Starting phenix.real_space_refine on Thu Aug 6 13:41:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnp_61624/08_2026/9jnp_61624.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnp_61624/08_2026/9jnp_61624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jnp_61624/08_2026/9jnp_61624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnp_61624/08_2026/9jnp_61624.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnp_61624/08_2026/9jnp_61624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnp_61624/08_2026/9jnp_61624.cif" } resolution = 2.3 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= 0.009 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: 6 Type Number sf(0) Gaussians P 295 5.49 5 Mg 1 5.21 5 S 25 5.16 5 C 9041 2.51 5 N 2902 2.21 5 O 3517 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15781 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3738 Classifications: {'peptide': 455} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 437} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.16, per 1000 atoms: 0.20 Number of scatterers: 15781 At special positions: 0 Unit cell: (98.5075, 122.322, 156.962, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 295 15.00 Mg 1 11.99 O 3517 8.00 N 2902 7.00 C 9041 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: 1.35 Conformation dependent library (CDL) restraints added in 578.1 milliseconds 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 12 sheets defined 64.9% alpha, 6.0% beta 144 base pairs and 278 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.849A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 15 through 19 removed outlier: 3.694A pdb=" N HIS B 18 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG B 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 15 through 19' Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.806A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.478A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.615A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.852A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.523A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.888A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 213 Processing helix chain 'K' and resid 226 through 241 Processing helix chain 'K' and resid 253 through 255 No H-bonds generated for 'chain 'K' and resid 253 through 255' Processing helix chain 'K' and resid 256 through 268 removed outlier: 3.561A pdb=" N ARG K 266 " --> pdb=" O ARG K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 303 through 309 removed outlier: 3.747A pdb=" N ILE K 307 " --> pdb=" O TYR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 314 removed outlier: 3.617A pdb=" N LEU K 313 " --> pdb=" O GLU K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 330 removed outlier: 3.688A pdb=" N ILE K 329 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS K 330 " --> pdb=" O HIS K 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 326 through 330' Processing helix chain 'K' and resid 334 through 341 Processing helix chain 'K' and resid 359 through 371 removed outlier: 4.154A pdb=" N LEU K 363 " --> pdb=" O ASN K 359 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE K 369 " --> pdb=" O ALA K 365 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 386 removed outlier: 3.667A pdb=" N PHE K 381 " --> pdb=" O ASP K 377 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE K 385 " --> pdb=" O PHE K 381 " (cutoff:3.500A) Processing helix chain 'K' and resid 397 through 406 Processing helix chain 'K' and resid 434 through 446 Processing helix chain 'K' and resid 467 through 478 Processing helix chain 'K' and resid 479 through 482 Processing helix chain 'K' and resid 495 through 500 removed outlier: 4.160A pdb=" N TYR K 499 " --> pdb=" O GLU K 495 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN K 500 " --> pdb=" O HIS K 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 495 through 500' Processing helix chain 'K' and resid 501 through 518 removed outlier: 3.580A pdb=" N LYS K 509 " --> pdb=" O GLN K 505 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 541 removed outlier: 3.557A pdb=" N LEU K 531 " --> pdb=" O MET K 527 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 566 Processing helix chain 'K' and resid 601 through 610 removed outlier: 3.749A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA K 608 " --> pdb=" O ALA K 604 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 649 removed outlier: 4.193A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP K 647 " --> pdb=" O LYS K 643 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.790A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.077A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.754A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.832A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.121A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 273 through 275 removed outlier: 6.463A pdb=" N PHE K 274 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N SER K 302 " --> pdb=" O PHE K 274 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE K 248 " --> pdb=" O VAL K 299 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA K 301 " --> pdb=" O PHE K 248 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL K 250 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU K 249 " --> pdb=" O ILE K 322 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASP K 324 " --> pdb=" O LEU K 249 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE K 251 " --> pdb=" O ASP K 324 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N TRP K 318 " --> pdb=" O ARG K 346 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ARG K 348 " --> pdb=" O TRP K 318 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N TYR K 320 " --> pdb=" O ARG K 348 " (cutoff:3.500A) removed outlier: 9.728A pdb=" N LEU K 350 " --> pdb=" O TYR K 320 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ILE K 322 " --> pdb=" O LEU K 350 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE K 218 " --> pdb=" O LEU K 410 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 425 through 431 removed outlier: 6.305A pdb=" N LEU K 522 " --> pdb=" O VAL K 594 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1650 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 732 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 278 stacking parallelities Total time for adding SS restraints: 3.89 Time building geometry restraints manager: 1.83 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: 2008 1.31 - 1.43: 5776 1.43 - 1.56: 8248 1.56 - 1.68: 588 1.68 - 1.81: 43 Bond restraints: 16663 Sorted by residual: bond pdb=" C4 ATP K1201 " pdb=" C5 ATP K1201 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" CA LEU K 422 " pdb=" C LEU K 422 " ideal model delta sigma weight residual 1.528 1.439 0.088 1.26e-02 6.30e+03 4.92e+01 bond pdb=" C5 ATP K1201 " pdb=" C6 ATP K1201 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.42e+01 bond pdb=" CA PRO K 423 " pdb=" CB PRO K 423 " ideal model delta sigma weight residual 1.534 1.468 0.066 1.23e-02 6.61e+03 2.87e+01 bond pdb=" C5 ATP K1201 " pdb=" N7 ATP K1201 " ideal model delta sigma weight residual 1.387 1.340 0.047 1.00e-02 1.00e+04 2.18e+01 ... (remaining 16658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 23702 3.84 - 7.69: 67 7.69 - 11.53: 6 11.53 - 15.37: 0 15.37 - 19.22: 3 Bond angle restraints: 23778 Sorted by residual: angle pdb=" PA ATP K1201 " pdb=" O3A ATP K1201 " pdb=" PB ATP K1201 " ideal model delta sigma weight residual 136.83 117.61 19.22 1.00e+00 1.00e+00 3.69e+02 angle pdb=" PB ATP K1201 " pdb=" O3B ATP K1201 " pdb=" PG ATP K1201 " ideal model delta sigma weight residual 139.87 122.17 17.70 1.00e+00 1.00e+00 3.13e+02 angle pdb=" CA PRO K 189 " pdb=" N PRO K 189 " pdb=" CD PRO K 189 " ideal model delta sigma weight residual 112.00 96.04 15.96 1.40e+00 5.10e-01 1.30e+02 angle pdb=" C5 ATP K1201 " pdb=" C4 ATP K1201 " pdb=" N3 ATP K1201 " ideal model delta sigma weight residual 126.80 119.00 7.80 1.00e+00 1.00e+00 6.08e+01 angle pdb=" N3 ATP K1201 " pdb=" C4 ATP K1201 " pdb=" N9 ATP K1201 " ideal model delta sigma weight residual 127.04 134.68 -7.64 1.15e+00 7.59e-01 4.42e+01 ... (remaining 23773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.16: 7439 31.16 - 62.32: 1816 62.32 - 93.48: 54 93.48 - 124.64: 0 124.64 - 155.81: 2 Dihedral angle restraints: 9311 sinusoidal: 5744 harmonic: 3567 Sorted by residual: dihedral pdb=" CA ASP K 568 " pdb=" C ASP K 568 " pdb=" N SER K 569 " pdb=" CA SER K 569 " ideal model delta harmonic sigma weight residual 180.00 152.57 27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA ILE K 585 " pdb=" C ILE K 585 " pdb=" N ASN K 586 " pdb=" CA ASN K 586 " ideal model delta harmonic sigma weight residual -180.00 -160.54 -19.46 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 64.19 155.81 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 9308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1653 0.041 - 0.081: 748 0.081 - 0.122: 260 0.122 - 0.162: 36 0.162 - 0.203: 5 Chirality restraints: 2702 Sorted by residual: chirality pdb=" C3' DT J 15 " pdb=" C4' DT J 15 " pdb=" O3' DT J 15 " pdb=" C2' DT J 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C3' DA I 98 " pdb=" C4' DA I 98 " pdb=" O3' DA I 98 " pdb=" C2' DA I 98 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA PRO K 423 " pdb=" N PRO K 423 " pdb=" C PRO K 423 " pdb=" CB PRO K 423 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.16e-01 ... (remaining 2699 not shown) Planarity restraints: 1999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 188 " 0.113 5.00e-02 4.00e+02 1.56e-01 3.88e+01 pdb=" N PRO K 189 " -0.269 5.00e-02 4.00e+02 pdb=" CA PRO K 189 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO K 189 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU K 422 " -0.050 5.00e-02 4.00e+02 7.52e-02 9.06e+00 pdb=" N PRO K 423 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO K 423 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO K 423 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER K 420 " -0.014 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" C SER K 420 " 0.044 2.00e-02 2.50e+03 pdb=" O SER K 420 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU K 421 " -0.015 2.00e-02 2.50e+03 ... (remaining 1996 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 230 2.63 - 3.20: 13101 3.20 - 3.77: 27743 3.77 - 4.33: 39055 4.33 - 4.90: 56673 Nonbonded interactions: 136802 Sorted by model distance: nonbonded pdb=" N2 DG I 6 " pdb=" O2 DC J 142 " model vdw 2.067 2.496 nonbonded pdb=" O3B ATP K1201 " pdb="MG MG K1202 " model vdw 2.093 2.170 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.207 3.040 nonbonded pdb=" O THR G 76 " pdb=" OG1 THR G 76 " model vdw 2.211 3.040 nonbonded pdb=" NZ LYS B 20 " pdb=" O VAL B 21 " model vdw 2.222 3.120 ... (remaining 136797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.840 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:7.180 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 : 0.009 0.147 16663 Z= 0.692 Angle : 0.867 19.216 23778 Z= 0.706 Chirality : 0.050 0.203 2702 Planarity : 0.006 0.156 1999 Dihedral : 26.686 155.806 7001 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.45 % Allowed : 19.77 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1199 helix: 1.77 (0.19), residues: 755 sheet: -0.76 (0.63), residues: 65 loop : -1.80 (0.27), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 186 TYR 0.016 0.002 TYR F 51 PHE 0.025 0.002 PHE K 185 TRP 0.016 0.001 TRP K 364 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00888 / 0.69 (16663) covalent geometry : angle 0.86670 / 0.71 (23778) hydrogen bonds : bond 0.10309 / 6.96 ( 928) hydrogen bonds : angle 4.09806 / 2.99 ( 2382) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.381 Fit side-chains REVERT: A 59 GLU cc_start: 0.8352 (pm20) cc_final: 0.8019 (pm20) REVERT: C 64 GLU cc_start: 0.8349 (tt0) cc_final: 0.8113 (tp30) REVERT: K 648 GLN cc_start: 0.8305 (tm130) cc_final: 0.8090 (tp-100) outliers start: 15 outliers final: 13 residues processed: 171 average time/residue: 0.8129 time to fit residues: 148.7161 Evaluate side-chains 167 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 496 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN E 68 GLN E 76 GLN ** K 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 652 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.084544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.060818 restraints weight = 32602.943| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.73 r_work: 0.2816 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16663 Z= 0.158 Angle : 0.658 8.618 23778 Z= 0.370 Chirality : 0.047 0.306 2702 Planarity : 0.005 0.072 1999 Dihedral : 29.626 157.249 4593 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.22 % Allowed : 19.19 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.20 (0.24), residues: 1199 helix: 2.04 (0.19), residues: 762 sheet: -0.56 (0.63), residues: 65 loop : -1.67 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 547 TYR 0.012 0.001 TYR F 51 PHE 0.016 0.001 PHE K 385 TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (16663) covalent geometry : angle 0.65786 / 0.37 (23778) hydrogen bonds : bond 0.05594 / 3.78 ( 928) hydrogen bonds : angle 3.43940 / 2.49 ( 2382) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8795 (pm20) cc_final: 0.8441 (pm20) REVERT: B 77 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8691 (mtmt) REVERT: C 64 GLU cc_start: 0.8995 (tt0) cc_final: 0.8666 (tp30) REVERT: E 59 GLU cc_start: 0.8900 (pm20) cc_final: 0.8313 (pm20) REVERT: E 120 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7845 (mtt) REVERT: H 105 LYS cc_start: 0.8765 (mttm) cc_final: 0.8554 (mtpp) REVERT: K 648 GLN cc_start: 0.8648 (tm130) cc_final: 0.8422 (tp-100) outliers start: 23 outliers final: 4 residues processed: 176 average time/residue: 0.7859 time to fit residues: 147.8275 Evaluate side-chains 165 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain K residue 398 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 139 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 68 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.085317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.061691 restraints weight = 32993.787| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.75 r_work: 0.2842 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16663 Z= 0.141 Angle : 0.610 10.735 23778 Z= 0.348 Chirality : 0.045 0.304 2702 Planarity : 0.004 0.056 1999 Dihedral : 29.466 156.886 4575 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.93 % Allowed : 19.67 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.53 (0.24), residues: 1199 helix: 2.25 (0.19), residues: 761 sheet: -0.41 (0.64), residues: 65 loop : -1.42 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 547 TYR 0.012 0.001 TYR F 51 PHE 0.025 0.001 PHE K 385 TRP 0.018 0.001 TRP K 364 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (16663) covalent geometry : angle 0.60983 / 0.35 (23778) hydrogen bonds : bond 0.04929 / 3.33 ( 928) hydrogen bonds : angle 3.22876 / 2.34 ( 2382) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.439 Fit side-chains REVERT: A 59 GLU cc_start: 0.8787 (pm20) cc_final: 0.8376 (pm20) REVERT: B 16 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8288 (ptpp) REVERT: B 24 ASP cc_start: 0.8183 (t0) cc_final: 0.7623 (m-30) REVERT: E 59 GLU cc_start: 0.8876 (pm20) cc_final: 0.8610 (pm20) REVERT: H 105 LYS cc_start: 0.8770 (mttm) cc_final: 0.8558 (mtpp) REVERT: K 569 SER cc_start: 0.6708 (OUTLIER) cc_final: 0.6363 (t) REVERT: K 646 LEU cc_start: 0.8952 (tm) cc_final: 0.8747 (tt) outliers start: 20 outliers final: 8 residues processed: 176 average time/residue: 0.8026 time to fit residues: 151.3515 Evaluate side-chains 168 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 569 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 129 optimal weight: 0.0980 chunk 124 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 46 HIS E 68 GLN E 76 GLN K 193 ASN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.085455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.061769 restraints weight = 32791.996| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.75 r_work: 0.2838 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16663 Z= 0.148 Angle : 0.613 12.771 23778 Z= 0.346 Chirality : 0.045 0.303 2702 Planarity : 0.004 0.051 1999 Dihedral : 29.406 155.965 4575 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.83 % Allowed : 20.54 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.76 (0.24), residues: 1199 helix: 2.40 (0.19), residues: 758 sheet: -0.31 (0.63), residues: 65 loop : -1.21 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 197 TYR 0.011 0.001 TYR F 51 PHE 0.015 0.001 PHE K 385 TRP 0.017 0.001 TRP K 364 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (16663) covalent geometry : angle 0.61293 / 0.35 (23778) hydrogen bonds : bond 0.04977 / 3.38 ( 928) hydrogen bonds : angle 3.16258 / 2.29 ( 2382) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8744 (pm20) cc_final: 0.8321 (pm20) REVERT: B 16 LYS cc_start: 0.8489 (ptpp) cc_final: 0.8286 (ptpp) REVERT: B 24 ASP cc_start: 0.8266 (t0) cc_final: 0.7632 (m-30) REVERT: C 95 LYS cc_start: 0.9200 (ttmm) cc_final: 0.8956 (tttp) REVERT: E 80 THR cc_start: 0.9350 (m) cc_final: 0.9098 (p) REVERT: H 31 LYS cc_start: 0.8333 (mptt) cc_final: 0.8053 (mptt) REVERT: H 105 LYS cc_start: 0.8731 (mttm) cc_final: 0.8512 (mtpp) REVERT: K 569 SER cc_start: 0.6651 (OUTLIER) cc_final: 0.6354 (t) outliers start: 19 outliers final: 9 residues processed: 172 average time/residue: 0.8041 time to fit residues: 147.9608 Evaluate side-chains 166 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 569 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 58 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 68 GLN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.085413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.061704 restraints weight = 32753.771| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.73 r_work: 0.2835 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16663 Z= 0.156 Angle : 0.613 13.807 23778 Z= 0.344 Chirality : 0.045 0.338 2702 Planarity : 0.004 0.046 1999 Dihedral : 29.392 155.725 4575 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.12 % Allowed : 20.54 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.86 (0.24), residues: 1199 helix: 2.45 (0.19), residues: 755 sheet: -0.25 (0.63), residues: 65 loop : -1.09 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 186 TYR 0.008 0.001 TYR H 37 PHE 0.009 0.001 PHE A 67 TRP 0.017 0.001 TRP K 364 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (16663) covalent geometry : angle 0.61265 / 0.34 (23778) hydrogen bonds : bond 0.05023 / 3.40 ( 928) hydrogen bonds : angle 3.12809 / 2.26 ( 2382) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8716 (pm20) cc_final: 0.8282 (pm20) REVERT: B 16 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8096 (ptpp) REVERT: B 24 ASP cc_start: 0.8349 (t0) cc_final: 0.7722 (m-30) REVERT: C 95 LYS cc_start: 0.9187 (ttmm) cc_final: 0.8949 (tttp) REVERT: E 80 THR cc_start: 0.9338 (OUTLIER) cc_final: 0.9095 (p) REVERT: G 64 GLU cc_start: 0.8886 (tt0) cc_final: 0.8616 (tp30) REVERT: H 31 LYS cc_start: 0.8383 (mptt) cc_final: 0.8093 (mptt) REVERT: H 105 LYS cc_start: 0.8744 (mttm) cc_final: 0.8524 (mtpp) REVERT: K 401 LEU cc_start: 0.9496 (mm) cc_final: 0.9160 (mm) REVERT: K 505 GLN cc_start: 0.9348 (tt0) cc_final: 0.9074 (tp40) REVERT: K 569 SER cc_start: 0.6612 (OUTLIER) cc_final: 0.6315 (t) outliers start: 22 outliers final: 9 residues processed: 174 average time/residue: 0.8081 time to fit residues: 150.3348 Evaluate side-chains 171 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 569 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 73 ASN E 68 GLN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.085438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.061754 restraints weight = 32703.956| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.74 r_work: 0.2839 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16663 Z= 0.153 Angle : 0.604 11.689 23778 Z= 0.340 Chirality : 0.044 0.302 2702 Planarity : 0.004 0.042 1999 Dihedral : 29.337 155.611 4573 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.31 % Allowed : 20.15 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.25), residues: 1199 helix: 2.49 (0.19), residues: 755 sheet: -0.52 (0.58), residues: 80 loop : -0.95 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG K 645 TYR 0.008 0.001 TYR K 499 PHE 0.010 0.001 PHE K 385 TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (16663) covalent geometry : angle 0.60430 / 0.34 (23778) hydrogen bonds : bond 0.04930 / 3.34 ( 928) hydrogen bonds : angle 3.09016 / 2.24 ( 2382) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8727 (pm20) cc_final: 0.8289 (pm20) REVERT: B 16 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8094 (ptpp) REVERT: B 24 ASP cc_start: 0.8370 (t0) cc_final: 0.7718 (m-30) REVERT: C 95 LYS cc_start: 0.9184 (ttmm) cc_final: 0.8955 (tttp) REVERT: E 80 THR cc_start: 0.9362 (OUTLIER) cc_final: 0.9123 (p) REVERT: G 64 GLU cc_start: 0.8894 (tt0) cc_final: 0.8623 (tp30) REVERT: H 31 LYS cc_start: 0.8395 (mptt) cc_final: 0.8129 (mptt) REVERT: H 105 LYS cc_start: 0.8739 (mttm) cc_final: 0.8519 (mtpp) REVERT: K 186 ARG cc_start: 0.8953 (tpp-160) cc_final: 0.8721 (mmm-85) REVERT: K 569 SER cc_start: 0.6632 (OUTLIER) cc_final: 0.6377 (t) outliers start: 24 outliers final: 11 residues processed: 176 average time/residue: 0.7532 time to fit residues: 142.0732 Evaluate side-chains 172 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 463 THR Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 569 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 84 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 73 ASN E 68 GLN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.085453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.061789 restraints weight = 32392.526| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.72 r_work: 0.2839 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16663 Z= 0.156 Angle : 0.611 14.957 23778 Z= 0.341 Chirality : 0.045 0.555 2702 Planarity : 0.004 0.040 1999 Dihedral : 29.328 155.489 4572 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.31 % Allowed : 20.44 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.25), residues: 1199 helix: 2.50 (0.19), residues: 755 sheet: -0.46 (0.58), residues: 80 loop : -0.93 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 645 TYR 0.008 0.001 TYR F 51 PHE 0.031 0.001 PHE K 385 TRP 0.017 0.001 TRP K 384 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (16663) covalent geometry : angle 0.61130 / 0.34 (23778) hydrogen bonds : bond 0.04962 / 3.37 ( 928) hydrogen bonds : angle 3.09161 / 2.23 ( 2382) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8722 (pm20) cc_final: 0.8311 (pm20) REVERT: B 16 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8097 (ptpp) REVERT: B 24 ASP cc_start: 0.8387 (t0) cc_final: 0.7731 (m-30) REVERT: C 95 LYS cc_start: 0.9180 (ttmm) cc_final: 0.8954 (tttp) REVERT: G 64 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8634 (tp30) REVERT: H 105 LYS cc_start: 0.8742 (mttm) cc_final: 0.8536 (mtpp) REVERT: K 401 LEU cc_start: 0.9525 (mm) cc_final: 0.9324 (mm) REVERT: K 569 SER cc_start: 0.6620 (OUTLIER) cc_final: 0.6348 (t) outliers start: 24 outliers final: 12 residues processed: 170 average time/residue: 0.8371 time to fit residues: 152.4106 Evaluate side-chains 171 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 463 THR Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 569 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 105 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 127 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 96 optimal weight: 10.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 73 ASN E 68 GLN E 76 GLN F 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.085368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.061698 restraints weight = 32541.911| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.73 r_work: 0.2837 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16663 Z= 0.158 Angle : 0.609 12.181 23778 Z= 0.340 Chirality : 0.044 0.329 2702 Planarity : 0.004 0.040 1999 Dihedral : 29.321 155.302 4572 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.22 % Allowed : 20.73 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.98 (0.25), residues: 1199 helix: 2.50 (0.19), residues: 756 sheet: -0.40 (0.58), residues: 80 loop : -0.91 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 645 TYR 0.010 0.001 TYR C 57 PHE 0.030 0.001 PHE K 385 TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (16663) covalent geometry : angle 0.60924 / 0.34 (23778) hydrogen bonds : bond 0.04990 / 3.39 ( 928) hydrogen bonds : angle 3.07442 / 2.22 ( 2382) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8731 (pm20) cc_final: 0.8318 (pm20) REVERT: B 16 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8076 (ptpp) REVERT: B 24 ASP cc_start: 0.8394 (t0) cc_final: 0.7732 (m-30) REVERT: C 95 LYS cc_start: 0.9183 (ttmm) cc_final: 0.8956 (tttp) REVERT: G 64 GLU cc_start: 0.8918 (tt0) cc_final: 0.8658 (tp30) REVERT: H 105 LYS cc_start: 0.8747 (mttm) cc_final: 0.8538 (mtpp) REVERT: H 113 LYS cc_start: 0.9157 (ttmm) cc_final: 0.8926 (ttpt) REVERT: K 186 ARG cc_start: 0.8955 (tpp-160) cc_final: 0.8737 (mmm-85) REVERT: K 569 SER cc_start: 0.6594 (OUTLIER) cc_final: 0.6365 (t) outliers start: 23 outliers final: 12 residues processed: 174 average time/residue: 0.8148 time to fit residues: 151.6140 Evaluate side-chains 171 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain K residue 463 THR Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 569 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 124 optimal weight: 6.9990 chunk 134 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 112 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 73 ASN E 68 GLN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.085495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.061789 restraints weight = 32710.969| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.75 r_work: 0.2840 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16663 Z= 0.149 Angle : 0.618 16.806 23778 Z= 0.342 Chirality : 0.046 0.818 2702 Planarity : 0.004 0.040 1999 Dihedral : 29.315 155.326 4572 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.83 % Allowed : 21.41 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.25), residues: 1199 helix: 2.52 (0.19), residues: 756 sheet: -0.38 (0.59), residues: 80 loop : -0.89 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 645 TYR 0.008 0.001 TYR F 51 PHE 0.014 0.001 PHE K 385 TRP 0.029 0.002 TRP K 384 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (16663) covalent geometry : angle 0.61819 / 0.34 (23778) hydrogen bonds : bond 0.04897 / 3.32 ( 928) hydrogen bonds : angle 3.08452 / 2.23 ( 2382) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8738 (pm20) cc_final: 0.8328 (pm20) REVERT: B 16 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8098 (ptpp) REVERT: B 24 ASP cc_start: 0.8391 (t0) cc_final: 0.7730 (m-30) REVERT: B 93 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8686 (mp10) REVERT: C 95 LYS cc_start: 0.9199 (ttmm) cc_final: 0.8979 (tttp) REVERT: G 64 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8681 (tp30) REVERT: H 31 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8349 (mptt) REVERT: H 105 LYS cc_start: 0.8770 (mttm) cc_final: 0.8566 (mtpp) REVERT: H 113 LYS cc_start: 0.9182 (ttmm) cc_final: 0.8953 (ttpt) REVERT: K 186 ARG cc_start: 0.8954 (tpp-160) cc_final: 0.8735 (mmm-85) REVERT: K 401 LEU cc_start: 0.9550 (mm) cc_final: 0.9304 (pp) REVERT: K 569 SER cc_start: 0.6621 (OUTLIER) cc_final: 0.6355 (t) outliers start: 19 outliers final: 12 residues processed: 169 average time/residue: 0.8598 time to fit residues: 155.1201 Evaluate side-chains 174 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain K residue 463 THR Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 569 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 136 optimal weight: 0.4980 chunk 139 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 73 ASN E 68 GLN E 76 GLN H 92 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.085622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.061979 restraints weight = 32305.832| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.73 r_work: 0.2844 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16663 Z= 0.140 Angle : 0.614 16.278 23778 Z= 0.341 Chirality : 0.046 0.796 2702 Planarity : 0.004 0.039 1999 Dihedral : 29.311 155.353 4572 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.83 % Allowed : 21.60 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.25), residues: 1199 helix: 2.53 (0.19), residues: 756 sheet: -0.38 (0.59), residues: 80 loop : -0.88 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.008 0.001 TYR K 499 PHE 0.020 0.001 PHE K 408 TRP 0.026 0.002 TRP K 384 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (16663) covalent geometry : angle 0.61392 / 0.34 (23778) hydrogen bonds : bond 0.04833 / 3.28 ( 928) hydrogen bonds : angle 3.07695 / 2.22 ( 2382) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8718 (pm20) cc_final: 0.8302 (pm20) REVERT: B 16 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8088 (ptpp) REVERT: B 24 ASP cc_start: 0.8391 (t0) cc_final: 0.7730 (m-30) REVERT: B 93 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8664 (mp10) REVERT: C 95 LYS cc_start: 0.9183 (ttmm) cc_final: 0.8959 (tttp) REVERT: G 64 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8655 (tp30) REVERT: H 31 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8315 (mptt) REVERT: H 105 LYS cc_start: 0.8746 (mttm) cc_final: 0.8539 (mtpp) REVERT: H 113 LYS cc_start: 0.9158 (ttmm) cc_final: 0.8928 (ttpt) REVERT: K 186 ARG cc_start: 0.8958 (tpp-160) cc_final: 0.8734 (mmm-85) REVERT: K 569 SER cc_start: 0.6562 (OUTLIER) cc_final: 0.6319 (t) outliers start: 19 outliers final: 13 residues processed: 170 average time/residue: 0.9271 time to fit residues: 168.5907 Evaluate side-chains 175 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 235 LEU Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain K residue 463 THR Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 569 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 82 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 73 ASN E 68 GLN E 76 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 652 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.085777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.062154 restraints weight = 32399.108| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.73 r_work: 0.2848 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16663 Z= 0.141 Angle : 0.613 20.270 23778 Z= 0.340 Chirality : 0.044 0.302 2702 Planarity : 0.004 0.039 1999 Dihedral : 29.288 155.407 4572 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.83 % Allowed : 21.70 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.25), residues: 1199 helix: 2.52 (0.19), residues: 755 sheet: -0.35 (0.59), residues: 80 loop : -0.86 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.008 0.001 TYR F 51 PHE 0.016 0.001 PHE K 385 TRP 0.024 0.002 TRP K 384 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (16663) covalent geometry : angle 0.61313 / 0.34 (23778) hydrogen bonds : bond 0.04755 / 3.23 ( 928) hydrogen bonds : angle 3.10647 / 2.26 ( 2382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6568.44 seconds wall clock time: 111 minutes 55.86 seconds (6715.86 seconds total)