: 0.7629 (ttm) REVERT: C 103 MET cc_start: 0.8831 (tpp) cc_final: 0.8581 (mmt) REVERT: C 136 ASP cc_start: 0.7419 (t0) cc_final: 0.6874 (t0) outliers start: 22 outliers final: 18 residues processed: 232 average time/residue: 0.0796 time to fit residues: 26.9050 Evaluate side-chains 224 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET 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 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: 0.4980 chunk 103 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3107 r_free = 0.3107 target = 0.112758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.094971 restraints weight = 13038.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.097308 restraints weight = 7744.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.099123 restraints weight = 5437.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.100224 restraints weight = 4257.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.100898 restraints weight = 3605.213| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9567 Z= 0.158 Angle : 0.601 7.946 13014 Z= 0.296 Chirality : 0.040 0.127 1614 Planarity : 0.004 0.044 1593 Dihedral : 7.535 70.720 1407 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.29 % Allowed : 20.06 % Favored : 76.65 % 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: 0.83 (0.24), residues: 1239 helix: 1.28 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -2.44 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.015 0.001 TYR C 299 PHE 0.011 0.001 PHE B 323 HIS 0.009 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 9567) covalent geometry : angle 0.60136 / 0.30 (13014) hydrogen bonds : bond 0.04360 / 2.97 ( 706) hydrogen bonds : angle 3.77813 / 2.69 ( 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 242 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.331 Fit side-chains REVERT: A 115 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7825 (pp) REVERT: A 194 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8815 (mmt) REVERT: A 269 MET cc_start: 0.8460 (mtp) cc_final: 0.8189 (mtm) REVERT: B 136 ASP cc_start: 0.7451 (t0) cc_final: 0.7006 (t0) REVERT: B 340 THR cc_start: 0.9095 (p) cc_final: 0.8887 (p) REVERT: C 103 MET cc_start: 0.8775 (tpp) cc_final: 0.8564 (mmt) REVERT: C 136 ASP cc_start: 0.7435 (t0) cc_final: 0.7013 (t0) REVERT: C 286 MET cc_start: 0.8890 (mtm) cc_final: 0.8435 (mtp) outliers start: 32 outliers final: 26 residues processed: 224 average time/residue: 0.0840 time to fit residues: 27.3003 Evaluate side-chains 227 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 115 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 194 MET 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 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=3.50 ------------------------------------------------------------------------------- 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: 5.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3072 r_free = 0.3072 target = 0.110029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.092426 restraints weight = 13264.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.094888 restraints weight = 7827.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.096596 restraints weight = 5452.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.097740 restraints weight = 4257.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.098339 restraints weight = 3609.355| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9567 Z= 0.188 Angle : 0.633 13.878 13014 Z= 0.311 Chirality : 0.041 0.167 1614 Planarity : 0.004 0.044 1593 Dihedral : 7.404 70.861 1407 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.63 % Allowed : 20.47 % Favored : 74.90 % 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: 0.95 (0.24), residues: 1239 helix: 1.37 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -2.43 (0.35), residues: 246 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 0.009 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 ( 9567) covalent geometry : angle 0.63296 / 0.31 (13014) hydrogen bonds : bond 0.04737 / 3.22 ( 706) hydrogen bonds : angle 3.90933 / 2.77 ( 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 244 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.335 Fit side-chains REVERT: A 269 MET cc_start: 0.8516 (mtp) cc_final: 0.8259 (mtm) REVERT: A 362 MET cc_start: 0.8060 (mtp) cc_final: 0.7578 (mtp) REVERT: B 136 ASP cc_start: 0.7492 (t0) cc_final: 0.7172 (t0) REVERT: C 136 ASP cc_start: 0.7420 (t0) cc_final: 0.7052 (t0) REVERT: C 286 MET cc_start: 0.8924 (mtm) cc_final: 0.8463 (mtp) outliers start: 45 outliers final: 36 residues processed: 227 average time/residue: 0.0836 time to fit residues: 27.4005 Evaluate side-chains 235 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 131 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 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 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: 0.2980 chunk 77 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 0.0870 chunk 82 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.115710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.097870 restraints weight = 12806.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.100434 restraints weight = 7515.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.102194 restraints weight = 5226.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.103422 restraints weight = 4073.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.104194 restraints weight = 3427.095| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2670 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= 0.119 Angle : 0.584 11.292 13014 Z= 0.284 Chirality : 0.039 0.154 1614 Planarity : 0.004 0.043 1593 Dihedral : 7.067 70.041 1407 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.50 % Allowed : 22.22 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.24), residues: 1239 helix: 1.65 (0.17), residues: 993 sheet: None (None), residues: 0 loop : -2.28 (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 0.011 0.001 PHE B 323 HIS 0.008 0.000 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 9567) covalent geometry : angle 0.58414 / 0.28 (13014) hydrogen bonds : bond 0.03800 / 2.59 ( 706) hydrogen bonds : angle 3.64098 / 2.60 ( 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 249 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.336 Fit side-chains REVERT: A 269 MET cc_start: 0.8474 (mtp) cc_final: 0.8218 (mtm) REVERT: A 362 MET cc_start: 0.7786 (mtp) cc_final: 0.7335 (mtp) REVERT: B 136 ASP cc_start: 0.7429 (t0) cc_final: 0.7047 (t0) REVERT: B 362 MET cc_start: 0.8109 (mtp) cc_final: 0.7873 (ttm) REVERT: C 136 ASP cc_start: 0.7243 (t0) cc_final: 0.6870 (t0) REVERT: C 286 MET cc_start: 0.8778 (mtm) cc_final: 0.8411 (mtp) outliers start: 34 outliers final: 31 residues processed: 240 average time/residue: 0.0804 time to fit residues: 28.2838 Evaluate side-chains 233 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 32 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3123 r_free = 0.3123 target = 0.113728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.096164 restraints weight = 13078.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.098766 restraints weight = 7592.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.100533 restraints weight = 5226.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.101611 restraints weight = 4067.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.102423 restraints weight = 3428.426| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9567 Z= 0.138 Angle : 0.593 10.109 13014 Z= 0.291 Chirality : 0.040 0.139 1614 Planarity : 0.004 0.043 1593 Dihedral : 7.036 69.736 1407 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.12 % Allowed : 23.05 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.24), residues: 1239 helix: 1.72 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -2.20 (0.37), residues: 243 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 0.011 0.001 PHE B 323 HIS 0.008 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9567) covalent geometry : angle 0.59349 / 0.29 (13014) hydrogen bonds : bond 0.04061 / 2.77 ( 706) hydrogen bonds : angle 3.65983 / 2.61 ( 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 244 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 0.248 Fit side-chains REVERT: A 194 MET cc_start: 0.8918 (mmt) cc_final: 0.8516 (mmt) REVERT: A 269 MET cc_start: 0.8416 (mtp) cc_final: 0.8148 (mtm) REVERT: A 362 MET cc_start: 0.7893 (mtp) cc_final: 0.7422 (mtp) REVERT: B 136 ASP cc_start: 0.7492 (t0) cc_final: 0.7130 (t0) REVERT: B 242 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.7144 (tp40) REVERT: C 136 ASP cc_start: 0.7344 (t0) cc_final: 0.6978 (t0) REVERT: C 286 MET cc_start: 0.8807 (mtm) cc_final: 0.8433 (mtp) outliers start: 40 outliers final: 29 residues processed: 235 average time/residue: 0.0754 time to fit residues: 26.0250 Evaluate side-chains 229 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 106 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 76 optimal weight: 0.0570 chunk 19 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.115742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.097871 restraints weight = 12919.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.100417 restraints weight = 7593.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.102143 restraints weight = 5285.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.103448 restraints weight = 4126.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.104142 restraints weight = 3471.043| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9567 Z= 0.123 Angle : 0.593 9.352 13014 Z= 0.288 Chirality : 0.039 0.203 1614 Planarity : 0.004 0.042 1593 Dihedral : 6.967 69.549 1407 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.91 % Allowed : 23.97 % Favored : 72.12 % 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: 1.79 (0.16), residues: 999 sheet: None (None), residues: 0 loop : -2.03 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 276 TYR 0.018 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/Z covalent geometry : bond 0.00274 / 0.12 ( 9567) covalent geometry : angle 0.59292 / 0.29 (13014) hydrogen bonds : bond 0.03759 / 2.57 ( 706) hydrogen bonds : angle 3.57334 / 2.55 ( 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 243 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.306 Fit side-chains REVERT: A 18 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8546 (mp) REVERT: A 269 MET cc_start: 0.8423 (mtp) cc_final: 0.8186 (mtm) REVERT: A 362 MET cc_start: 0.7782 (mtp) cc_final: 0.7342 (mtp) REVERT: B 136 ASP cc_start: 0.7463 (t0) cc_final: 0.7098 (t0) REVERT: B 242 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.6910 (tp40) REVERT: B 340 THR cc_start: 0.8931 (p) cc_final: 0.8637 (p) REVERT: B 362 MET cc_start: 0.8110 (mtp) cc_final: 0.7583 (ttm) REVERT: C 136 ASP cc_start: 0.7258 (t0) cc_final: 0.6932 (t0) REVERT: C 286 MET cc_start: 0.8734 (mtm) cc_final: 0.8371 (mtp) outliers start: 38 outliers final: 32 residues processed: 232 average time/residue: 0.0748 time to fit residues: 25.7830 Evaluate side-chains 238 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 56 MET Chi-restraints excluded: chain A residue 91 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 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 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 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: 0.9980 chunk 79 optimal weight: 0.2980 chunk 82 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3142 r_free = 0.3142 target = 0.115289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.097882 restraints weight = 12926.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.100381 restraints weight = 7647.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.102099 restraints weight = 5327.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.103241 restraints weight = 4160.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.104133 restraints weight = 3494.454| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9567 Z= 0.127 Angle : 0.608 17.418 13014 Z= 0.293 Chirality : 0.040 0.181 1614 Planarity : 0.004 0.042 1593 Dihedral : 6.931 69.662 1407 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.91 % Allowed : 24.38 % 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: 1.75 (0.24), residues: 1239 helix: 1.88 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -2.00 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 276 TYR 0.019 0.001 TYR A 88 PHE 0.009 0.001 PHE A 323 HIS 0.008 0.000 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9567) covalent geometry : angle 0.60781 / 0.29 (13014) hydrogen bonds : bond 0.03824 / 2.61 ( 706) hydrogen bonds : angle 3.58711 / 2.56 ( 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 240 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.317 Fit side-chains REVERT: A 18 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8548 (mp) REVERT: A 269 MET cc_start: 0.8436 (mtp) cc_final: 0.8201 (mtm) REVERT: A 362 MET cc_start: 0.7812 (mtp) cc_final: 0.7372 (mtp) REVERT: B 136 ASP cc_start: 0.7524 (t0) cc_final: 0.7271 (t0) REVERT: B 242 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.6780 (tp40) REVERT: B 362 MET cc_start: 0.8136 (mtp) cc_final: 0.7879 (ttm) REVERT: C 136 ASP cc_start: 0.7267 (t0) cc_final: 0.6946 (t0) outliers start: 38 outliers final: 34 residues processed: 228 average time/residue: 0.0734 time to fit residues: 24.9636 Evaluate side-chains 236 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 56 MET Chi-restraints excluded: chain A residue 91 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 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 45 optimal weight: 1.9990 chunk 30 optimal weight: 0.0770 chunk 11 optimal weight: 0.0870 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 89 optimal weight: 0.0670 overall best weight: 0.4254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 HIS C 332 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.117893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.100302 restraints weight = 12866.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.102840 restraints weight = 7646.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.104479 restraints weight = 5326.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.105600 restraints weight = 4174.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.106516 restraints weight = 3521.547| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9567 Z= 0.115 Angle : 0.604 16.942 13014 Z= 0.288 Chirality : 0.039 0.161 1614 Planarity : 0.003 0.041 1593 Dihedral : 6.823 69.323 1407 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.60 % Allowed : 24.79 % Favored : 71.60 % 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: 1.91 (0.24), residues: 1239 helix: 2.00 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -1.91 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 276 TYR 0.016 0.001 TYR A 88 PHE 0.008 0.001 PHE C 323 HIS 0.009 0.000 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 9567) covalent geometry : angle 0.60404 / 0.29 (13014) hydrogen bonds : bond 0.03499 / 2.39 ( 706) hydrogen bonds : angle 3.48071 / 2.49 ( 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 248 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 0.261 Fit side-chains REVERT: A 13 LEU cc_start: 0.8353 (mt) cc_final: 0.8105 (mt) REVERT: A 18 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8495 (mp) REVERT: A 269 MET cc_start: 0.8432 (mtp) cc_final: 0.8206 (mtm) REVERT: A 362 MET cc_start: 0.7661 (mtp) cc_final: 0.7276 (mtp) REVERT: B 136 ASP cc_start: 0.7688 (t0) cc_final: 0.7350 (t0) REVERT: B 242 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.6420 (tp40) REVERT: B 362 MET cc_start: 0.7945 (mtp) cc_final: 0.7510 (ttm) REVERT: C 136 ASP cc_start: 0.7263 (t0) cc_final: 0.6955 (t0) REVERT: C 286 MET cc_start: 0.8795 (mtm) cc_final: 0.8327 (mtp) outliers start: 35 outliers final: 29 residues processed: 239 average time/residue: 0.0767 time to fit residues: 27.0842 Evaluate side-chains 231 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 113 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 HIS B 223 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.115659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.098204 restraints weight = 12918.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.100542 restraints weight = 7667.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.102356 restraints weight = 5380.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.103367 restraints weight = 4192.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.104231 restraints weight = 3558.185| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9567 Z= 0.130 Angle : 0.611 16.717 13014 Z= 0.294 Chirality : 0.040 0.179 1614 Planarity : 0.004 0.042 1593 Dihedral : 6.847 70.389 1407 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.70 % Allowed : 25.10 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.24), residues: 1239 helix: 2.02 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -1.92 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 276 TYR 0.016 0.001 TYR A 88 PHE 0.009 0.001 PHE C 323 HIS 0.009 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 9567) covalent geometry : angle 0.61065 / 0.29 (13014) hydrogen bonds : bond 0.03801 / 2.59 ( 706) hydrogen bonds : angle 3.56512 / 2.54 ( 2118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1469.19 seconds wall clock time: 26 minutes 4.06 seconds (1564.06 seconds total)