Starting phenix.real_space_refine on Wed Sep 17 19:56:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cnu_45760/09_2025/9cnu_45760.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cnu_45760/09_2025/9cnu_45760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cnu_45760/09_2025/9cnu_45760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cnu_45760/09_2025/9cnu_45760.map" model { file = "/net/cci-nas-00/data/ceres_data/9cnu_45760/09_2025/9cnu_45760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cnu_45760/09_2025/9cnu_45760.cif" } resolution = 2.99 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= 0.014 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 72 5.16 5 C 6864 2.51 5 N 1872 2.21 5 O 2292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 11172 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1735 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 55 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'IHP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, E, G, I, K, D, F, H, J, L Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" C1 IHP A 301 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP A 301 " occ=0.17 residue: pdb=" C1 IHP A 302 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP A 302 " occ=0.17 residue: pdb=" C1 IHP C 301 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP C 301 " occ=0.17 residue: pdb=" C1 IHP C 302 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP C 302 " occ=0.17 residue: pdb=" C1 IHP E 301 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP E 301 " occ=0.17 residue: pdb=" C1 IHP E 302 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP E 302 " occ=0.17 residue: pdb=" C1 IHP G 301 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP G 301 " occ=0.17 residue: pdb=" C1 IHP G 302 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP G 302 " occ=0.17 residue: pdb=" C1 IHP I 301 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP I 301 " occ=0.17 residue: pdb=" C1 IHP I 302 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP I 302 " occ=0.17 residue: pdb=" C1 IHP K 301 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP K 301 " occ=0.17 residue: pdb=" C1 IHP K 302 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP K 302 " occ=0.17 Time building chain proxies: 1.45, per 1000 atoms: 0.13 Number of scatterers: 11172 At special positions: 0 Unit cell: (112.14, 112.14, 75.828, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 72 15.00 O 2292 8.00 N 1872 7.00 C 6864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS G 198 " - pdb=" SG CYS G 218 " distance=2.03 Simple disulfide: pdb=" SG CYS I 198 " - pdb=" SG CYS I 218 " distance=2.03 Simple disulfide: pdb=" SG CYS K 198 " - pdb=" SG CYS K 218 " distance=2.03 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 Atom "HETATM 7387 O15 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1801 O15 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11111 O15 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5525 O15 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9249 O15 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3663 O15 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11108 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5522 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7384 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1798 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3660 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9246 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9250 O16 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3664 O16 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7388 O16 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5526 O16 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1802 O16 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11112 O16 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7420 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9282 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3696 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5558 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11144 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11144 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7420 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5558 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9282 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3696 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3699 O15 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5561 O15 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11147 O15 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9285 O15 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7384 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1837 O15 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7423 O15 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1798 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11108 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5522 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5522 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11108 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7384 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1798 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3660 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9246 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3660 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9246 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3661 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9247 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7385 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1799 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5523 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11109 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7420 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9282 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3696 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5558 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11144 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3661 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9247 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7385 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1799 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5523 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11109 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9245 O11 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3659 O11 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5521 O11 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11107 O11 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7383 O11 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1797 O11 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1802 O16 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7388 O16 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5526 O16 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3664 O16 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9250 O16 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11112 O16 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11143 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5557 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9281 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3695 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1833 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7419 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11110 O14 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5524 O14 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3662 O14 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9248 O14 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7386 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1800 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11143 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5557 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9281 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3695 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7419 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1833 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7384 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1798 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9246 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3660 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11108 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5522 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9248 O14 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3662 O14 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11110 O14 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5524 O14 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1800 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7386 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9286 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3700 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1838 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7424 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11148 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5562 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11112 O16 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5526 O16 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9250 O16 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3664 O16 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1802 O16 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7388 O16 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5524 O14 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11110 O14 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7386 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1800 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3662 O14 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9248 O14 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3700 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9286 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7424 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1838 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11148 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5562 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1798 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7384 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9246 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3660 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5522 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11108 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9247 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3661 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7385 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1799 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5523 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11109 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1797 O11 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7383 O11 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9245 O11 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3659 O11 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5521 O11 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11107 O11 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1838 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7424 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5562 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11148 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3700 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9286 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7421 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3697 O13 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9283 O13 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5559 O13 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11145 O13 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5524 O14 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11110 O14 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3662 O14 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7386 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1800 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9248 O14 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9281 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3695 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11143 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5557 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7419 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1833 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7421 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9283 O13 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3697 O13 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5559 O13 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11145 O13 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11144 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5558 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9282 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3696 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7420 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11143 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5557 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1798 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7384 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7388 O16 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1802 O16 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5522 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11108 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9246 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3660 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9281 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3695 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9250 O16 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3664 O16 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1833 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7419 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5526 O16 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11112 O16 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11109 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5523 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3661 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9247 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1799 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7385 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11143 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5557 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7419 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1833 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9281 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3695 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7385 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1799 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9247 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3661 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11109 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5523 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5562 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11148 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1838 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7424 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3700 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9286 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7385 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9247 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3661 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1799 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5523 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11109 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3699 O15 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9285 O15 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5561 O15 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11147 O15 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1837 O15 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7423 O15 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1838 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7424 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5562 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11148 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3700 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9286 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11144 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5558 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5559 O13 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11145 O13 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7420 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7421 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9282 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3696 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3697 O13 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9283 O13 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7384 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1798 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9246 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3660 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11108 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5522 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9284 O14 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3698 O14 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5560 O14 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11146 O14 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1836 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7422 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9284 O14 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3698 O14 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1836 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7422 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5560 O14 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7421 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11146 O14 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11145 O13 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5559 O13 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3663 O15 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9283 O13 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3697 O13 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9249 O15 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5525 O15 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11111 O15 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1801 O15 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7387 O15 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11109 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5523 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3661 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9247 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7385 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1799 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7419 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1833 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9281 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3695 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5557 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11143 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11144 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5558 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7420 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3696 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9282 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7388 O16 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1802 O16 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5526 O16 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11112 O16 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11109 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5523 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9250 O16 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3664 O16 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1798 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7384 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1799 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7385 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5522 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11108 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9246 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3660 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3661 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9247 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7384 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1798 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9246 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3660 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7421 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11108 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5522 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5559 O13 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11145 O13 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9283 O13 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3697 O13 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1797 O11 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7383 O11 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7387 O15 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1801 O15 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11107 O11 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9245 O11 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3659 O11 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5521 O11 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9249 O15 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3663 O15 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5525 O15 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11111 O15 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9286 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3700 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11148 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5562 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7424 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1838 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11144 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5558 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7420 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9282 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3696 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11148 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5562 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9286 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3700 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1838 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7424 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11144 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7420 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5558 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9282 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3696 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9245 O11 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3659 O11 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1797 O11 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7383 O11 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5521 O11 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11107 O11 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11107 O11 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9284 O14 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3698 O14 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5521 O11 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1836 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7422 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9245 O11 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3659 O11 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1797 O11 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7383 O11 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11146 O14 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3700 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9286 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5560 O14 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11107 O11 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11148 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5521 O11 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5562 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1838 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7424 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3659 O11 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9245 O11 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7383 O11 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1797 O11 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5524 O14 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11110 O14 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3662 O14 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9248 O14 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1800 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7386 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7422 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1836 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11146 O14 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5560 O14 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3698 O14 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9284 O14 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9283 O13 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3697 O13 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7421 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11145 O13 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5559 O13 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7385 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1799 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9247 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3661 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1800 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9248 O14 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3662 O14 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7386 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5523 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11109 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1833 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7419 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11110 O14 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5524 O14 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9281 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3695 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5557 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11143 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11112 O16 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5526 O16 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3664 O16 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9250 O16 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1802 O16 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7388 O16 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1836 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7422 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11146 O14 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3698 O14 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9284 O14 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5560 O14 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7383 O11 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3696 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1797 O11 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9282 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11107 O11 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5521 O11 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7420 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11144 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5558 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3697 O13 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9283 O13 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9245 O11 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3659 O11 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11145 O13 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5559 O13 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7421 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11111 O15 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5525 O15 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1801 O15 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7387 O15 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9249 O15 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3663 O15 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3662 O14 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9248 O14 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1800 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7386 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11109 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5523 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11110 O14 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5524 O14 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9247 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3661 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11147 O15 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5561 O15 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1837 O15 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7423 O15 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1799 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7385 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9285 O15 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3699 O15 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11144 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5558 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9282 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3696 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7420 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11143 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5557 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7419 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1833 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9281 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3695 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5560 O14 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11146 O14 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3698 O14 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9284 O14 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1836 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7422 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7422 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1836 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9284 O14 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3698 O14 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11146 O14 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5560 O14 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5562 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11148 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7424 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1838 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3700 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9286 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5524 O14 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11110 O14 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7386 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1800 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3662 O14 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9248 O14 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7420 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5558 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11144 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9282 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5557 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11143 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3696 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1833 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7419 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9281 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3695 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9247 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3661 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5523 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11109 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9248 O14 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3662 O14 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7385 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1799 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7385 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11144 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5558 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3660 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9246 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1799 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7384 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1798 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7420 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9282 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11110 O14 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5522 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11108 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9248 O14 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3696 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5524 O14 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3662 O14 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7386 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1800 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3661 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9247 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11144 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11110 O14 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5524 O14 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5523 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11109 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9282 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5558 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3696 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7420 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7386 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1800 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 521.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 67.7% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 18 through 30 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.546A pdb=" N VAL A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.405A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.643A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'C' and resid 18 through 30 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 59 removed outlier: 3.547A pdb=" N VAL C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 99 through 105 Processing helix chain 'C' and resid 110 through 118 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.405A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE C 191 " --> pdb=" O GLN C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.644A pdb=" N GLY C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'E' and resid 18 through 30 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 59 removed outlier: 3.546A pdb=" N VAL E 59 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 99 through 105 Processing helix chain 'E' and resid 110 through 118 Processing helix chain 'E' and resid 125 through 146 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.406A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE E 191 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.643A pdb=" N GLY E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'G' and resid 18 through 30 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 59 removed outlier: 3.546A pdb=" N VAL G 59 " --> pdb=" O MET G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 99 through 105 Processing helix chain 'G' and resid 110 through 118 Processing helix chain 'G' and resid 125 through 146 Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 160 through 176 Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.405A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE G 191 " --> pdb=" O GLN G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.643A pdb=" N GLY G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 218 Processing helix chain 'I' and resid 18 through 30 Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 48 through 59 removed outlier: 3.546A pdb=" N VAL I 59 " --> pdb=" O MET I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 84 Processing helix chain 'I' and resid 99 through 105 Processing helix chain 'I' and resid 110 through 118 Processing helix chain 'I' and resid 125 through 146 Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'I' and resid 160 through 176 Processing helix chain 'I' and resid 178 through 193 removed outlier: 4.405A pdb=" N LEU I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE I 191 " --> pdb=" O GLN I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 206 removed outlier: 3.643A pdb=" N GLY I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 218 Processing helix chain 'K' and resid 18 through 30 Processing helix chain 'K' and resid 35 through 44 Processing helix chain 'K' and resid 48 through 59 removed outlier: 3.546A pdb=" N VAL K 59 " --> pdb=" O MET K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 84 Processing helix chain 'K' and resid 99 through 105 Processing helix chain 'K' and resid 110 through 118 Processing helix chain 'K' and resid 125 through 146 Processing helix chain 'K' and resid 149 through 153 Processing helix chain 'K' and resid 160 through 176 Processing helix chain 'K' and resid 178 through 193 removed outlier: 4.406A pdb=" N LEU K 190 " --> pdb=" O THR K 186 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE K 191 " --> pdb=" O GLN K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 206 removed outlier: 3.643A pdb=" N GLY K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 218 Processing sheet with id=1, first strand: chain 'A' and resid 2 through 5 removed outlier: 3.507A pdb=" N ASN A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'C' and resid 2 through 5 removed outlier: 3.507A pdb=" N ASN C 9 " --> pdb=" O THR C 5 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'E' and resid 2 through 5 removed outlier: 3.507A pdb=" N ASN E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'G' and resid 2 through 5 removed outlier: 3.507A pdb=" N ASN G 9 " --> pdb=" O THR G 5 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'I' and resid 2 through 5 removed outlier: 3.507A pdb=" N ASN I 9 " --> pdb=" O THR I 5 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'K' and resid 2 through 5 removed outlier: 3.506A pdb=" N ASN K 9 " --> pdb=" O THR K 5 " (cutoff:3.500A) 642 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2250 1.32 - 1.45: 2351 1.45 - 1.57: 6643 1.57 - 1.69: 72 1.69 - 1.82: 114 Bond restraints: 11430 Sorted by residual: bond pdb=" CA SER C 44 " pdb=" CB SER C 44 " ideal model delta sigma weight residual 1.529 1.469 0.059 1.40e-02 5.10e+03 1.80e+01 bond pdb=" CA SER A 44 " pdb=" CB SER A 44 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.40e-02 5.10e+03 1.78e+01 bond pdb=" CA SER G 44 " pdb=" CB SER G 44 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.40e-02 5.10e+03 1.78e+01 bond pdb=" CA SER K 44 " pdb=" CB SER K 44 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.40e-02 5.10e+03 1.77e+01 bond pdb=" CA SER E 44 " pdb=" CB SER E 44 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.40e-02 5.10e+03 1.77e+01 ... (remaining 11425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 11743 2.26 - 4.51: 3561 4.51 - 6.77: 302 6.77 - 9.03: 72 9.03 - 11.29: 12 Bond angle restraints: 15690 Sorted by residual: angle pdb=" N ILE C 191 " pdb=" CA ILE C 191 " pdb=" C ILE C 191 " ideal model delta sigma weight residual 111.44 102.99 8.45 1.34e+00 5.57e-01 3.98e+01 angle pdb=" N ILE I 191 " pdb=" CA ILE I 191 " pdb=" C ILE I 191 " ideal model delta sigma weight residual 111.44 103.00 8.44 1.34e+00 5.57e-01 3.96e+01 angle pdb=" N ILE E 191 " pdb=" CA ILE E 191 " pdb=" C ILE E 191 " ideal model delta sigma weight residual 111.44 103.01 8.43 1.34e+00 5.57e-01 3.96e+01 angle pdb=" N ILE A 191 " pdb=" CA ILE A 191 " pdb=" C ILE A 191 " ideal model delta sigma weight residual 111.44 103.02 8.42 1.34e+00 5.57e-01 3.95e+01 angle pdb=" N ILE G 191 " pdb=" CA ILE G 191 " pdb=" C ILE G 191 " ideal model delta sigma weight residual 111.44 103.02 8.42 1.34e+00 5.57e-01 3.95e+01 ... (remaining 15685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.31: 6024 12.31 - 24.62: 672 24.62 - 36.93: 260 36.93 - 49.23: 52 49.23 - 61.54: 162 Dihedral angle restraints: 7170 sinusoidal: 3246 harmonic: 3924 Sorted by residual: dihedral pdb=" CB CYS I 198 " pdb=" SG CYS I 198 " pdb=" SG CYS I 218 " pdb=" CB CYS I 218 " ideal model delta sinusoidal sigma weight residual -86.00 -146.07 60.07 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CB CYS K 198 " pdb=" SG CYS K 198 " pdb=" SG CYS K 218 " pdb=" CB CYS K 218 " ideal model delta sinusoidal sigma weight residual -86.00 -146.06 60.06 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CB CYS E 198 " pdb=" SG CYS E 198 " pdb=" SG CYS E 218 " pdb=" CB CYS E 218 " ideal model delta sinusoidal sigma weight residual -86.00 -146.06 60.06 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 7167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 384 0.064 - 0.127: 640 0.127 - 0.190: 435 0.190 - 0.253: 215 0.253 - 0.316: 24 Chirality restraints: 1698 Sorted by residual: chirality pdb=" CA LEU E 20 " pdb=" N LEU E 20 " pdb=" C LEU E 20 " pdb=" CB LEU E 20 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA LEU G 20 " pdb=" N LEU G 20 " pdb=" C LEU G 20 " pdb=" CB LEU G 20 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA LEU A 20 " pdb=" N LEU A 20 " pdb=" C LEU A 20 " pdb=" CB LEU A 20 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.48e+00 ... (remaining 1695 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 173 " 0.594 9.50e-02 1.11e+02 2.67e-01 4.35e+01 pdb=" NE ARG C 173 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG C 173 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 173 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 173 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 173 " -0.594 9.50e-02 1.11e+02 2.66e-01 4.35e+01 pdb=" NE ARG I 173 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG I 173 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG I 173 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG I 173 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 173 " -0.594 9.50e-02 1.11e+02 2.66e-01 4.34e+01 pdb=" NE ARG G 173 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG G 173 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG G 173 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG G 173 " -0.017 2.00e-02 2.50e+03 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 0.24 - 1.17: 786 1.17 - 2.11: 2116 2.11 - 3.04: 11437 3.04 - 3.97: 37146 3.97 - 4.90: 64014 Warning: very small nonbonded interaction distances. Nonbonded interactions: 115499 Sorted by model distance: nonbonded pdb=" O26 IHP E 301 " pdb=" O33 IHP K 301 " model vdw 0.243 3.040 nonbonded pdb=" O33 IHP E 301 " pdb=" O26 IHP K 301 " model vdw 0.243 3.040 nonbonded pdb=" O23 IHP A 301 " pdb=" O36 IHP G 301 " model vdw 0.246 3.040 nonbonded pdb=" O36 IHP A 301 " pdb=" O23 IHP G 301 " model vdw 0.246 3.040 nonbonded pdb=" O26 IHP A 301 " pdb=" O33 IHP G 301 " model vdw 0.248 3.040 ... (remaining 115494 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } 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=0.17 max=1.00 mean=0.97 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: 0.400 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.780 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:8.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 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 : 0.058 1.326 11460 Z= 5.713 Angle : 1.988 11.285 15702 Z= 1.425 Chirality : 0.133 0.316 1698 Planarity : 0.029 0.267 1986 Dihedral : 15.679 61.543 4632 Min Nonbonded Distance : 0.243 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.20), residues: 1350 helix: -0.70 (0.16), residues: 834 sheet: -2.87 (0.36), residues: 54 loop : -2.50 (0.24), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.003 ARG I 131 TYR 0.035 0.006 TYR I 118 PHE 0.012 0.003 PHE K 40 TRP 0.041 0.005 TRP I 116 HIS 0.013 0.006 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.01416 (11430) covalent geometry : angle 1.98852 (15690) SS BOND : bond 0.00149 ( 6) SS BOND : angle 0.23574 ( 12) hydrogen bonds : bond 0.22435 ( 642) hydrogen bonds : angle 8.03701 ( 1890) Misc. bond : bond 1.23116 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 4 residues processed: 326 average time/residue: 0.7604 time to fit residues: 262.2288 Evaluate side-chains 249 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 245 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain K residue 61 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN C 21 ASN C 162 GLN E 21 ASN E 162 GLN G 162 GLN I 21 ASN I 162 GLN K 21 ASN K 162 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.087830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.066589 restraints weight = 49860.833| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 5.37 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 1.523 11460 Z= 4.277 Angle : 5.771 96.511 15702 Z= 1.964 Chirality : 0.485 4.878 1698 Planarity : 0.008 0.107 1986 Dihedral : 22.006 133.908 1976 Min Nonbonded Distance : 1.141 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.39 % Allowed : 14.10 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.22), residues: 1350 helix: 0.29 (0.16), residues: 888 sheet: -2.84 (0.51), residues: 54 loop : -1.62 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.003 ARG E 18 TYR 0.014 0.002 TYR K 50 PHE 0.009 0.002 PHE L 7 TRP 0.015 0.002 TRP G 116 HIS 0.003 0.001 HIS G 84 Details of bonding type rmsd covalent geometry : bond 0.08445 (11430) covalent geometry : angle 5.77038 (15690) SS BOND : bond 0.00926 ( 6) SS BOND : angle 6.87221 ( 12) hydrogen bonds : bond 0.06117 ( 642) hydrogen bonds : angle 5.36387 ( 1890) Misc. bond : bond 0.09551 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 282 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8671 (t80) cc_final: 0.8458 (t80) REVERT: A 175 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8123 (mt-10) REVERT: A 182 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.9134 (ptpt) REVERT: A 214 MET cc_start: 0.9252 (mtt) cc_final: 0.8679 (mpp) REVERT: C 76 GLU cc_start: 0.9115 (mp0) cc_final: 0.8629 (mp0) REVERT: C 144 MET cc_start: 0.8938 (mmm) cc_final: 0.8420 (mpt) REVERT: C 203 LYS cc_start: 0.9616 (mtpm) cc_final: 0.9399 (ptpp) REVERT: C 214 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.8833 (mpp) REVERT: E 25 LYS cc_start: 0.8359 (mtmm) cc_final: 0.8140 (mtpp) REVERT: E 29 ASP cc_start: 0.8884 (m-30) cc_final: 0.8555 (m-30) REVERT: E 175 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8045 (mt-10) REVERT: E 182 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.9168 (ptpp) REVERT: E 189 LEU cc_start: 0.9342 (tp) cc_final: 0.9119 (tm) REVERT: E 214 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8861 (mpt) REVERT: G 130 TYR cc_start: 0.8662 (t80) cc_final: 0.8449 (t80) REVERT: G 175 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8131 (mt-10) REVERT: G 182 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9136 (ptpt) REVERT: G 214 MET cc_start: 0.9245 (mtt) cc_final: 0.8665 (mpp) REVERT: I 76 GLU cc_start: 0.9120 (mp0) cc_final: 0.8638 (mp0) REVERT: I 144 MET cc_start: 0.8932 (mmm) cc_final: 0.8411 (mpt) REVERT: I 203 LYS cc_start: 0.9614 (mtpm) cc_final: 0.9397 (ptpp) REVERT: I 214 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8822 (mpp) REVERT: K 25 LYS cc_start: 0.8344 (mtmm) cc_final: 0.8125 (mtpp) REVERT: K 29 ASP cc_start: 0.8873 (m-30) cc_final: 0.8545 (m-30) REVERT: K 70 ARG cc_start: 0.8891 (tpt170) cc_final: 0.8593 (mtp85) REVERT: K 175 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8050 (mt-10) REVERT: K 182 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9176 (ptpp) REVERT: K 189 LEU cc_start: 0.9343 (tp) cc_final: 0.9116 (tm) REVERT: K 214 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8853 (mpt) outliers start: 28 outliers final: 6 residues processed: 288 average time/residue: 0.7970 time to fit residues: 242.7064 Evaluate side-chains 252 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain K residue 182 LYS Chi-restraints excluded: chain K residue 214 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS G 12 HIS I 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.086160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.066345 restraints weight = 33185.870| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 4.40 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.061 1.285 11460 Z= 3.077 Angle : 5.138 92.922 15702 Z= 1.740 Chirality : 0.362 4.304 1698 Planarity : 0.006 0.044 1986 Dihedral : 25.972 175.631 1972 Min Nonbonded Distance : 1.274 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.37 % Allowed : 16.92 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.22), residues: 1350 helix: 1.07 (0.17), residues: 888 sheet: -2.71 (0.55), residues: 54 loop : -1.17 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG E 18 TYR 0.020 0.003 TYR A 10 PHE 0.012 0.002 PHE B 7 TRP 0.010 0.001 TRP G 116 HIS 0.004 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.06051 (11430) covalent geometry : angle 5.13907 (15690) SS BOND : bond 0.00299 ( 6) SS BOND : angle 4.17802 ( 12) hydrogen bonds : bond 0.05116 ( 642) hydrogen bonds : angle 5.04922 ( 1890) Misc. bond : bond 0.12560 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 279 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.9207 (t0) cc_final: 0.8620 (p0) REVERT: A 175 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8143 (mt-10) REVERT: A 182 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.9182 (ptpp) REVERT: A 214 MET cc_start: 0.9096 (mtt) cc_final: 0.8685 (mpp) REVERT: C 76 GLU cc_start: 0.9179 (mp0) cc_final: 0.8565 (mp0) REVERT: C 144 MET cc_start: 0.8961 (mmm) cc_final: 0.8388 (mpt) REVERT: C 159 GLU cc_start: 0.7928 (tt0) cc_final: 0.7708 (tm-30) REVERT: C 175 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7331 (mp0) REVERT: C 203 LYS cc_start: 0.9506 (mtpm) cc_final: 0.9283 (ptpt) REVERT: C 214 MET cc_start: 0.9252 (mtp) cc_final: 0.8898 (mpp) REVERT: E 175 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8069 (mt-10) REVERT: E 182 LYS cc_start: 0.9501 (ptmt) cc_final: 0.9201 (ptpp) REVERT: E 214 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8890 (mpt) REVERT: G 97 ASP cc_start: 0.9213 (t0) cc_final: 0.8629 (p0) REVERT: G 175 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8124 (mt-10) REVERT: G 182 LYS cc_start: 0.9466 (OUTLIER) cc_final: 0.9186 (ptpp) REVERT: G 214 MET cc_start: 0.9094 (mtt) cc_final: 0.8684 (mpp) REVERT: I 75 ASP cc_start: 0.9528 (m-30) cc_final: 0.9206 (m-30) REVERT: I 76 GLU cc_start: 0.9183 (mp0) cc_final: 0.8573 (mp0) REVERT: I 97 ASP cc_start: 0.9142 (t0) cc_final: 0.8421 (p0) REVERT: I 144 MET cc_start: 0.8964 (mmm) cc_final: 0.8396 (mpt) REVERT: I 159 GLU cc_start: 0.7922 (tt0) cc_final: 0.7698 (tm-30) REVERT: I 175 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7320 (mp0) REVERT: I 203 LYS cc_start: 0.9487 (mtpm) cc_final: 0.9275 (ptpp) REVERT: I 214 MET cc_start: 0.9276 (mtp) cc_final: 0.8857 (mpp) REVERT: K 175 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8057 (mt-10) REVERT: K 182 LYS cc_start: 0.9502 (ptmt) cc_final: 0.9205 (ptpp) REVERT: K 214 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8891 (mpt) outliers start: 16 outliers final: 7 residues processed: 283 average time/residue: 0.8482 time to fit residues: 253.0389 Evaluate side-chains 252 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 241 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 214 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 112 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 0.0270 chunk 31 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 overall best weight: 2.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 HIS I 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.081793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.061154 restraints weight = 31903.260| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 4.35 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.053 1.022 11460 Z= 2.699 Angle : 4.719 93.508 15702 Z= 1.601 Chirality : 0.332 3.731 1698 Planarity : 0.006 0.072 1986 Dihedral : 26.343 178.306 1972 Min Nonbonded Distance : 1.405 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.14 % Allowed : 17.26 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.23), residues: 1350 helix: 1.07 (0.17), residues: 930 sheet: -2.58 (0.55), residues: 54 loop : -1.05 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 18 TYR 0.025 0.003 TYR G 10 PHE 0.009 0.002 PHE K 32 TRP 0.007 0.001 TRP I 116 HIS 0.004 0.001 HIS I 84 Details of bonding type rmsd covalent geometry : bond 0.05298 (11430) covalent geometry : angle 4.71998 (15690) SS BOND : bond 0.00225 ( 6) SS BOND : angle 3.20272 ( 12) hydrogen bonds : bond 0.04723 ( 642) hydrogen bonds : angle 4.81884 ( 1890) Misc. bond : bond 0.11914 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.8968 (mtp85) cc_final: 0.8660 (mmm160) REVERT: A 76 GLU cc_start: 0.9456 (mm-30) cc_final: 0.9103 (mp0) REVERT: A 175 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8357 (mt-10) REVERT: A 182 LYS cc_start: 0.9485 (ptmt) cc_final: 0.9225 (ptpp) REVERT: A 214 MET cc_start: 0.9017 (mtt) cc_final: 0.8717 (mpp) REVERT: C 70 ARG cc_start: 0.8886 (ttm-80) cc_final: 0.8404 (mtp85) REVERT: C 76 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8893 (mp0) REVERT: C 159 GLU cc_start: 0.7921 (tt0) cc_final: 0.7694 (tm-30) REVERT: C 175 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7614 (mp0) REVERT: C 182 LYS cc_start: 0.9369 (ptpp) cc_final: 0.9082 (pttm) REVERT: C 199 LYS cc_start: 0.9559 (tttt) cc_final: 0.9341 (mtmm) REVERT: C 214 MET cc_start: 0.9092 (mtp) cc_final: 0.8651 (mpp) REVERT: E 76 GLU cc_start: 0.9206 (mp0) cc_final: 0.8996 (mp0) REVERT: E 112 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8408 (pt0) REVERT: E 175 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7904 (mp0) REVERT: E 182 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9251 (ptpp) REVERT: E 214 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8892 (mpt) REVERT: G 18 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7902 (ptm160) REVERT: G 70 ARG cc_start: 0.8966 (mtp85) cc_final: 0.8659 (mmm160) REVERT: G 76 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9108 (mp0) REVERT: G 175 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8356 (mt-10) REVERT: G 182 LYS cc_start: 0.9490 (ptmt) cc_final: 0.9229 (ptpp) REVERT: G 214 MET cc_start: 0.9021 (mtt) cc_final: 0.8722 (mpp) REVERT: I 70 ARG cc_start: 0.8895 (ttm-80) cc_final: 0.8546 (mtp85) REVERT: I 76 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8645 (mp0) REVERT: I 118 TYR cc_start: 0.8881 (m-80) cc_final: 0.8448 (m-80) REVERT: I 159 GLU cc_start: 0.7928 (tt0) cc_final: 0.7696 (tm-30) REVERT: I 175 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7628 (mp0) REVERT: I 199 LYS cc_start: 0.9475 (tttt) cc_final: 0.9238 (mtmm) REVERT: I 214 MET cc_start: 0.9260 (mtp) cc_final: 0.8649 (mpp) REVERT: K 76 GLU cc_start: 0.9209 (mp0) cc_final: 0.9000 (mp0) REVERT: K 112 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8409 (pt0) REVERT: K 175 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7917 (mp0) REVERT: K 182 LYS cc_start: 0.9488 (OUTLIER) cc_final: 0.9253 (ptpp) REVERT: K 214 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8894 (mpt) outliers start: 25 outliers final: 9 residues processed: 284 average time/residue: 0.8546 time to fit residues: 255.3641 Evaluate side-chains 261 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 245 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 76 GLU Chi-restraints excluded: chain I residue 141 CYS Chi-restraints excluded: chain K residue 182 LYS Chi-restraints excluded: chain K residue 214 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 52 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 12 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.082887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.061696 restraints weight = 32422.513| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 4.34 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 1.057 11460 Z= 2.580 Angle : 4.460 98.222 15702 Z= 1.518 Chirality : 0.324 4.028 1698 Planarity : 0.007 0.142 1986 Dihedral : 26.793 174.316 1970 Min Nonbonded Distance : 1.431 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.88 % Allowed : 21.54 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.23), residues: 1350 helix: 1.14 (0.17), residues: 906 sheet: -2.10 (0.52), residues: 54 loop : -0.28 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG E 18 TYR 0.021 0.002 TYR C 10 PHE 0.008 0.001 PHE I 161 TRP 0.007 0.001 TRP I 23 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.05054 (11430) covalent geometry : angle 4.46069 (15690) SS BOND : bond 0.00264 ( 6) SS BOND : angle 2.67080 ( 12) hydrogen bonds : bond 0.04485 ( 642) hydrogen bonds : angle 4.80282 ( 1890) Misc. bond : bond 0.11985 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 282 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.8969 (mtp85) cc_final: 0.8549 (mmm160) REVERT: A 76 GLU cc_start: 0.9445 (mm-30) cc_final: 0.9142 (mp0) REVERT: A 97 ASP cc_start: 0.9336 (t0) cc_final: 0.8300 (p0) REVERT: A 118 TYR cc_start: 0.8812 (m-80) cc_final: 0.8579 (m-80) REVERT: A 175 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8099 (mp0) REVERT: A 182 LYS cc_start: 0.9485 (ptmt) cc_final: 0.9207 (ptpt) REVERT: A 214 MET cc_start: 0.9018 (mtt) cc_final: 0.8697 (mpp) REVERT: C 45 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8575 (mm-30) REVERT: C 70 ARG cc_start: 0.8926 (ttm-80) cc_final: 0.8463 (mtp85) REVERT: C 76 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8871 (mp0) REVERT: C 118 TYR cc_start: 0.8887 (m-80) cc_final: 0.8404 (m-80) REVERT: C 144 MET cc_start: 0.8800 (mmm) cc_final: 0.8170 (mpt) REVERT: C 175 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7468 (mp0) REVERT: E 75 ASP cc_start: 0.9442 (m-30) cc_final: 0.9169 (m-30) REVERT: E 112 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8374 (pt0) REVERT: E 152 ASP cc_start: 0.9168 (m-30) cc_final: 0.8815 (p0) REVERT: E 163 SER cc_start: 0.8879 (m) cc_final: 0.8551 (p) REVERT: E 175 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7917 (mp0) REVERT: E 182 LYS cc_start: 0.9533 (ptmt) cc_final: 0.9103 (ptpp) REVERT: E 214 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8833 (mpt) REVERT: G 70 ARG cc_start: 0.8971 (mtp85) cc_final: 0.8553 (mmm160) REVERT: G 76 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9131 (mp0) REVERT: G 97 ASP cc_start: 0.9340 (t0) cc_final: 0.8310 (p0) REVERT: G 118 TYR cc_start: 0.8806 (m-80) cc_final: 0.8575 (m-80) REVERT: G 175 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8108 (mp0) REVERT: G 182 LYS cc_start: 0.9489 (ptmt) cc_final: 0.9205 (ptpt) REVERT: G 214 MET cc_start: 0.9023 (mtt) cc_final: 0.8707 (mpp) REVERT: I 45 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8567 (mm-30) REVERT: I 70 ARG cc_start: 0.8916 (ttm-80) cc_final: 0.8489 (mtp85) REVERT: I 76 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8902 (mp0) REVERT: I 97 ASP cc_start: 0.9189 (t0) cc_final: 0.8849 (t0) REVERT: I 118 TYR cc_start: 0.8870 (m-80) cc_final: 0.8557 (m-80) REVERT: I 144 MET cc_start: 0.8805 (mmm) cc_final: 0.8170 (mpt) REVERT: I 175 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7481 (mp0) REVERT: I 182 LYS cc_start: 0.9222 (ptpp) cc_final: 0.9011 (pttm) REVERT: I 214 MET cc_start: 0.9177 (mtp) cc_final: 0.8879 (mpp) REVERT: K 70 ARG cc_start: 0.8923 (tpt170) cc_final: 0.8712 (mmm160) REVERT: K 76 GLU cc_start: 0.9258 (mp0) cc_final: 0.8723 (mp0) REVERT: K 112 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8380 (pt0) REVERT: K 152 ASP cc_start: 0.9165 (m-30) cc_final: 0.8807 (p0) REVERT: K 163 SER cc_start: 0.8866 (m) cc_final: 0.8551 (p) REVERT: K 175 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7934 (mp0) REVERT: K 182 LYS cc_start: 0.9530 (ptmt) cc_final: 0.9103 (ptpp) REVERT: K 214 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8889 (mpt) outliers start: 22 outliers final: 6 residues processed: 289 average time/residue: 0.8770 time to fit residues: 267.1111 Evaluate side-chains 256 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 246 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 76 GLU Chi-restraints excluded: chain K residue 214 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 6.9990 chunk 97 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.079500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.058384 restraints weight = 32555.493| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 4.33 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.6719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 1.043 11460 Z= 2.548 Angle : 4.367 99.439 15702 Z= 1.487 Chirality : 0.322 3.956 1698 Planarity : 0.006 0.092 1986 Dihedral : 27.144 179.768 1970 Min Nonbonded Distance : 1.425 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.31 % Allowed : 23.25 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.23), residues: 1350 helix: 1.11 (0.17), residues: 912 sheet: -1.92 (0.48), residues: 54 loop : -0.01 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 18 TYR 0.019 0.002 TYR E 118 PHE 0.006 0.001 PHE A 32 TRP 0.008 0.001 TRP C 23 HIS 0.003 0.001 HIS E 84 Details of bonding type rmsd covalent geometry : bond 0.04990 (11430) covalent geometry : angle 4.36825 (15690) SS BOND : bond 0.00128 ( 6) SS BOND : angle 2.49845 ( 12) hydrogen bonds : bond 0.04358 ( 642) hydrogen bonds : angle 4.63236 ( 1890) Misc. bond : bond 0.11883 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 281 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.8961 (t80) cc_final: 0.8573 (t80) REVERT: A 70 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8694 (mmm160) REVERT: A 76 GLU cc_start: 0.9446 (mm-30) cc_final: 0.9132 (mp0) REVERT: A 175 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8191 (mp0) REVERT: A 213 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8592 (pm20) REVERT: A 214 MET cc_start: 0.9044 (mtt) cc_final: 0.8722 (mpp) REVERT: C 45 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8862 (mm-30) REVERT: C 50 TYR cc_start: 0.8985 (t80) cc_final: 0.8626 (t80) REVERT: C 70 ARG cc_start: 0.8940 (ttm-80) cc_final: 0.8648 (mtp85) REVERT: C 76 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8891 (mp0) REVERT: C 118 TYR cc_start: 0.8768 (m-80) cc_final: 0.8558 (m-80) REVERT: C 144 MET cc_start: 0.8782 (mmm) cc_final: 0.8186 (mpt) REVERT: C 175 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7726 (mp0) REVERT: C 182 LYS cc_start: 0.9419 (ptpp) cc_final: 0.8912 (pttt) REVERT: C 185 MET cc_start: 0.9553 (mtp) cc_final: 0.9156 (mtm) REVERT: E 45 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8755 (mm-30) REVERT: E 70 ARG cc_start: 0.9069 (mtp85) cc_final: 0.8657 (mmm160) REVERT: E 163 SER cc_start: 0.8950 (m) cc_final: 0.8654 (p) REVERT: E 175 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7937 (mp0) REVERT: E 182 LYS cc_start: 0.9462 (ptmt) cc_final: 0.9166 (ptpp) REVERT: E 203 LYS cc_start: 0.9551 (mppt) cc_final: 0.9304 (ptpt) REVERT: E 214 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8860 (mpt) REVERT: G 50 TYR cc_start: 0.8935 (t80) cc_final: 0.8542 (t80) REVERT: G 70 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8691 (mmm160) REVERT: G 76 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9136 (mp0) REVERT: G 175 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8193 (mp0) REVERT: G 213 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8588 (pm20) REVERT: G 214 MET cc_start: 0.9060 (mtt) cc_final: 0.8733 (mpp) REVERT: I 45 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8874 (mm-30) REVERT: I 50 TYR cc_start: 0.8984 (t80) cc_final: 0.8623 (t80) REVERT: I 70 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8602 (mtp85) REVERT: I 76 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.8878 (mp0) REVERT: I 144 MET cc_start: 0.8778 (mmm) cc_final: 0.8172 (mpt) REVERT: I 175 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7745 (mp0) REVERT: I 182 LYS cc_start: 0.9324 (ptpp) cc_final: 0.8826 (pttm) REVERT: I 185 MET cc_start: 0.9545 (mtp) cc_final: 0.9150 (mtm) REVERT: I 212 GLU cc_start: 0.9326 (pm20) cc_final: 0.8906 (pm20) REVERT: I 213 GLU cc_start: 0.9069 (pt0) cc_final: 0.8783 (pm20) REVERT: I 214 MET cc_start: 0.9100 (mtp) cc_final: 0.8825 (mtt) REVERT: K 45 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8700 (mm-30) REVERT: K 70 ARG cc_start: 0.8965 (tpt170) cc_final: 0.8742 (mmm160) REVERT: K 163 SER cc_start: 0.8942 (m) cc_final: 0.8651 (p) REVERT: K 175 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7931 (mp0) REVERT: K 182 LYS cc_start: 0.9470 (ptmt) cc_final: 0.9167 (ptpp) REVERT: K 203 LYS cc_start: 0.9548 (mppt) cc_final: 0.9304 (ptpt) REVERT: K 214 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8879 (mpt) outliers start: 27 outliers final: 6 residues processed: 289 average time/residue: 0.8240 time to fit residues: 251.5351 Evaluate side-chains 250 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 237 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain G residue 70 ARG Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 76 GLU Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 185 MET Chi-restraints excluded: chain K residue 214 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 131 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 123 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN G 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.080210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.058679 restraints weight = 32898.750| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 4.28 r_work: 0.2836 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.7070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 1.031 11460 Z= 2.539 Angle : 4.351 99.187 15702 Z= 1.488 Chirality : 0.328 4.077 1698 Planarity : 0.005 0.062 1986 Dihedral : 27.441 179.852 1968 Min Nonbonded Distance : 1.409 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.05 % Allowed : 24.36 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.23), residues: 1350 helix: 1.10 (0.17), residues: 906 sheet: -1.61 (0.45), residues: 54 loop : 0.45 (0.37), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 18 TYR 0.023 0.003 TYR I 118 PHE 0.006 0.001 PHE A 161 TRP 0.008 0.001 TRP C 23 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.04973 (11430) covalent geometry : angle 4.35209 (15690) SS BOND : bond 0.00140 ( 6) SS BOND : angle 2.41477 ( 12) hydrogen bonds : bond 0.04406 ( 642) hydrogen bonds : angle 4.78925 ( 1890) Misc. bond : bond 0.11832 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 276 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9565 (tt) cc_final: 0.9287 (pp) REVERT: A 70 ARG cc_start: 0.9197 (mtp85) cc_final: 0.8820 (mmm160) REVERT: A 76 GLU cc_start: 0.9503 (mm-30) cc_final: 0.9102 (mp0) REVERT: A 97 ASP cc_start: 0.9272 (t0) cc_final: 0.8917 (t0) REVERT: A 163 SER cc_start: 0.8924 (m) cc_final: 0.8662 (p) REVERT: A 175 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8491 (mp0) REVERT: A 182 LYS cc_start: 0.9478 (ptmt) cc_final: 0.9252 (ptpt) REVERT: A 214 MET cc_start: 0.9219 (mtt) cc_final: 0.8815 (mpp) REVERT: C 76 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8986 (mp0) REVERT: C 144 MET cc_start: 0.9137 (mmm) cc_final: 0.8660 (mpt) REVERT: C 163 SER cc_start: 0.9003 (m) cc_final: 0.8744 (p) REVERT: C 175 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8230 (mm-30) REVERT: C 182 LYS cc_start: 0.9443 (ptpp) cc_final: 0.9071 (pttt) REVERT: C 212 GLU cc_start: 0.9280 (pm20) cc_final: 0.8831 (pm20) REVERT: C 213 GLU cc_start: 0.9113 (pt0) cc_final: 0.8823 (pm20) REVERT: C 214 MET cc_start: 0.9283 (mpp) cc_final: 0.9076 (mpt) REVERT: E 11 ILE cc_start: 0.9541 (tt) cc_final: 0.9246 (pp) REVERT: E 70 ARG cc_start: 0.9283 (mtp85) cc_final: 0.8788 (mmm160) REVERT: E 76 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8808 (mp0) REVERT: E 163 SER cc_start: 0.9083 (m) cc_final: 0.8817 (p) REVERT: E 175 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8321 (mp0) REVERT: E 182 LYS cc_start: 0.9519 (ptmt) cc_final: 0.9138 (ptpp) REVERT: E 214 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8780 (mpp) REVERT: G 11 ILE cc_start: 0.9561 (tt) cc_final: 0.9282 (pp) REVERT: G 18 ARG cc_start: 0.8900 (ptm160) cc_final: 0.8333 (ptm160) REVERT: G 70 ARG cc_start: 0.9194 (mtp85) cc_final: 0.8814 (mmm160) REVERT: G 76 GLU cc_start: 0.9492 (mm-30) cc_final: 0.9099 (mp0) REVERT: G 97 ASP cc_start: 0.9273 (t0) cc_final: 0.8920 (t0) REVERT: G 163 SER cc_start: 0.8936 (m) cc_final: 0.8673 (p) REVERT: G 175 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8473 (mp0) REVERT: G 182 LYS cc_start: 0.9483 (ptmt) cc_final: 0.9260 (ptpt) REVERT: G 214 MET cc_start: 0.9265 (mtt) cc_final: 0.8849 (mpp) REVERT: I 18 ARG cc_start: 0.8385 (ptm-80) cc_final: 0.7884 (ptm-80) REVERT: I 70 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8871 (mmp-170) REVERT: I 76 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.8921 (mp0) REVERT: I 144 MET cc_start: 0.9102 (mmm) cc_final: 0.8672 (mpt) REVERT: I 163 SER cc_start: 0.9004 (m) cc_final: 0.8747 (p) REVERT: I 175 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8294 (mm-30) REVERT: I 182 LYS cc_start: 0.9349 (ptpp) cc_final: 0.9097 (ptpp) REVERT: I 185 MET cc_start: 0.9507 (mtp) cc_final: 0.9205 (mtm) REVERT: K 11 ILE cc_start: 0.9528 (tt) cc_final: 0.9221 (pp) REVERT: K 70 ARG cc_start: 0.9188 (tpt170) cc_final: 0.8936 (mmm160) REVERT: K 163 SER cc_start: 0.9075 (m) cc_final: 0.8840 (p) REVERT: K 175 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8350 (mp0) REVERT: K 182 LYS cc_start: 0.9523 (ptmt) cc_final: 0.9134 (ptpp) REVERT: K 214 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.8929 (mpt) outliers start: 24 outliers final: 10 residues processed: 288 average time/residue: 0.8361 time to fit residues: 254.1596 Evaluate side-chains 266 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 250 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 76 GLU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 214 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 34 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.079623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.058068 restraints weight = 32060.059| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.36 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.7252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.999 11460 Z= 2.528 Angle : 4.306 99.182 15702 Z= 1.474 Chirality : 0.334 4.125 1698 Planarity : 0.005 0.045 1986 Dihedral : 28.037 173.593 1968 Min Nonbonded Distance : 1.423 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.39 % Allowed : 25.73 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.24), residues: 1350 helix: 1.05 (0.17), residues: 906 sheet: -1.38 (0.44), residues: 54 loop : 0.58 (0.37), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 96 TYR 0.027 0.003 TYR A 50 PHE 0.008 0.001 PHE E 32 TRP 0.008 0.001 TRP K 23 HIS 0.002 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.04950 (11430) covalent geometry : angle 4.30761 (15690) SS BOND : bond 0.00206 ( 6) SS BOND : angle 2.18359 ( 12) hydrogen bonds : bond 0.04367 ( 642) hydrogen bonds : angle 4.69065 ( 1890) Misc. bond : bond 0.11789 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 273 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9503 (tt) cc_final: 0.9226 (pp) REVERT: A 50 TYR cc_start: 0.8855 (t80) cc_final: 0.8559 (t80) REVERT: A 70 ARG cc_start: 0.9013 (mtp85) cc_final: 0.8634 (mmm160) REVERT: A 76 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9246 (mp0) REVERT: A 163 SER cc_start: 0.8816 (m) cc_final: 0.8556 (p) REVERT: A 175 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8163 (mp0) REVERT: A 182 LYS cc_start: 0.9506 (ptmt) cc_final: 0.9229 (ptpt) REVERT: C 45 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8732 (mm-30) REVERT: C 50 TYR cc_start: 0.8872 (t80) cc_final: 0.8555 (OUTLIER) REVERT: C 75 ASP cc_start: 0.9592 (m-30) cc_final: 0.9123 (p0) REVERT: C 97 ASP cc_start: 0.9342 (t0) cc_final: 0.9012 (t0) REVERT: C 144 MET cc_start: 0.8673 (mmm) cc_final: 0.8240 (mpt) REVERT: C 163 SER cc_start: 0.8906 (m) cc_final: 0.8677 (p) REVERT: C 175 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7918 (mm-30) REVERT: C 182 LYS cc_start: 0.9426 (ptpp) cc_final: 0.8938 (pttm) REVERT: C 185 MET cc_start: 0.9488 (mtm) cc_final: 0.9287 (mtm) REVERT: C 212 GLU cc_start: 0.9277 (pm20) cc_final: 0.8710 (pm20) REVERT: C 213 GLU cc_start: 0.8969 (pt0) cc_final: 0.8654 (pm20) REVERT: C 214 MET cc_start: 0.9215 (mpp) cc_final: 0.8946 (mpt) REVERT: D 4 VAL cc_start: 0.8947 (m) cc_final: 0.8720 (t) REVERT: E 11 ILE cc_start: 0.9511 (tt) cc_final: 0.9213 (pp) REVERT: E 70 ARG cc_start: 0.9067 (mtp85) cc_final: 0.8531 (mmm160) REVERT: E 76 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8792 (mp0) REVERT: E 154 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8772 (mmmt) REVERT: E 163 SER cc_start: 0.8963 (m) cc_final: 0.8721 (p) REVERT: E 175 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7969 (mp0) REVERT: E 177 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8214 (m) REVERT: E 182 LYS cc_start: 0.9508 (ptmt) cc_final: 0.9126 (ptpt) REVERT: E 212 GLU cc_start: 0.9296 (pm20) cc_final: 0.9037 (pm20) REVERT: E 213 GLU cc_start: 0.9036 (pt0) cc_final: 0.8630 (pm20) REVERT: E 214 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8717 (mpp) REVERT: G 11 ILE cc_start: 0.9505 (tt) cc_final: 0.9230 (pp) REVERT: G 18 ARG cc_start: 0.8655 (ptm160) cc_final: 0.8360 (ptm160) REVERT: G 50 TYR cc_start: 0.8845 (t80) cc_final: 0.8545 (t80) REVERT: G 70 ARG cc_start: 0.9012 (mtp85) cc_final: 0.8638 (mmm160) REVERT: G 76 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9253 (mp0) REVERT: G 163 SER cc_start: 0.8839 (m) cc_final: 0.8585 (p) REVERT: G 175 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8164 (mp0) REVERT: G 182 LYS cc_start: 0.9505 (ptmt) cc_final: 0.9222 (ptpt) REVERT: I 45 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8749 (mm-30) REVERT: I 144 MET cc_start: 0.8637 (mmm) cc_final: 0.8210 (mpt) REVERT: I 163 SER cc_start: 0.8893 (m) cc_final: 0.8657 (p) REVERT: I 175 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7920 (mm-30) REVERT: I 182 LYS cc_start: 0.9305 (ptpp) cc_final: 0.9048 (ptpp) REVERT: I 185 MET cc_start: 0.9477 (mtp) cc_final: 0.9182 (mtm) REVERT: I 212 GLU cc_start: 0.9301 (pm20) cc_final: 0.8954 (pm20) REVERT: J 4 VAL cc_start: 0.8963 (m) cc_final: 0.8739 (t) REVERT: K 11 ILE cc_start: 0.9507 (tt) cc_final: 0.9201 (pp) REVERT: K 154 LYS cc_start: 0.9007 (mmmt) cc_final: 0.8805 (mmmt) REVERT: K 163 SER cc_start: 0.8969 (m) cc_final: 0.8732 (p) REVERT: K 175 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7966 (mp0) REVERT: K 177 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8213 (m) REVERT: K 182 LYS cc_start: 0.9509 (ptmt) cc_final: 0.9128 (ptpt) REVERT: K 214 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.8884 (mpt) outliers start: 28 outliers final: 11 residues processed: 287 average time/residue: 0.7868 time to fit residues: 238.9782 Evaluate side-chains 269 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 202 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 214 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 0.0770 chunk 81 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.080815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.059285 restraints weight = 32943.899| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 4.33 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.7505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.963 11460 Z= 2.519 Angle : 4.329 100.068 15702 Z= 1.485 Chirality : 0.339 4.253 1698 Planarity : 0.005 0.039 1986 Dihedral : 28.665 177.543 1968 Min Nonbonded Distance : 1.427 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.39 % Allowed : 25.64 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.24), residues: 1350 helix: 1.04 (0.17), residues: 894 sheet: -1.46 (0.42), residues: 54 loop : 0.61 (0.36), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 96 TYR 0.026 0.003 TYR C 50 PHE 0.010 0.001 PHE L 7 TRP 0.015 0.001 TRP E 23 HIS 0.003 0.001 HIS G 84 Details of bonding type rmsd covalent geometry : bond 0.04938 (11430) covalent geometry : angle 4.33006 (15690) SS BOND : bond 0.00170 ( 6) SS BOND : angle 2.32953 ( 12) hydrogen bonds : bond 0.04346 ( 642) hydrogen bonds : angle 4.67510 ( 1890) Misc. bond : bond 0.11566 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 257 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9543 (tt) cc_final: 0.9271 (pp) REVERT: A 50 TYR cc_start: 0.8905 (t80) cc_final: 0.8594 (t80) REVERT: A 70 ARG cc_start: 0.8977 (mtp85) cc_final: 0.8594 (mmm160) REVERT: A 76 GLU cc_start: 0.9483 (mm-30) cc_final: 0.9234 (mp0) REVERT: A 163 SER cc_start: 0.8880 (m) cc_final: 0.8641 (p) REVERT: A 175 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8213 (mp0) REVERT: A 203 LYS cc_start: 0.9493 (mppt) cc_final: 0.9220 (pmmt) REVERT: C 45 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8748 (mm-30) REVERT: C 76 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8913 (mp0) REVERT: C 144 MET cc_start: 0.8651 (mmm) cc_final: 0.8249 (mpt) REVERT: C 163 SER cc_start: 0.9007 (m) cc_final: 0.8776 (p) REVERT: C 175 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7944 (mm-30) REVERT: C 182 LYS cc_start: 0.9463 (ptpp) cc_final: 0.9204 (ptpp) REVERT: C 185 MET cc_start: 0.9479 (mtm) cc_final: 0.9237 (mtm) REVERT: C 212 GLU cc_start: 0.9294 (pm20) cc_final: 0.8705 (pm20) REVERT: C 213 GLU cc_start: 0.8964 (pt0) cc_final: 0.8633 (pm20) REVERT: C 214 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8886 (mpt) REVERT: E 11 ILE cc_start: 0.9539 (tt) cc_final: 0.9261 (pp) REVERT: E 45 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8887 (mm-30) REVERT: E 70 ARG cc_start: 0.9054 (mtp85) cc_final: 0.8593 (mmm160) REVERT: E 76 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8740 (mp0) REVERT: E 163 SER cc_start: 0.9036 (m) cc_final: 0.8789 (p) REVERT: E 175 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8018 (mp0) REVERT: E 177 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8537 (m) REVERT: E 182 LYS cc_start: 0.9546 (ptmt) cc_final: 0.9215 (ptpp) REVERT: E 214 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8711 (mpp) REVERT: G 11 ILE cc_start: 0.9546 (tt) cc_final: 0.9272 (pp) REVERT: G 18 ARG cc_start: 0.8747 (ptm160) cc_final: 0.8341 (ptm160) REVERT: G 50 TYR cc_start: 0.8890 (t80) cc_final: 0.8575 (t80) REVERT: G 70 ARG cc_start: 0.8989 (mtp85) cc_final: 0.8615 (mmm160) REVERT: G 76 GLU cc_start: 0.9482 (mm-30) cc_final: 0.9235 (mp0) REVERT: G 163 SER cc_start: 0.8895 (m) cc_final: 0.8657 (p) REVERT: G 175 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8207 (mp0) REVERT: G 203 LYS cc_start: 0.9488 (mppt) cc_final: 0.9212 (pmmt) REVERT: I 18 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.8104 (mtm-85) REVERT: I 45 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8744 (mm-30) REVERT: I 144 MET cc_start: 0.8618 (mmm) cc_final: 0.8208 (mpt) REVERT: I 163 SER cc_start: 0.8989 (m) cc_final: 0.8751 (p) REVERT: I 175 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7945 (mm-30) REVERT: I 214 MET cc_start: 0.9065 (mtp) cc_final: 0.8714 (mtt) REVERT: K 11 ILE cc_start: 0.9540 (tt) cc_final: 0.9251 (pp) REVERT: K 45 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8913 (mm-30) REVERT: K 163 SER cc_start: 0.9045 (m) cc_final: 0.8801 (p) REVERT: K 175 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8058 (mp0) REVERT: K 177 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8540 (m) REVERT: K 182 LYS cc_start: 0.9542 (ptmt) cc_final: 0.9210 (ptpp) REVERT: K 214 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8815 (mpt) outliers start: 28 outliers final: 12 residues processed: 271 average time/residue: 0.8253 time to fit residues: 236.6724 Evaluate side-chains 272 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 253 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 214 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 107 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 12 HIS E 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.078974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.057765 restraints weight = 33692.977| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.29 r_work: 0.2816 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.7593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.957 11460 Z= 2.510 Angle : 4.308 98.672 15702 Z= 1.476 Chirality : 0.343 4.306 1698 Planarity : 0.005 0.038 1986 Dihedral : 29.005 178.686 1968 Min Nonbonded Distance : 1.425 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.97 % Allowed : 25.90 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.24), residues: 1350 helix: 1.26 (0.18), residues: 870 sheet: -1.64 (0.41), residues: 54 loop : 0.63 (0.35), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 96 TYR 0.026 0.003 TYR C 118 PHE 0.011 0.001 PHE I 32 TRP 0.012 0.001 TRP E 23 HIS 0.003 0.001 HIS G 62 Details of bonding type rmsd covalent geometry : bond 0.04924 (11430) covalent geometry : angle 4.30879 (15690) SS BOND : bond 0.00154 ( 6) SS BOND : angle 2.41816 ( 12) hydrogen bonds : bond 0.04393 ( 642) hydrogen bonds : angle 4.68372 ( 1890) Misc. bond : bond 0.11436 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9534 (tt) cc_final: 0.9249 (pp) REVERT: A 70 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8777 (mmm160) REVERT: A 76 GLU cc_start: 0.9511 (mm-30) cc_final: 0.9292 (mp0) REVERT: A 163 SER cc_start: 0.9015 (m) cc_final: 0.8788 (p) REVERT: A 175 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8515 (mp0) REVERT: A 182 LYS cc_start: 0.9560 (ptmt) cc_final: 0.9216 (ptpt) REVERT: A 203 LYS cc_start: 0.9524 (mppt) cc_final: 0.9236 (pmmt) REVERT: C 50 TYR cc_start: 0.8991 (t80) cc_final: 0.8661 (t80) REVERT: C 144 MET cc_start: 0.9117 (mmm) cc_final: 0.8751 (mpt) REVERT: C 163 SER cc_start: 0.9094 (m) cc_final: 0.8880 (p) REVERT: C 175 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8345 (mm-30) REVERT: C 182 LYS cc_start: 0.9496 (ptpp) cc_final: 0.9262 (ptpp) REVERT: C 212 GLU cc_start: 0.9330 (pm20) cc_final: 0.8801 (pm20) REVERT: C 213 GLU cc_start: 0.9102 (pt0) cc_final: 0.8773 (pm20) REVERT: C 214 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.9005 (mpt) REVERT: E 11 ILE cc_start: 0.9539 (tt) cc_final: 0.9234 (pp) REVERT: E 70 ARG cc_start: 0.9261 (mtp85) cc_final: 0.8784 (mmm160) REVERT: E 76 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8866 (mp0) REVERT: E 163 SER cc_start: 0.9176 (m) cc_final: 0.8940 (p) REVERT: E 175 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8583 (mm-30) REVERT: E 177 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8203 (m) REVERT: E 182 LYS cc_start: 0.9531 (ptmt) cc_final: 0.9073 (ptpp) REVERT: E 212 GLU cc_start: 0.9282 (pm20) cc_final: 0.9046 (pm20) REVERT: E 213 GLU cc_start: 0.9207 (pt0) cc_final: 0.8870 (pm20) REVERT: E 214 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.8815 (mpp) REVERT: G 11 ILE cc_start: 0.9550 (tt) cc_final: 0.9273 (pp) REVERT: G 70 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8766 (mmm160) REVERT: G 76 GLU cc_start: 0.9505 (mm-30) cc_final: 0.9285 (mp0) REVERT: G 163 SER cc_start: 0.9015 (m) cc_final: 0.8794 (p) REVERT: G 175 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8521 (mp0) REVERT: G 182 LYS cc_start: 0.9562 (ptmt) cc_final: 0.9224 (ptpt) REVERT: G 203 LYS cc_start: 0.9528 (mppt) cc_final: 0.9242 (pmmt) REVERT: I 144 MET cc_start: 0.9083 (mmm) cc_final: 0.8710 (mpt) REVERT: I 163 SER cc_start: 0.9095 (m) cc_final: 0.8863 (p) REVERT: I 175 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8332 (mm-30) REVERT: I 182 LYS cc_start: 0.9300 (ptpp) cc_final: 0.8896 (pttt) REVERT: I 214 MET cc_start: 0.9291 (mtp) cc_final: 0.8810 (mpp) REVERT: K 11 ILE cc_start: 0.9535 (tt) cc_final: 0.9221 (pp) REVERT: K 70 ARG cc_start: 0.9223 (mmm160) cc_final: 0.8576 (mmm160) REVERT: K 163 SER cc_start: 0.9193 (m) cc_final: 0.8949 (p) REVERT: K 175 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8568 (mm-30) REVERT: K 177 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8178 (m) REVERT: K 182 LYS cc_start: 0.9528 (ptmt) cc_final: 0.9068 (ptpp) REVERT: K 214 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.8926 (mpt) outliers start: 23 outliers final: 11 residues processed: 262 average time/residue: 0.8362 time to fit residues: 230.9904 Evaluate side-chains 267 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 248 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 70 ARG Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 214 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 116 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 12 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.079840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.057977 restraints weight = 32326.408| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.29 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.7720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.958 11460 Z= 2.505 Angle : 4.312 98.032 15702 Z= 1.480 Chirality : 0.353 4.364 1698 Planarity : 0.005 0.103 1986 Dihedral : 29.294 179.313 1968 Min Nonbonded Distance : 1.416 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.97 % Allowed : 25.30 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.24), residues: 1350 helix: 1.31 (0.18), residues: 870 sheet: -1.68 (0.41), residues: 54 loop : 0.56 (0.35), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 18 TYR 0.026 0.003 TYR C 118 PHE 0.007 0.001 PHE L 7 TRP 0.011 0.001 TRP E 23 HIS 0.014 0.002 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.04913 (11430) covalent geometry : angle 4.31365 (15690) SS BOND : bond 0.00132 ( 6) SS BOND : angle 2.24180 ( 12) hydrogen bonds : bond 0.04318 ( 642) hydrogen bonds : angle 4.65620 ( 1890) Misc. bond : bond 0.11414 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4531.82 seconds wall clock time: 77 minutes 53.11 seconds (4673.11 seconds total)