Starting phenix.real_space_refine on Fri Jun 13 23:21:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnp_61624/06_2025/9jnp_61624.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnp_61624/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jnp_61624/06_2025/9jnp_61624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnp_61624/06_2025/9jnp_61624.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnp_61624/06_2025/9jnp_61624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnp_61624/06_2025/9jnp_61624.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.23, per 1000 atoms: 0.58 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: 4.21 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 7.14 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: 8.09 Time building geometry restraints manager: 4.80 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: 2.200 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: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 43.630 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 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:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.410 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.001 TRP K 364 HIS 0.006 0.001 HIS G 31 PHE 0.025 0.002 PHE K 185 TYR 0.016 0.002 TYR F 51 ARG 0.009 0.001 ARG K 186 Details of bonding type rmsd hydrogen bonds : bond 0.10309 ( 928) hydrogen bonds : angle 4.09806 ( 2382) covalent geometry : bond 0.00818 (16663) covalent geometry : angle 0.75254 (23778) *********************** 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 : 1.526 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: 1.9618 time to fit residues: 358.4809 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 : 1.325 ------------------------------------------------------------------------------- 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 122 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3609 r_free = 0.3609 target = 0.088014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.064753 restraints weight = 32439.615| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.68 r_work: 0.2956 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16663 Z= 0.157 Angle : 0.555 7.685 23778 Z= 0.329 Chirality : 0.036 0.181 2702 Planarity : 0.004 0.068 1999 Dihedral : 28.986 153.978 4593 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.93 % Allowed : 18.51 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.24), residues: 1199 helix: 2.14 (0.19), residues: 768 sheet: -0.41 (0.64), residues: 65 loop : -1.56 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 364 HIS 0.004 0.001 HIS B 75 PHE 0.017 0.001 PHE K 385 TYR 0.012 0.001 TYR F 51 ARG 0.006 0.000 ARG K 547 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 928) hydrogen bonds : angle 3.20403 ( 2382) covalent geometry : bond 0.00345 (16663) covalent geometry : angle 0.55527 (23778) *********************** 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 190 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 1.429 Fit side-chains REVERT: A 59 GLU cc_start: 0.8781 (pm20) cc_final: 0.8427 (pm20) REVERT: C 64 GLU cc_start: 0.8970 (tt0) cc_final: 0.8653 (tp30) REVERT: C 95 LYS cc_start: 0.9217 (ttmm) cc_final: 0.8980 (tttp) REVERT: E 59 GLU cc_start: 0.8865 (pm20) cc_final: 0.8578 (pm20) REVERT: K 645 ARG cc_start: 0.8560 (tmm-80) cc_final: 0.8345 (tmm-80) REVERT: K 648 GLN cc_start: 0.8581 (tm130) cc_final: 0.8332 (tp-100) outliers start: 20 outliers final: 4 residues processed: 181 average time/residue: 1.9579 time to fit residues: 379.5494 Evaluate side-chains 165 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 161 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain K residue 320 TYR 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 46 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN E 76 GLN K 193 ASN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 648 GLN ** K 652 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 = 0.3602 r_free = 0.3602 target = 0.087502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.064161 restraints weight = 32145.565| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.67 r_work: 0.2989 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16663 Z= 0.173 Angle : 0.546 8.182 23778 Z= 0.323 Chirality : 0.036 0.181 2702 Planarity : 0.004 0.049 1999 Dihedral : 28.902 151.382 4575 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.74 % Allowed : 19.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1199 helix: 2.38 (0.19), residues: 756 sheet: -0.16 (0.65), residues: 65 loop : -1.22 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS B 75 PHE 0.016 0.001 PHE K 385 TYR 0.009 0.001 TYR H 37 ARG 0.004 0.000 ARG K 547 Details of bonding type rmsd hydrogen bonds : bond 0.04626 ( 928) hydrogen bonds : angle 3.09618 ( 2382) covalent geometry : bond 0.00387 (16663) covalent geometry : angle 0.54550 (23778) *********************** 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 190 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 1.301 Fit side-chains REVERT: A 59 GLU cc_start: 0.8788 (pm20) cc_final: 0.8418 (pm20) REVERT: B 24 ASP cc_start: 0.8593 (t0) cc_final: 0.7955 (m-30) REVERT: B 93 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8648 (mm-40) REVERT: C 95 LYS cc_start: 0.9221 (ttmm) cc_final: 0.9005 (tttp) REVERT: E 80 THR cc_start: 0.9313 (m) cc_final: 0.9067 (p) REVERT: F 93 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8433 (mm-40) REVERT: F 95 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8321 (mtp85) REVERT: H 31 LYS cc_start: 0.8348 (mptt) cc_final: 0.8076 (mptt) REVERT: H 105 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8418 (mttm) REVERT: H 113 LYS cc_start: 0.9166 (ttmm) cc_final: 0.8946 (ttpt) REVERT: K 505 GLN cc_start: 0.9299 (tt0) cc_final: 0.9054 (tp40) REVERT: K 569 SER cc_start: 0.6651 (OUTLIER) cc_final: 0.6380 (t) REVERT: K 645 ARG cc_start: 0.8608 (tmm-80) cc_final: 0.8328 (ttp80) outliers start: 18 outliers final: 5 residues processed: 184 average time/residue: 1.9346 time to fit residues: 381.1663 Evaluate side-chains 171 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 435 SER 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 130 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.0170 chunk 108 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- 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 D 46 HIS 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 = 0.3602 r_free = 0.3602 target = 0.087592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.064262 restraints weight = 32268.644| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.67 r_work: 0.2917 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1322 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= 0.164 Angle : 0.544 11.170 23778 Z= 0.320 Chirality : 0.035 0.197 2702 Planarity : 0.004 0.043 1999 Dihedral : 28.855 151.086 4572 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.03 % Allowed : 20.15 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.24), residues: 1199 helix: 2.49 (0.19), residues: 756 sheet: -0.10 (0.64), residues: 65 loop : -1.10 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS B 75 PHE 0.023 0.001 PHE K 385 TYR 0.010 0.001 TYR F 51 ARG 0.005 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.04447 ( 928) hydrogen bonds : angle 3.03276 ( 2382) covalent geometry : bond 0.00366 (16663) covalent geometry : angle 0.54376 (23778) *********************** 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 188 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 1.412 Fit side-chains REVERT: A 59 GLU cc_start: 0.8770 (pm20) cc_final: 0.8367 (pm20) REVERT: B 24 ASP cc_start: 0.8568 (t0) cc_final: 0.7954 (m-30) REVERT: C 95 LYS cc_start: 0.9217 (ttmm) cc_final: 0.8992 (tttp) REVERT: E 80 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.9091 (p) REVERT: F 95 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8360 (mtp85) REVERT: G 64 GLU cc_start: 0.8908 (tt0) cc_final: 0.8663 (tp30) REVERT: H 31 LYS cc_start: 0.8383 (mptt) cc_final: 0.8100 (mptt) REVERT: H 82 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9131 (mtmm) REVERT: K 569 SER cc_start: 0.6594 (OUTLIER) cc_final: 0.6343 (t) REVERT: K 645 ARG cc_start: 0.8647 (tmm-80) cc_final: 0.8368 (ttp80) REVERT: K 646 LEU cc_start: 0.8964 (tt) cc_final: 0.8662 (tm) outliers start: 21 outliers final: 8 residues processed: 180 average time/residue: 2.0722 time to fit residues: 399.1109 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 : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 435 SER 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 8 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN C 73 ASN E 68 GLN E 76 GLN F 93 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.085697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.061978 restraints weight = 32780.874| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.74 r_work: 0.2840 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1389 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= 0.179 Angle : 0.547 12.498 23778 Z= 0.321 Chirality : 0.036 0.321 2702 Planarity : 0.004 0.038 1999 Dihedral : 28.824 149.915 4572 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.60 % Allowed : 20.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.24), residues: 1199 helix: 2.56 (0.19), residues: 755 sheet: -0.00 (0.64), residues: 65 loop : -1.00 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.010 0.001 TYR F 51 ARG 0.005 0.000 ARG K 186 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 928) hydrogen bonds : angle 2.99283 ( 2382) covalent geometry : bond 0.00403 (16663) covalent geometry : angle 0.54749 (23778) *********************** 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 191 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 2.083 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8720 (pm20) cc_final: 0.8291 (pm20) REVERT: B 24 ASP cc_start: 0.8652 (t0) cc_final: 0.7944 (m-30) REVERT: C 64 GLU cc_start: 0.8989 (tt0) cc_final: 0.8644 (tp30) REVERT: C 95 LYS cc_start: 0.9198 (ttmm) cc_final: 0.8972 (tttp) REVERT: F 52 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8149 (mp0) REVERT: G 64 GLU cc_start: 0.8894 (tt0) cc_final: 0.8617 (tp30) REVERT: H 82 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9131 (mtmm) REVERT: H 105 LYS cc_start: 0.8625 (mtpp) cc_final: 0.8335 (mttm) REVERT: H 113 LYS cc_start: 0.9155 (ttmm) cc_final: 0.8927 (ttpt) REVERT: K 186 ARG cc_start: 0.8965 (tpp-160) cc_final: 0.8710 (mmm-85) REVERT: K 569 SER cc_start: 0.6665 (OUTLIER) cc_final: 0.6424 (t) REVERT: K 642 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8407 (mp10) REVERT: K 645 ARG cc_start: 0.8672 (tmm-80) cc_final: 0.8357 (ttp80) outliers start: 27 outliers final: 11 residues processed: 181 average time/residue: 2.0076 time to fit residues: 389.9391 Evaluate side-chains 178 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 117 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 422 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 40 optimal weight: 0.0470 chunk 134 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.0882 ------------------------------------------------------------------------------- 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 F 93 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 = 0.3603 r_free = 0.3603 target = 0.087654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.064328 restraints weight = 32310.835| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.66 r_work: 0.2993 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1498 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= 0.178 Angle : 0.546 10.167 23778 Z= 0.320 Chirality : 0.035 0.219 2702 Planarity : 0.004 0.038 1999 Dihedral : 28.744 149.249 4572 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.99 % Allowed : 19.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.25), residues: 1199 helix: 2.61 (0.19), residues: 755 sheet: 0.11 (0.63), residues: 65 loop : -0.93 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS B 75 PHE 0.012 0.001 PHE K 408 TYR 0.009 0.001 TYR F 51 ARG 0.005 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.04580 ( 928) hydrogen bonds : angle 2.95381 ( 2382) covalent geometry : bond 0.00400 (16663) covalent geometry : angle 0.54589 (23778) *********************** 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 196 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.416 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8705 (pm20) cc_final: 0.8284 (pm20) REVERT: B 24 ASP cc_start: 0.8578 (t0) cc_final: 0.7891 (m-30) REVERT: C 73 ASN cc_start: 0.8150 (m-40) cc_final: 0.7628 (t0) REVERT: C 95 LYS cc_start: 0.9216 (ttmm) cc_final: 0.9008 (tttp) REVERT: F 52 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8199 (mp0) REVERT: F 95 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8016 (mtp85) REVERT: G 64 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8668 (tp30) REVERT: H 113 LYS cc_start: 0.9176 (ttmm) cc_final: 0.8972 (ttpt) REVERT: K 401 LEU cc_start: 0.9428 (mm) cc_final: 0.9011 (mt) REVERT: K 569 SER cc_start: 0.6774 (OUTLIER) cc_final: 0.6538 (t) REVERT: K 642 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8436 (mp10) REVERT: K 645 ARG cc_start: 0.8670 (tmm-80) cc_final: 0.8355 (ttp80) REVERT: K 646 LEU cc_start: 0.9034 (tt) cc_final: 0.8759 (tm) outliers start: 31 outliers final: 12 residues processed: 185 average time/residue: 1.8917 time to fit residues: 374.4482 Evaluate side-chains 179 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 117 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 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 68 GLU Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 548 ILE 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 82 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3580 r_free = 0.3580 target = 0.086390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.062982 restraints weight = 32312.884| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.66 r_work: 0.2968 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16663 Z= 0.226 Angle : 0.570 9.845 23778 Z= 0.332 Chirality : 0.037 0.188 2702 Planarity : 0.004 0.040 1999 Dihedral : 28.877 148.806 4572 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.80 % Allowed : 20.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.24), residues: 1199 helix: 2.52 (0.19), residues: 755 sheet: 0.17 (0.63), residues: 65 loop : -1.00 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.009 0.001 TYR F 51 ARG 0.005 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.05241 ( 928) hydrogen bonds : angle 3.03779 ( 2382) covalent geometry : bond 0.00514 (16663) covalent geometry : angle 0.56976 (23778) *********************** 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 192 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 3.678 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8764 (pm20) cc_final: 0.8349 (pm20) REVERT: B 24 ASP cc_start: 0.8584 (t0) cc_final: 0.7890 (m-30) REVERT: C 95 LYS cc_start: 0.9209 (ttmm) cc_final: 0.8998 (tttp) REVERT: F 93 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7335 (mp10) REVERT: G 64 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8661 (tp30) REVERT: H 105 LYS cc_start: 0.8722 (mtpp) cc_final: 0.8430 (mttm) REVERT: K 186 ARG cc_start: 0.8906 (tpp-160) cc_final: 0.8674 (mmm-85) REVERT: K 401 LEU cc_start: 0.9424 (mm) cc_final: 0.9020 (mt) REVERT: K 569 SER cc_start: 0.6659 (OUTLIER) cc_final: 0.6448 (t) REVERT: K 642 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8420 (mp10) REVERT: K 645 ARG cc_start: 0.8661 (tmm-80) cc_final: 0.8341 (ttp80) outliers start: 29 outliers final: 11 residues processed: 180 average time/residue: 2.5278 time to fit residues: 489.4804 Evaluate side-chains 178 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 117 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 93 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 68 GLU Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 548 ILE 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 109 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.086087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.062604 restraints weight = 32127.506| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.66 r_work: 0.2901 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16663 Z= 0.233 Angle : 0.572 8.991 23778 Z= 0.333 Chirality : 0.037 0.156 2702 Planarity : 0.004 0.041 1999 Dihedral : 28.933 148.947 4572 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.89 % Allowed : 20.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.24), residues: 1199 helix: 2.46 (0.19), residues: 755 sheet: 0.09 (0.63), residues: 65 loop : -1.03 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 PHE 0.011 0.002 PHE K 408 TYR 0.011 0.001 TYR F 51 ARG 0.005 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.05321 ( 928) hydrogen bonds : angle 3.03917 ( 2382) covalent geometry : bond 0.00530 (16663) covalent geometry : angle 0.57182 (23778) *********************** 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 194 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 1.875 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8751 (pm20) cc_final: 0.8317 (pm20) REVERT: C 64 GLU cc_start: 0.8972 (tt0) cc_final: 0.8639 (tp30) REVERT: C 95 LYS cc_start: 0.9206 (ttmm) cc_final: 0.8994 (tttp) REVERT: F 93 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7305 (mp10) REVERT: G 64 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8664 (tp30) REVERT: H 105 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8414 (mttm) REVERT: H 113 LYS cc_start: 0.9190 (ttmm) cc_final: 0.8963 (ttpt) REVERT: K 569 SER cc_start: 0.6517 (OUTLIER) cc_final: 0.6311 (t) REVERT: K 642 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8422 (mp10) REVERT: K 645 ARG cc_start: 0.8658 (tmm-80) cc_final: 0.8277 (ttp80) outliers start: 30 outliers final: 15 residues processed: 181 average time/residue: 2.1227 time to fit residues: 414.1462 Evaluate side-chains 181 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 117 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR 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 376 SER Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 463 THR Chi-restraints excluded: chain K residue 548 ILE 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 69 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 F 93 GLN H 92 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.086832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.063435 restraints weight = 31990.298| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.66 r_work: 0.2931 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16663 Z= 0.164 Angle : 0.573 14.962 23778 Z= 0.330 Chirality : 0.036 0.250 2702 Planarity : 0.004 0.047 1999 Dihedral : 28.925 149.287 4572 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.83 % Allowed : 21.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.25), residues: 1199 helix: 2.53 (0.19), residues: 755 sheet: 0.07 (0.63), residues: 65 loop : -0.95 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 PHE 0.011 0.001 PHE K 385 TYR 0.010 0.001 TYR F 51 ARG 0.006 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.04834 ( 928) hydrogen bonds : angle 3.02280 ( 2382) covalent geometry : bond 0.00364 (16663) covalent geometry : angle 0.57280 (23778) *********************** 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 183 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8740 (pm20) cc_final: 0.8304 (pm20) REVERT: C 64 GLU cc_start: 0.8956 (tt0) cc_final: 0.8662 (tp30) REVERT: C 95 LYS cc_start: 0.9202 (ttmm) cc_final: 0.8976 (tttp) REVERT: G 64 GLU cc_start: 0.8902 (tt0) cc_final: 0.8632 (tp30) REVERT: H 105 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8392 (mttm) REVERT: H 113 LYS cc_start: 0.9181 (ttmm) cc_final: 0.8953 (ttpt) REVERT: K 401 LEU cc_start: 0.9391 (mm) cc_final: 0.9178 (mm) REVERT: K 470 MET cc_start: 0.9135 (tpt) cc_final: 0.8791 (tpp) REVERT: K 569 SER cc_start: 0.6745 (OUTLIER) cc_final: 0.6506 (t) REVERT: K 642 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8450 (mp10) REVERT: K 645 ARG cc_start: 0.8633 (tmm-80) cc_final: 0.8254 (ttp80) outliers start: 19 outliers final: 13 residues processed: 178 average time/residue: 2.2279 time to fit residues: 427.0657 Evaluate side-chains 177 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 117 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain K residue 235 LEU Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 463 THR Chi-restraints excluded: chain K residue 548 ILE 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 5 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3593 r_free = 0.3593 target = 0.087130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.063787 restraints weight = 32371.477| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.66 r_work: 0.2991 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1489 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= 0.168 Angle : 0.566 13.344 23778 Z= 0.327 Chirality : 0.035 0.153 2702 Planarity : 0.004 0.047 1999 Dihedral : 28.883 149.284 4572 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.74 % Allowed : 22.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.24), residues: 1199 helix: 2.54 (0.19), residues: 753 sheet: 0.08 (0.64), residues: 65 loop : -0.93 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS B 75 PHE 0.013 0.001 PHE K 408 TYR 0.009 0.001 TYR F 51 ARG 0.007 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 928) hydrogen bonds : angle 3.01149 ( 2382) covalent geometry : bond 0.00374 (16663) covalent geometry : angle 0.56608 (23778) ********************** 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 180 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.453 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8728 (pm20) cc_final: 0.8294 (pm20) REVERT: C 64 GLU cc_start: 0.8955 (tt0) cc_final: 0.8656 (tp30) REVERT: C 95 LYS cc_start: 0.9205 (ttmm) cc_final: 0.8989 (tttp) REVERT: G 64 GLU cc_start: 0.8901 (tt0) cc_final: 0.8630 (tp30) REVERT: H 105 LYS cc_start: 0.8703 (mtpp) cc_final: 0.8441 (mttm) REVERT: H 113 LYS cc_start: 0.9190 (ttmm) cc_final: 0.8965 (ttpt) REVERT: K 569 SER cc_start: 0.6722 (OUTLIER) cc_final: 0.6483 (t) REVERT: K 642 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8468 (mp10) REVERT: K 645 ARG cc_start: 0.8624 (tmm-80) cc_final: 0.8254 (ttp80) outliers start: 18 outliers final: 13 residues processed: 175 average time/residue: 1.9649 time to fit residues: 368.4391 Evaluate side-chains 174 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 117 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain K residue 235 LEU Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 463 THR Chi-restraints excluded: chain K residue 548 ILE 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 21 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.085958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.062417 restraints weight = 32379.263| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.67 r_work: 0.2913 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 16663 Z= 0.246 Angle : 0.598 13.204 23778 Z= 0.343 Chirality : 0.038 0.152 2702 Planarity : 0.004 0.044 1999 Dihedral : 28.944 148.577 4572 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.93 % Allowed : 22.18 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.24), residues: 1199 helix: 2.44 (0.19), residues: 754 sheet: 0.05 (0.64), residues: 65 loop : -1.02 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 364 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.010 0.001 TYR A 54 ARG 0.005 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.05556 ( 928) hydrogen bonds : angle 3.12988 ( 2382) covalent geometry : bond 0.00562 (16663) covalent geometry : angle 0.59787 (23778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17921.23 seconds wall clock time: 314 minutes 44.16 seconds (18884.16 seconds total)