Starting phenix.real_space_refine on Thu Sep 18 08:59:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnp_61624/09_2025/9jnp_61624.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnp_61624/09_2025/9jnp_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jnp_61624/09_2025/9jnp_61624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnp_61624/09_2025/9jnp_61624.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jnp_61624/09_2025/9jnp_61624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnp_61624/09_2025/9jnp_61624.map" } 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-2.0-5805/lib/python3.9/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: 4.36, per 1000 atoms: 0.28 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: 1.50 Conformation dependent library (CDL) restraints added in 559.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 2.72 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: 4.08 Time building geometry restraints manager: 2.04 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: 23706 3.84 - 7.69: 63 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 - 0.038: 1764 0.038 - 0.077: 746 0.077 - 0.115: 161 0.115 - 0.153: 26 0.153 - 0.191: 5 Chirality restraints: 2702 Sorted by residual: 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 chirality pdb=" CG LEU K 649 " pdb=" CB LEU K 649 " pdb=" CD1 LEU K 649 " pdb=" CD2 LEU K 649 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA PRO A 43 " pdb=" N PRO A 43 " pdb=" C PRO A 43 " pdb=" CB PRO A 43 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.21e-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: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.900 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 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 : 0.008 0.147 16663 Z= 0.384 Angle : 0.753 19.216 23778 Z= 0.480 Chirality : 0.042 0.191 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 aren 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 covalent geometry : bond 0.00818 (16663) covalent geometry : angle 0.75254 (23778) hydrogen bonds : bond 0.10309 ( 928) hydrogen bonds : angle 4.09806 ( 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 : 0.499 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: 1.0272 time to fit residues: 187.1362 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 : 0.485 ------------------------------------------------------------------------------- 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: 3.9990 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: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3545 r_free = 0.3545 target = 0.084784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.061091 restraints weight = 32655.336| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.73 r_work: 0.2819 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16663 Z= 0.173 Angle : 0.584 9.334 23778 Z= 0.343 Chirality : 0.037 0.206 2702 Planarity : 0.005 0.070 1999 Dihedral : 29.411 154.731 4593 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.31 % Allowed : 18.90 % 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 aren not related in a simple way. whole: 1.23 (0.24), residues: 1199 helix: 2.06 (0.19), residues: 762 sheet: -0.55 (0.63), residues: 65 loop : -1.65 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 547 TYR 0.012 0.001 TYR F 51 PHE 0.018 0.002 PHE K 385 TRP 0.017 0.001 TRP K 364 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00386 (16663) covalent geometry : angle 0.58427 (23778) hydrogen bonds : bond 0.05061 ( 928) hydrogen bonds : angle 3.35149 ( 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 188 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.518 Fit side-chains REVERT: A 59 GLU cc_start: 0.8788 (pm20) cc_final: 0.8427 (pm20) REVERT: B 24 ASP cc_start: 0.8233 (t0) cc_final: 0.7657 (m-30) REVERT: C 64 GLU cc_start: 0.8986 (tt0) cc_final: 0.8651 (tp30) REVERT: E 59 GLU cc_start: 0.8907 (pm20) cc_final: 0.8318 (pm20) REVERT: H 105 LYS cc_start: 0.8748 (mttm) cc_final: 0.8537 (mtpp) REVERT: K 648 GLN cc_start: 0.8634 (tm130) cc_final: 0.8358 (tp-100) outliers start: 24 outliers final: 5 residues processed: 178 average time/residue: 0.9759 time to fit residues: 185.6399 Evaluate side-chains 162 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU 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 398 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 29 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 46 HIS E 68 GLN E 76 GLN K 193 ASN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 648 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 = 0.3569 r_free = 0.3569 target = 0.086022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.062336 restraints weight = 32897.945| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.75 r_work: 0.2851 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16663 Z= 0.163 Angle : 0.547 10.347 23778 Z= 0.323 Chirality : 0.035 0.172 2702 Planarity : 0.004 0.049 1999 Dihedral : 28.867 151.579 4575 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.74 % Allowed : 20.06 % Favored : 78.21 % 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 aren not related in a simple way. whole: 1.70 (0.24), residues: 1199 helix: 2.37 (0.19), residues: 756 sheet: -0.32 (0.65), residues: 65 loop : -1.29 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 547 TYR 0.012 0.001 TYR K 499 PHE 0.012 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 covalent geometry : bond 0.00361 (16663) covalent geometry : angle 0.54685 (23778) hydrogen bonds : bond 0.04416 ( 928) hydrogen bonds : angle 3.07629 ( 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 187 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.614 Fit side-chains REVERT: A 59 GLU cc_start: 0.8765 (pm20) cc_final: 0.8376 (pm20) REVERT: B 24 ASP cc_start: 0.8292 (t0) cc_final: 0.7758 (m-30) REVERT: C 95 LYS cc_start: 0.9209 (ttmm) cc_final: 0.8972 (tttp) REVERT: H 31 LYS cc_start: 0.8310 (mptt) cc_final: 0.8034 (mptt) REVERT: H 105 LYS cc_start: 0.8732 (mttm) cc_final: 0.8523 (mtpp) REVERT: H 113 LYS cc_start: 0.9159 (ttmm) cc_final: 0.8948 (ttpt) REVERT: K 569 SER cc_start: 0.6644 (OUTLIER) cc_final: 0.6373 (t) REVERT: K 645 ARG cc_start: 0.8597 (tmm-80) cc_final: 0.8382 (tmm-80) REVERT: K 646 LEU cc_start: 0.8957 (tm) cc_final: 0.8718 (tt) outliers start: 18 outliers final: 4 residues processed: 178 average time/residue: 1.0392 time to fit residues: 197.1883 Evaluate side-chains 166 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 161 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain K residue 320 TYR 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: 0.9980 chunk 61 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 124 optimal weight: 0.0770 chunk 82 optimal weight: 3.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN E 68 GLN E 76 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.086397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.062747 restraints weight = 32800.839| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.75 r_work: 0.2862 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16663 Z= 0.153 Angle : 0.542 13.641 23778 Z= 0.319 Chirality : 0.036 0.428 2702 Planarity : 0.004 0.045 1999 Dihedral : 28.837 151.405 4574 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.64 % Allowed : 19.86 % Favored : 78.50 % 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 aren not related in a simple way. whole: 1.93 (0.24), residues: 1199 helix: 2.52 (0.19), residues: 755 sheet: -0.24 (0.64), residues: 65 loop : -1.10 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.009 0.001 TYR K 499 PHE 0.014 0.001 PHE K 408 TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00337 (16663) covalent geometry : angle 0.54213 (23778) hydrogen bonds : bond 0.04263 ( 928) hydrogen bonds : angle 3.02885 ( 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: 17 poor density : 165 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8711 (pm20) cc_final: 0.8296 (pm20) REVERT: B 24 ASP cc_start: 0.8353 (t0) cc_final: 0.7761 (m-30) REVERT: B 93 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8444 (mp10) REVERT: C 95 LYS cc_start: 0.9188 (ttmm) cc_final: 0.8960 (tttp) REVERT: E 120 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7603 (mtt) REVERT: G 64 GLU cc_start: 0.8872 (tt0) cc_final: 0.8626 (tp30) REVERT: H 31 LYS cc_start: 0.8348 (mptt) cc_final: 0.8068 (mptt) REVERT: H 82 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9108 (mtmm) REVERT: H 105 LYS cc_start: 0.8707 (mttm) cc_final: 0.8499 (mtpp) REVERT: K 401 LEU cc_start: 0.9515 (mm) cc_final: 0.9166 (mm) REVERT: K 569 SER cc_start: 0.6607 (OUTLIER) cc_final: 0.6347 (t) REVERT: K 645 ARG cc_start: 0.8671 (tmm-80) cc_final: 0.8440 (ttp80) REVERT: K 646 LEU cc_start: 0.8931 (tm) cc_final: 0.8633 (tt) REVERT: K 648 GLN cc_start: 0.8706 (tp-100) cc_final: 0.8397 (tm-30) outliers start: 17 outliers final: 7 residues processed: 175 average time/residue: 1.0161 time to fit residues: 189.3634 Evaluate side-chains 174 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 362 GLU 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: 0.9990 chunk 95 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3564 r_free = 0.3564 target = 0.085747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.062028 restraints weight = 32576.009| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.74 r_work: 0.2841 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16663 Z= 0.180 Angle : 0.546 9.457 23778 Z= 0.321 Chirality : 0.036 0.237 2702 Planarity : 0.004 0.043 1999 Dihedral : 28.855 150.112 4574 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.60 % Allowed : 20.15 % 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 aren not related in a simple way. whole: 2.00 (0.25), residues: 1199 helix: 2.55 (0.19), residues: 755 sheet: -0.15 (0.63), residues: 65 loop : -1.01 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.010 0.001 TYR F 51 PHE 0.009 0.001 PHE A 67 TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00405 (16663) covalent geometry : angle 0.54616 (23778) hydrogen bonds : bond 0.04665 ( 928) hydrogen bonds : angle 3.01304 ( 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 193 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8702 (pm20) cc_final: 0.8273 (pm20) REVERT: B 24 ASP cc_start: 0.8370 (t0) cc_final: 0.7743 (m-30) REVERT: C 95 LYS cc_start: 0.9183 (ttmm) cc_final: 0.8957 (tttp) REVERT: E 80 THR cc_start: 0.9357 (p) cc_final: 0.9146 (p) REVERT: G 64 GLU cc_start: 0.8904 (tt0) cc_final: 0.8636 (tp30) REVERT: H 82 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.9126 (mtmm) REVERT: H 105 LYS cc_start: 0.8729 (mttm) cc_final: 0.8515 (mtpp) REVERT: H 113 LYS cc_start: 0.9145 (ttmm) cc_final: 0.8918 (ttpt) REVERT: K 569 SER cc_start: 0.6609 (OUTLIER) cc_final: 0.6358 (t) REVERT: K 645 ARG cc_start: 0.8719 (tmm-80) cc_final: 0.8471 (ttp80) REVERT: K 646 LEU cc_start: 0.8974 (tm) cc_final: 0.8683 (tt) REVERT: K 648 GLN cc_start: 0.8704 (tp-100) cc_final: 0.8466 (tp40) outliers start: 27 outliers final: 7 residues processed: 181 average time/residue: 1.0003 time to fit residues: 193.1616 Evaluate side-chains 172 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 48 ASP 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 82 LYS 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: 0.0980 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN E 68 GLN E 76 GLN H 92 GLN ** 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 = 0.3569 r_free = 0.3569 target = 0.086106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.062366 restraints weight = 32575.881| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.75 r_work: 0.2850 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16663 Z= 0.153 Angle : 0.560 18.551 23778 Z= 0.322 Chirality : 0.037 0.679 2702 Planarity : 0.004 0.041 1999 Dihedral : 28.873 150.238 4574 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.83 % Allowed : 21.22 % Favored : 76.95 % 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 aren not related in a simple way. whole: 2.09 (0.25), residues: 1199 helix: 2.61 (0.19), residues: 755 sheet: -0.10 (0.63), residues: 65 loop : -0.96 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 186 TYR 0.009 0.001 TYR F 51 PHE 0.013 0.001 PHE K 408 TRP 0.026 0.001 TRP K 384 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00335 (16663) covalent geometry : angle 0.56046 (23778) hydrogen bonds : bond 0.04427 ( 928) hydrogen bonds : angle 3.00724 ( 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 183 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8691 (pm20) cc_final: 0.8250 (pm20) REVERT: B 24 ASP cc_start: 0.8367 (t0) cc_final: 0.7733 (m-30) REVERT: C 64 GLU cc_start: 0.8977 (tt0) cc_final: 0.8650 (tp30) REVERT: C 95 LYS cc_start: 0.9180 (ttmm) cc_final: 0.8955 (tttp) REVERT: G 64 GLU cc_start: 0.8881 (tt0) cc_final: 0.8609 (tp30) REVERT: H 31 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8230 (mptp) REVERT: H 82 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9127 (mtmm) REVERT: H 105 LYS cc_start: 0.8717 (mttm) cc_final: 0.8506 (mtpp) REVERT: H 113 LYS cc_start: 0.9138 (ttmm) cc_final: 0.8918 (ttpt) REVERT: K 401 LEU cc_start: 0.9454 (mm) cc_final: 0.9247 (pp) REVERT: K 569 SER cc_start: 0.6622 (OUTLIER) cc_final: 0.6384 (t) REVERT: K 642 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8394 (mp10) REVERT: K 645 ARG cc_start: 0.8708 (tmm-80) cc_final: 0.8443 (ttp80) REVERT: K 646 LEU cc_start: 0.8972 (tm) cc_final: 0.8691 (tt) REVERT: K 648 GLN cc_start: 0.8729 (tp-100) cc_final: 0.8472 (tp40) outliers start: 19 outliers final: 8 residues processed: 175 average time/residue: 1.0255 time to fit residues: 191.3883 Evaluate side-chains 172 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain K residue 384 TRP Chi-restraints excluded: chain K residue 511 LEU Chi-restraints excluded: chain K residue 569 SER Chi-restraints excluded: chain K residue 642 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN E 68 GLN E 76 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.086336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.062641 restraints weight = 32246.455| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.73 r_work: 0.2859 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16663 Z= 0.165 Angle : 0.543 12.237 23778 Z= 0.318 Chirality : 0.035 0.223 2702 Planarity : 0.004 0.040 1999 Dihedral : 28.705 149.501 4572 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.93 % Allowed : 20.93 % Favored : 77.15 % 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 aren not related in a simple way. whole: 2.15 (0.25), residues: 1199 helix: 2.65 (0.19), residues: 755 sheet: -0.03 (0.63), residues: 65 loop : -0.91 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 186 TYR 0.008 0.001 TYR K 499 PHE 0.009 0.001 PHE A 67 TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00367 (16663) covalent geometry : angle 0.54339 (23778) hydrogen bonds : bond 0.04368 ( 928) hydrogen bonds : angle 2.95998 ( 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 186 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8677 (pm20) cc_final: 0.8229 (pm20) REVERT: B 24 ASP cc_start: 0.8389 (t0) cc_final: 0.7741 (m-30) REVERT: C 95 LYS cc_start: 0.9151 (ttmm) cc_final: 0.8934 (tttp) REVERT: G 64 GLU cc_start: 0.8899 (tt0) cc_final: 0.8634 (tp30) REVERT: H 105 LYS cc_start: 0.8714 (mttm) cc_final: 0.8505 (mtpp) REVERT: K 186 ARG cc_start: 0.8971 (tpp-160) cc_final: 0.8730 (mmm-85) REVERT: K 569 SER cc_start: 0.6789 (OUTLIER) cc_final: 0.6552 (t) REVERT: K 642 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8427 (mp10) REVERT: K 645 ARG cc_start: 0.8771 (tmm-80) cc_final: 0.8468 (ttp80) REVERT: K 646 LEU cc_start: 0.9011 (tm) cc_final: 0.8748 (tt) REVERT: K 648 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8411 (tp40) outliers start: 20 outliers final: 9 residues processed: 177 average time/residue: 1.0084 time to fit residues: 190.6375 Evaluate side-chains 174 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU 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 F residue 93 GLN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 569 SER Chi-restraints excluded: chain K residue 642 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 105 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.085723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.061992 restraints weight = 32436.793| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.73 r_work: 0.2846 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16663 Z= 0.183 Angle : 0.552 9.478 23778 Z= 0.323 Chirality : 0.036 0.228 2702 Planarity : 0.004 0.043 1999 Dihedral : 28.734 148.873 4572 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.22 % Allowed : 21.22 % 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 aren not related in a simple way. whole: 2.12 (0.25), residues: 1199 helix: 2.60 (0.19), residues: 755 sheet: 0.09 (0.64), residues: 65 loop : -0.91 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.009 0.001 TYR F 51 PHE 0.009 0.001 PHE A 67 TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00412 (16663) covalent geometry : angle 0.55244 (23778) hydrogen bonds : bond 0.04694 ( 928) hydrogen bonds : angle 2.97469 ( 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 186 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8745 (pm20) cc_final: 0.8345 (pm20) REVERT: B 24 ASP cc_start: 0.8382 (t0) cc_final: 0.7657 (m-30) REVERT: C 64 GLU cc_start: 0.8988 (tt0) cc_final: 0.8699 (tp30) REVERT: C 73 ASN cc_start: 0.8130 (m-40) cc_final: 0.7593 (t0) REVERT: C 95 LYS cc_start: 0.9200 (ttmm) cc_final: 0.8985 (tttp) REVERT: G 64 GLU cc_start: 0.8927 (tt0) cc_final: 0.8667 (tp30) REVERT: K 569 SER cc_start: 0.6753 (OUTLIER) cc_final: 0.6536 (t) REVERT: K 642 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8456 (mp10) REVERT: K 645 ARG cc_start: 0.8741 (tmm-80) cc_final: 0.8424 (ttp80) REVERT: K 646 LEU cc_start: 0.9108 (tm) cc_final: 0.8852 (tt) REVERT: K 648 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8353 (tp40) outliers start: 23 outliers final: 10 residues processed: 177 average time/residue: 0.9943 time to fit residues: 187.4463 Evaluate side-chains 174 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 569 SER Chi-restraints excluded: chain K residue 642 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 124 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 76 GLN ** K 230 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 = 0.3572 r_free = 0.3572 target = 0.086178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.062411 restraints weight = 32526.836| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.74 r_work: 0.2852 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16663 Z= 0.170 Angle : 0.560 11.923 23778 Z= 0.325 Chirality : 0.035 0.151 2702 Planarity : 0.004 0.044 1999 Dihedral : 28.700 148.952 4572 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.35 % Allowed : 22.47 % Favored : 76.18 % 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 aren not related in a simple way. whole: 2.15 (0.25), residues: 1199 helix: 2.61 (0.19), residues: 756 sheet: -0.20 (0.59), residues: 80 loop : -0.81 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 186 TYR 0.008 0.001 TYR F 51 PHE 0.009 0.001 PHE A 67 TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00382 (16663) covalent geometry : angle 0.55965 (23778) hydrogen bonds : bond 0.04457 ( 928) hydrogen bonds : angle 2.98568 ( 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: 14 poor density : 163 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8706 (pm20) cc_final: 0.8295 (pm20) REVERT: B 24 ASP cc_start: 0.8390 (t0) cc_final: 0.7671 (m-30) REVERT: C 64 GLU cc_start: 0.8975 (tt0) cc_final: 0.8671 (tp30) REVERT: C 73 ASN cc_start: 0.8112 (m-40) cc_final: 0.7616 (t0) REVERT: C 95 LYS cc_start: 0.9152 (ttmm) cc_final: 0.8934 (tttp) REVERT: G 64 GLU cc_start: 0.8902 (tt0) cc_final: 0.8638 (tp30) REVERT: H 105 LYS cc_start: 0.8588 (mtpp) cc_final: 0.8261 (mttm) REVERT: K 569 SER cc_start: 0.6729 (OUTLIER) cc_final: 0.6521 (t) REVERT: K 642 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8434 (mp10) REVERT: K 645 ARG cc_start: 0.8729 (tmm-80) cc_final: 0.8422 (ttp80) REVERT: K 646 LEU cc_start: 0.9105 (tm) cc_final: 0.8851 (tt) outliers start: 14 outliers final: 7 residues processed: 171 average time/residue: 0.9703 time to fit residues: 176.7390 Evaluate side-chains 171 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 569 SER Chi-restraints excluded: chain K residue 642 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 141 optimal weight: 0.5980 chunk 136 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 76 GLN ** K 230 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 = 0.3575 r_free = 0.3575 target = 0.086370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.062639 restraints weight = 32114.801| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.73 r_work: 0.2859 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16663 Z= 0.157 Angle : 0.563 12.259 23778 Z= 0.325 Chirality : 0.035 0.235 2702 Planarity : 0.004 0.046 1999 Dihedral : 28.696 148.992 4572 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.16 % Allowed : 22.47 % Favored : 76.37 % 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 aren not related in a simple way. whole: 2.18 (0.25), residues: 1199 helix: 2.63 (0.19), residues: 756 sheet: -0.19 (0.59), residues: 80 loop : -0.81 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.008 0.001 TYR F 51 PHE 0.009 0.001 PHE A 67 TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00350 (16663) covalent geometry : angle 0.56264 (23778) hydrogen bonds : bond 0.04379 ( 928) hydrogen bonds : angle 2.96767 ( 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 176 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8704 (pm20) cc_final: 0.8292 (pm20) REVERT: B 24 ASP cc_start: 0.8381 (t0) cc_final: 0.7670 (m-30) REVERT: C 64 GLU cc_start: 0.8967 (tt0) cc_final: 0.8662 (tp30) REVERT: C 73 ASN cc_start: 0.8091 (m-40) cc_final: 0.7604 (t0) REVERT: C 95 LYS cc_start: 0.9155 (ttmm) cc_final: 0.8933 (tttp) REVERT: G 64 GLU cc_start: 0.8900 (tt0) cc_final: 0.8635 (tp30) REVERT: K 569 SER cc_start: 0.6694 (OUTLIER) cc_final: 0.6475 (t) REVERT: K 642 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8427 (mp10) REVERT: K 645 ARG cc_start: 0.8722 (tmm-80) cc_final: 0.8410 (ttp80) REVERT: K 646 LEU cc_start: 0.9096 (tm) cc_final: 0.8840 (tt) outliers start: 12 outliers final: 8 residues processed: 169 average time/residue: 0.9765 time to fit residues: 175.4729 Evaluate side-chains 173 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 569 SER Chi-restraints excluded: chain K residue 642 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 82 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 137 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.086335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.062611 restraints weight = 32213.586| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.73 r_work: 0.2855 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16663 Z= 0.169 Angle : 0.563 12.214 23778 Z= 0.325 Chirality : 0.035 0.149 2702 Planarity : 0.004 0.045 1999 Dihedral : 28.662 148.830 4572 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.35 % Allowed : 22.57 % Favored : 76.08 % 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 aren not related in a simple way. whole: 2.17 (0.25), residues: 1199 helix: 2.63 (0.19), residues: 756 sheet: -0.18 (0.59), residues: 80 loop : -0.81 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.009 0.001 TYR C 57 PHE 0.009 0.001 PHE A 67 TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00379 (16663) covalent geometry : angle 0.56344 (23778) hydrogen bonds : bond 0.04418 ( 928) hydrogen bonds : angle 2.96287 ( 2382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8017.79 seconds wall clock time: 136 minutes 37.75 seconds (8197.75 seconds total)