Starting phenix.real_space_refine on Mon Jun 9 20:11:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cnu_45760/06_2025/9cnu_45760.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cnu_45760/06_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_45760/06_2025/9cnu_45760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cnu_45760/06_2025/9cnu_45760.map" model { file = "/net/cci-nas-00/data/ceres_data/9cnu_45760/06_2025/9cnu_45760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cnu_45760/06_2025/9cnu_45760.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: D, F, H, J, L, C, E, G, I, K 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: 4.16, per 1000 atoms: 0.37 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: 5.47 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.00 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: 2.95 Time building geometry restraints manager: 5.97 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: 0.09 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.120 Process input model: 27.130 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.490 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (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 TRP 0.041 0.005 TRP I 116 HIS 0.013 0.006 HIS E 62 PHE 0.012 0.003 PHE K 40 TYR 0.035 0.006 TYR I 118 ARG 0.011 0.003 ARG I 131 Details of bonding type rmsd hydrogen bonds : bond 0.22435 ( 642) hydrogen bonds : angle 8.03701 ( 1890) SS BOND : bond 0.00149 ( 6) SS BOND : angle 0.23574 ( 12) covalent geometry : bond 0.01416 (11430) covalent geometry : angle 1.98852 (15690) 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 : 1.173 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 outliers start: 0 outliers final: 4 residues processed: 326 average time/residue: 1.5645 time to fit residues: 540.9150 Evaluate side-chains 244 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 240 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 111 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.087981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.067440 restraints weight = 48037.124| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 5.20 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 1.596 11460 Z= 4.202 Angle : 5.694 91.772 15702 Z= 1.930 Chirality : 0.464 4.677 1698 Planarity : 0.008 0.086 1986 Dihedral : 22.303 138.331 1976 Min Nonbonded Distance : 1.121 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.99 % Allowed : 13.68 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1350 helix: 0.28 (0.16), residues: 888 sheet: -2.83 (0.51), residues: 54 loop : -1.62 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 116 HIS 0.003 0.001 HIS G 84 PHE 0.009 0.002 PHE L 7 TYR 0.014 0.002 TYR K 50 ARG 0.068 0.003 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.06092 ( 642) hydrogen bonds : angle 5.36298 ( 1890) SS BOND : bond 0.00912 ( 6) SS BOND : angle 6.91129 ( 12) covalent geometry : bond 0.08365 (11430) covalent geometry : angle 5.69298 (15690) Misc. bond : bond 0.10530 ( 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 317 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 1.236 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: symmetry clash REVERT: A 175 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8140 (mt-10) REVERT: A 182 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9134 (ptpt) REVERT: A 214 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8719 (mpt) REVERT: C 76 GLU cc_start: 0.9097 (mp0) cc_final: 0.8604 (mp0) REVERT: C 144 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8145 (mpt) REVERT: C 175 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7909 (mt-10) REVERT: C 182 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.9282 (ptpp) REVERT: C 214 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.8840 (mpp) REVERT: E 175 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7816 (mm-30) REVERT: E 214 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8881 (mpt) REVERT: G 175 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8134 (mt-10) REVERT: G 182 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9134 (ptpt) REVERT: G 214 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8712 (mpt) REVERT: I 76 GLU cc_start: 0.9105 (mp0) cc_final: 0.8616 (mp0) REVERT: I 144 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8141 (mpt) REVERT: I 175 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7909 (mt-10) REVERT: I 182 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9286 (ptpp) REVERT: I 214 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8824 (mpp) REVERT: K 175 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7809 (mm-30) REVERT: K 214 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8832 (mpt) outliers start: 35 outliers final: 7 residues processed: 290 average time/residue: 1.6181 time to fit residues: 496.9408 Evaluate side-chains 258 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 239 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 214 MET 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 G residue 214 MET Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 182 LYS Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain K residue 199 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 21 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 5 optimal weight: 0.3980 chunk 108 optimal weight: 0.6980 chunk 55 optimal weight: 0.0370 chunk 27 optimal weight: 0.6980 chunk 131 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.087580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.066950 restraints weight = 34051.912| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 4.54 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 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 = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.061 1.333 11460 Z= 3.089 Angle : 5.134 89.598 15702 Z= 1.740 Chirality : 0.382 4.543 1698 Planarity : 0.006 0.047 1986 Dihedral : 26.186 177.799 1972 Min Nonbonded Distance : 1.230 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.62 % Allowed : 15.81 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.23), residues: 1350 helix: 1.09 (0.17), residues: 888 sheet: -2.75 (0.55), residues: 54 loop : -1.20 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 116 HIS 0.003 0.001 HIS I 84 PHE 0.008 0.002 PHE G 161 TYR 0.020 0.002 TYR A 10 ARG 0.055 0.002 ARG G 18 Details of bonding type rmsd hydrogen bonds : bond 0.05096 ( 642) hydrogen bonds : angle 5.03267 ( 1890) SS BOND : bond 0.00415 ( 6) SS BOND : angle 4.43159 ( 12) covalent geometry : bond 0.06099 (11430) covalent geometry : angle 5.13406 (15690) Misc. bond : bond 0.11342 ( 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 306 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 287 time to evaluate : 1.262 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 75 ASP cc_start: 0.9517 (m-30) cc_final: 0.9292 (m-30) REVERT: A 76 GLU cc_start: 0.9429 (mm-30) cc_final: 0.9050 (mp0) REVERT: A 97 ASP cc_start: 0.9211 (t0) cc_final: 0.8625 (p0) REVERT: A 175 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8168 (mt-10) REVERT: A 182 LYS cc_start: 0.9450 (OUTLIER) cc_final: 0.9189 (ptpt) REVERT: A 214 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8728 (mpt) REVERT: C 76 GLU cc_start: 0.9183 (mp0) cc_final: 0.8586 (mp0) REVERT: C 182 LYS cc_start: 0.9513 (ptmt) cc_final: 0.9256 (ptpp) REVERT: C 214 MET cc_start: 0.9279 (mtp) cc_final: 0.8850 (mpp) REVERT: E 75 ASP cc_start: 0.9513 (m-30) cc_final: 0.9187 (m-30) REVERT: E 76 GLU cc_start: 0.9150 (mp0) cc_final: 0.8872 (mp0) REVERT: E 175 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8063 (mt-10) REVERT: E 182 LYS cc_start: 0.9330 (ptpp) cc_final: 0.8946 (pttm) REVERT: E 212 GLU cc_start: 0.9238 (pm20) cc_final: 0.9035 (pm20) REVERT: E 214 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8901 (mpt) REVERT: G 75 ASP cc_start: 0.9519 (m-30) cc_final: 0.9294 (m-30) REVERT: G 76 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9043 (mp0) REVERT: G 97 ASP cc_start: 0.9212 (t0) cc_final: 0.8628 (p0) REVERT: G 175 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8147 (mt-10) REVERT: G 182 LYS cc_start: 0.9456 (OUTLIER) cc_final: 0.9194 (ptpt) REVERT: G 214 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8728 (mpt) REVERT: I 76 GLU cc_start: 0.9183 (mp0) cc_final: 0.8602 (mp0) REVERT: I 97 ASP cc_start: 0.9130 (t0) cc_final: 0.8423 (p0) REVERT: I 182 LYS cc_start: 0.9519 (ptmt) cc_final: 0.9269 (ptpp) REVERT: I 214 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8850 (mpp) REVERT: K 32 PHE cc_start: 0.8689 (m-80) cc_final: 0.8487 (m-80) REVERT: K 75 ASP cc_start: 0.9513 (m-30) cc_final: 0.9199 (m-30) REVERT: K 76 GLU cc_start: 0.9151 (mp0) cc_final: 0.8871 (mp0) REVERT: K 118 TYR cc_start: 0.8657 (m-80) cc_final: 0.8422 (m-80) REVERT: K 175 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8047 (mt-10) REVERT: K 182 LYS cc_start: 0.9330 (ptpp) cc_final: 0.8946 (pttm) REVERT: K 189 LEU cc_start: 0.9441 (tp) cc_final: 0.9241 (tp) REVERT: K 214 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8847 (mpt) outliers start: 19 outliers final: 6 residues processed: 291 average time/residue: 1.5906 time to fit residues: 490.3181 Evaluate side-chains 241 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 228 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 214 MET 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 G residue 214 MET 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 214 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 27 optimal weight: 0.0370 chunk 110 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 HIS I 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 = 0.3537 r_free = 0.3537 target = 0.080899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.060320 restraints weight = 32090.376| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 4.26 r_work: 0.2855 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.053 1.058 11460 Z= 2.664 Angle : 4.641 95.184 15702 Z= 1.578 Chirality : 0.355 3.809 1698 Planarity : 0.007 0.118 1986 Dihedral : 27.595 176.996 1972 Min Nonbonded Distance : 1.434 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.56 % Allowed : 16.75 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.22), residues: 1350 helix: 1.20 (0.17), residues: 894 sheet: -2.62 (0.53), residues: 54 loop : -0.77 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 116 HIS 0.005 0.002 HIS I 84 PHE 0.011 0.002 PHE G 32 TYR 0.026 0.003 TYR A 10 ARG 0.017 0.001 ARG I 18 Details of bonding type rmsd hydrogen bonds : bond 0.04779 ( 642) hydrogen bonds : angle 5.00275 ( 1890) SS BOND : bond 0.00107 ( 6) SS BOND : angle 3.87406 ( 12) covalent geometry : bond 0.05230 (11430) covalent geometry : angle 4.64167 (15690) Misc. bond : bond 0.11829 ( 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 306 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 1.229 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 76 GLU cc_start: 0.9475 (mm-30) cc_final: 0.9103 (mp0) REVERT: A 175 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8694 (mt-10) REVERT: A 182 LYS cc_start: 0.9475 (ptmt) cc_final: 0.9200 (ptpp) REVERT: A 212 GLU cc_start: 0.9326 (pm20) cc_final: 0.9121 (pm20) REVERT: A 214 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.8947 (mpt) REVERT: C 70 ARG cc_start: 0.9107 (ttm-80) cc_final: 0.8813 (mtp85) REVERT: C 76 GLU cc_start: 0.9298 (OUTLIER) cc_final: 0.8674 (mp0) REVERT: C 175 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8320 (tm-30) REVERT: C 182 LYS cc_start: 0.9557 (ptmt) cc_final: 0.9155 (ptpp) REVERT: C 185 MET cc_start: 0.9641 (mtp) cc_final: 0.9313 (mtm) REVERT: C 214 MET cc_start: 0.9361 (mtp) cc_final: 0.8954 (mpp) REVERT: E 76 GLU cc_start: 0.9334 (mp0) cc_final: 0.9083 (mp0) REVERT: E 112 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8578 (pt0) REVERT: E 163 SER cc_start: 0.8944 (m) cc_final: 0.8654 (p) REVERT: E 175 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8252 (mp0) REVERT: E 182 LYS cc_start: 0.9322 (ptpp) cc_final: 0.8986 (pttm) REVERT: E 199 LYS cc_start: 0.9453 (ttpp) cc_final: 0.9185 (mtmm) REVERT: E 214 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.8776 (mpp) REVERT: G 76 GLU cc_start: 0.9490 (mm-30) cc_final: 0.9124 (mp0) REVERT: G 175 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8700 (mt-10) REVERT: G 182 LYS cc_start: 0.9476 (ptmt) cc_final: 0.9199 (ptpp) REVERT: G 214 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.8951 (mpt) REVERT: I 70 ARG cc_start: 0.9100 (ttm-80) cc_final: 0.8809 (mtp85) REVERT: I 76 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8672 (mp0) REVERT: I 175 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8298 (tm-30) REVERT: I 182 LYS cc_start: 0.9558 (ptmt) cc_final: 0.9170 (ptpp) REVERT: I 185 MET cc_start: 0.9631 (mtp) cc_final: 0.9301 (mtm) REVERT: I 214 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.8798 (mpp) REVERT: K 18 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8177 (ppp80) REVERT: K 76 GLU cc_start: 0.9333 (mp0) cc_final: 0.9083 (mp0) REVERT: K 112 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8553 (pt0) REVERT: K 163 SER cc_start: 0.8949 (m) cc_final: 0.8654 (p) REVERT: K 175 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8262 (mp0) REVERT: K 182 LYS cc_start: 0.9329 (ptpp) cc_final: 0.9000 (pttm) REVERT: K 214 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.8989 (mpt) outliers start: 30 outliers final: 4 residues processed: 285 average time/residue: 1.6752 time to fit residues: 504.1842 Evaluate side-chains 245 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 233 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain C residue 76 GLU 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 214 MET Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 76 GLU Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain K residue 18 ARG 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 37 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.077502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.055818 restraints weight = 31658.304| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 4.25 r_work: 0.2729 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.6513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 1.047 11460 Z= 2.556 Angle : 4.351 98.688 15702 Z= 1.482 Chirality : 0.346 3.931 1698 Planarity : 0.006 0.081 1986 Dihedral : 28.306 176.989 1970 Min Nonbonded Distance : 1.428 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.31 % Allowed : 19.49 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.23), residues: 1350 helix: 1.40 (0.17), residues: 870 sheet: -2.36 (0.49), residues: 54 loop : -0.18 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 116 HIS 0.004 0.001 HIS A 84 PHE 0.008 0.002 PHE K 32 TYR 0.021 0.003 TYR I 10 ARG 0.017 0.001 ARG I 18 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 642) hydrogen bonds : angle 4.98999 ( 1890) SS BOND : bond 0.00273 ( 6) SS BOND : angle 2.84112 ( 12) covalent geometry : bond 0.05008 (11430) covalent geometry : angle 4.35221 (15690) Misc. bond : bond 0.11864 ( 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 308 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 281 time to evaluate : 1.141 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 75 ASP cc_start: 0.9670 (m-30) cc_final: 0.9438 (m-30) REVERT: A 76 GLU cc_start: 0.9489 (mm-30) cc_final: 0.9200 (mp0) REVERT: A 97 ASP cc_start: 0.9321 (t0) cc_final: 0.8396 (p0) REVERT: A 118 TYR cc_start: 0.8868 (m-80) cc_final: 0.8666 (m-80) REVERT: A 175 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8737 (mt-10) REVERT: A 182 LYS cc_start: 0.9522 (ptmt) cc_final: 0.9261 (ptpt) REVERT: A 214 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.8965 (mpt) REVERT: C 45 GLU cc_start: 0.9372 (mm-30) cc_final: 0.9115 (mm-30) REVERT: C 70 ARG cc_start: 0.9128 (ttm-80) cc_final: 0.8751 (mtp85) REVERT: C 76 GLU cc_start: 0.9391 (OUTLIER) cc_final: 0.9007 (mp0) REVERT: C 182 LYS cc_start: 0.9539 (ptmt) cc_final: 0.9321 (ptpp) REVERT: E 32 PHE cc_start: 0.9503 (m-80) cc_final: 0.9299 (m-80) REVERT: E 70 ARG cc_start: 0.9191 (ttm-80) cc_final: 0.8934 (mtp85) REVERT: E 71 GLU cc_start: 0.9037 (mp0) cc_final: 0.8798 (mp0) REVERT: E 97 ASP cc_start: 0.9040 (t0) cc_final: 0.8777 (t0) REVERT: E 112 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8484 (pt0) REVERT: E 163 SER cc_start: 0.9104 (m) cc_final: 0.8830 (p) REVERT: E 175 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8232 (mp0) REVERT: E 182 LYS cc_start: 0.9361 (ptpp) cc_final: 0.8844 (pttm) REVERT: E 214 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.8982 (mpt) REVERT: G 75 ASP cc_start: 0.9670 (m-30) cc_final: 0.9442 (m-30) REVERT: G 76 GLU cc_start: 0.9497 (mm-30) cc_final: 0.9217 (mp0) REVERT: G 97 ASP cc_start: 0.9318 (t0) cc_final: 0.8395 (p0) REVERT: G 118 TYR cc_start: 0.8872 (m-80) cc_final: 0.8666 (m-80) REVERT: G 175 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8744 (mt-10) REVERT: G 182 LYS cc_start: 0.9523 (ptmt) cc_final: 0.9259 (ptpt) REVERT: G 214 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8890 (mpt) REVERT: I 45 GLU cc_start: 0.9380 (mm-30) cc_final: 0.9124 (mm-30) REVERT: I 70 ARG cc_start: 0.9128 (ttm-80) cc_final: 0.8758 (mtp85) REVERT: I 76 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.9133 (mp0) REVERT: I 97 ASP cc_start: 0.9309 (t0) cc_final: 0.8989 (t0) REVERT: I 118 TYR cc_start: 0.8905 (m-80) cc_final: 0.8569 (m-80) REVERT: I 175 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8465 (tm-30) REVERT: I 182 LYS cc_start: 0.9552 (ptmt) cc_final: 0.9322 (ptpp) REVERT: K 112 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8482 (pt0) REVERT: K 163 SER cc_start: 0.9108 (m) cc_final: 0.8826 (p) REVERT: K 175 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8270 (mp0) REVERT: K 182 LYS cc_start: 0.9362 (ptpp) cc_final: 0.8858 (pttm) REVERT: K 214 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.9008 (mpt) outliers start: 27 outliers final: 6 residues processed: 289 average time/residue: 1.7000 time to fit residues: 518.8106 Evaluate side-chains 264 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 252 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 76 GLU Chi-restraints excluded: chain I residue 214 MET 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 41 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 54 optimal weight: 0.2980 chunk 8 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.080099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.058621 restraints weight = 32116.656| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 4.31 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.6942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 1.058 11460 Z= 2.523 Angle : 4.182 99.165 15702 Z= 1.425 Chirality : 0.331 4.015 1698 Planarity : 0.006 0.157 1986 Dihedral : 29.112 177.152 1970 Min Nonbonded Distance : 1.436 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.50 % Allowed : 20.94 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1350 helix: 1.35 (0.17), residues: 870 sheet: -1.96 (0.45), residues: 54 loop : 0.17 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 23 HIS 0.003 0.001 HIS A 84 PHE 0.009 0.001 PHE I 32 TYR 0.023 0.002 TYR K 50 ARG 0.038 0.001 ARG I 18 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 642) hydrogen bonds : angle 4.77642 ( 1890) SS BOND : bond 0.00279 ( 6) SS BOND : angle 2.25035 ( 12) covalent geometry : bond 0.04945 (11430) covalent geometry : angle 4.18318 (15690) Misc. bond : bond 0.11463 ( 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 325 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 284 time to evaluate : 1.165 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 50 TYR cc_start: 0.8993 (t80) cc_final: 0.8764 (t80) REVERT: A 70 ARG cc_start: 0.9057 (mmm160) cc_final: 0.8542 (mmm160) REVERT: A 76 GLU cc_start: 0.9481 (mm-30) cc_final: 0.9141 (mp0) REVERT: A 163 SER cc_start: 0.8959 (m) cc_final: 0.8668 (p) REVERT: A 175 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8275 (mt-10) REVERT: A 182 LYS cc_start: 0.9477 (ptmt) cc_final: 0.9249 (ptpp) REVERT: A 214 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8880 (mpt) REVERT: C 70 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8623 (mtp85) REVERT: C 76 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8832 (mp0) REVERT: C 182 LYS cc_start: 0.9566 (ptmt) cc_final: 0.9362 (ptpp) REVERT: C 214 MET cc_start: 0.9300 (mtp) cc_final: 0.8950 (mpp) REVERT: E 163 SER cc_start: 0.9047 (m) cc_final: 0.8828 (p) REVERT: E 175 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8074 (mp0) REVERT: E 182 LYS cc_start: 0.9338 (ptpp) cc_final: 0.8991 (pttm) REVERT: E 199 LYS cc_start: 0.9333 (ttpp) cc_final: 0.9129 (ptpt) REVERT: E 214 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8834 (mpt) REVERT: G 50 TYR cc_start: 0.8993 (t80) cc_final: 0.8762 (t80) REVERT: G 70 ARG cc_start: 0.9048 (mmm160) cc_final: 0.8529 (mmm160) REVERT: G 76 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9128 (mp0) REVERT: G 163 SER cc_start: 0.8983 (m) cc_final: 0.8697 (p) REVERT: G 175 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8267 (mt-10) REVERT: G 182 LYS cc_start: 0.9469 (ptmt) cc_final: 0.9244 (ptpp) REVERT: G 214 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8866 (mpt) REVERT: I 70 ARG cc_start: 0.8906 (ttm-80) cc_final: 0.8616 (mtp85) REVERT: I 118 TYR cc_start: 0.8885 (m-80) cc_final: 0.8682 (m-80) REVERT: I 182 LYS cc_start: 0.9566 (OUTLIER) cc_final: 0.9339 (ptpp) REVERT: K 70 ARG cc_start: 0.9053 (mmm160) cc_final: 0.8538 (mmm160) REVERT: K 163 SER cc_start: 0.9037 (m) cc_final: 0.8802 (p) REVERT: K 175 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8045 (mp0) REVERT: K 182 LYS cc_start: 0.9336 (ptpp) cc_final: 0.9034 (pttm) REVERT: K 212 GLU cc_start: 0.9210 (pm20) cc_final: 0.8913 (pm20) REVERT: K 214 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8849 (mpt) outliers start: 41 outliers final: 13 residues processed: 306 average time/residue: 1.5831 time to fit residues: 512.9352 Evaluate side-chains 272 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain C residue 13 VAL 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 214 MET Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 154 LYS Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 182 LYS Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 31 LYS 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 7 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.078576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.056870 restraints weight = 32201.112| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 4.34 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.7111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 1.029 11460 Z= 2.509 Angle : 4.160 99.314 15702 Z= 1.423 Chirality : 0.336 4.029 1698 Planarity : 0.007 0.234 1986 Dihedral : 28.996 179.260 1968 Min Nonbonded Distance : 1.429 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.99 % Allowed : 23.33 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.23), residues: 1350 helix: 1.25 (0.17), residues: 870 sheet: -1.60 (0.44), residues: 54 loop : 0.46 (0.34), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 23 HIS 0.003 0.001 HIS E 84 PHE 0.008 0.001 PHE G 32 TYR 0.025 0.003 TYR I 50 ARG 0.011 0.001 ARG I 18 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 642) hydrogen bonds : angle 4.85639 ( 1890) SS BOND : bond 0.00133 ( 6) SS BOND : angle 2.36147 ( 12) covalent geometry : bond 0.04920 (11430) covalent geometry : angle 4.16063 (15690) Misc. bond : bond 0.11312 ( 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 312 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 277 time to evaluate : 1.215 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: A 11 ILE cc_start: 0.9512 (tt) cc_final: 0.9218 (pp) REVERT: A 50 TYR cc_start: 0.9014 (t80) cc_final: 0.8608 (t80) REVERT: A 70 ARG cc_start: 0.9116 (mmm160) cc_final: 0.8637 (mmm160) REVERT: A 76 GLU cc_start: 0.9492 (mm-30) cc_final: 0.9189 (mp0) REVERT: A 97 ASP cc_start: 0.9235 (t0) cc_final: 0.8873 (t0) REVERT: A 158 LYS cc_start: 0.9027 (mmmt) cc_final: 0.8648 (mmmt) REVERT: A 163 SER cc_start: 0.8896 (m) cc_final: 0.8614 (p) REVERT: A 175 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8172 (mt-10) REVERT: A 182 LYS cc_start: 0.9486 (ptmt) cc_final: 0.9198 (ptpt) REVERT: A 214 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8867 (mpt) REVERT: C 45 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8811 (mm-30) REVERT: C 50 TYR cc_start: 0.8895 (t80) cc_final: 0.8524 (t80) REVERT: C 170 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8619 (ttmt) REVERT: C 182 LYS cc_start: 0.9542 (ptmt) cc_final: 0.9272 (ptpp) REVERT: C 185 MET cc_start: 0.9359 (mtp) cc_final: 0.9083 (mtm) REVERT: C 214 MET cc_start: 0.9215 (mtp) cc_final: 0.8885 (mpp) REVERT: E 11 ILE cc_start: 0.9518 (tt) cc_final: 0.9229 (pp) REVERT: E 32 PHE cc_start: 0.9451 (m-80) cc_final: 0.9216 (m-80) REVERT: E 45 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8733 (mm-30) REVERT: E 50 TYR cc_start: 0.8987 (t80) cc_final: 0.8774 (t80) REVERT: E 70 ARG cc_start: 0.9025 (mtp85) cc_final: 0.8532 (mmm160) REVERT: E 163 SER cc_start: 0.9015 (m) cc_final: 0.8782 (p) REVERT: E 175 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8024 (mp0) REVERT: E 182 LYS cc_start: 0.9345 (ptpp) cc_final: 0.9019 (pttm) REVERT: E 214 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8906 (mpt) REVERT: G 11 ILE cc_start: 0.9528 (tt) cc_final: 0.9233 (pp) REVERT: G 50 TYR cc_start: 0.8993 (t80) cc_final: 0.8545 (t80) REVERT: G 70 ARG cc_start: 0.9119 (mmm160) cc_final: 0.8637 (mmm160) REVERT: G 76 GLU cc_start: 0.9489 (mm-30) cc_final: 0.9184 (mp0) REVERT: G 97 ASP cc_start: 0.9230 (t0) cc_final: 0.8867 (t0) REVERT: G 158 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8679 (mmmt) REVERT: G 163 SER cc_start: 0.8909 (m) cc_final: 0.8624 (p) REVERT: G 175 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8159 (mt-10) REVERT: G 182 LYS cc_start: 0.9485 (ptmt) cc_final: 0.9195 (ptpt) REVERT: G 214 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8883 (mpt) REVERT: I 45 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8817 (mm-30) REVERT: I 50 TYR cc_start: 0.8906 (t80) cc_final: 0.8553 (t80) REVERT: I 97 ASP cc_start: 0.9341 (t0) cc_final: 0.8950 (t0) REVERT: I 170 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8624 (ttmt) REVERT: I 214 MET cc_start: 0.9230 (mtp) cc_final: 0.8857 (mpp) REVERT: K 11 ILE cc_start: 0.9529 (tt) cc_final: 0.9223 (pp) REVERT: K 70 ARG cc_start: 0.9098 (mmm160) cc_final: 0.8533 (mmm160) REVERT: K 163 SER cc_start: 0.9035 (m) cc_final: 0.8795 (p) REVERT: K 175 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8015 (mp0) REVERT: K 182 LYS cc_start: 0.9342 (ptpp) cc_final: 0.9007 (pttm) REVERT: K 203 LYS cc_start: 0.9468 (mppt) cc_final: 0.9208 (pmmt) REVERT: K 214 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8836 (mpt) outliers start: 35 outliers final: 12 residues processed: 293 average time/residue: 1.7300 time to fit residues: 536.9913 Evaluate side-chains 272 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 254 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 170 LYS Chi-restraints excluded: chain K residue 13 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 84 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 0.0670 chunk 131 optimal weight: 30.0000 chunk 91 optimal weight: 0.1980 overall best weight: 2.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.078875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.057158 restraints weight = 32392.755| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 4.31 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.7395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.994 11460 Z= 2.497 Angle : 4.131 99.506 15702 Z= 1.418 Chirality : 0.340 4.195 1698 Planarity : 0.005 0.122 1986 Dihedral : 29.126 176.883 1968 Min Nonbonded Distance : 1.424 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.82 % Allowed : 24.79 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1350 helix: 1.32 (0.18), residues: 870 sheet: -1.63 (0.42), residues: 54 loop : 0.62 (0.35), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 116 HIS 0.004 0.001 HIS I 84 PHE 0.010 0.002 PHE I 32 TYR 0.027 0.003 TYR I 118 ARG 0.013 0.001 ARG I 18 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 642) hydrogen bonds : angle 4.95357 ( 1890) SS BOND : bond 0.00165 ( 6) SS BOND : angle 2.60146 ( 12) covalent geometry : bond 0.04897 (11430) covalent geometry : angle 4.13244 (15690) Misc. bond : bond 0.11322 ( 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: 33 poor density : 268 time to evaluate : 1.165 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 11 ILE cc_start: 0.9540 (tt) cc_final: 0.9246 (pp) REVERT: A 50 TYR cc_start: 0.9035 (t80) cc_final: 0.8830 (t80) REVERT: A 70 ARG cc_start: 0.9150 (mmm160) cc_final: 0.8623 (mmm160) REVERT: A 76 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9165 (mp0) REVERT: A 158 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8679 (mmmt) REVERT: A 163 SER cc_start: 0.9012 (m) cc_final: 0.8734 (p) REVERT: A 175 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8456 (tm-30) REVERT: A 214 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8917 (mpt) REVERT: C 50 TYR cc_start: 0.8999 (t80) cc_final: 0.8645 (t80) REVERT: C 158 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8600 (mmmt) REVERT: C 163 SER cc_start: 0.9041 (m) cc_final: 0.8706 (p) REVERT: C 170 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8733 (ttmt) REVERT: C 175 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8396 (mt-10) REVERT: C 182 LYS cc_start: 0.9548 (ptmt) cc_final: 0.9239 (ptpp) REVERT: C 185 MET cc_start: 0.9428 (mtp) cc_final: 0.9163 (mtm) REVERT: C 212 GLU cc_start: 0.9305 (pm20) cc_final: 0.9098 (pm20) REVERT: C 214 MET cc_start: 0.9230 (mtp) cc_final: 0.8879 (mpp) REVERT: E 11 ILE cc_start: 0.9529 (tt) cc_final: 0.9238 (pp) REVERT: E 70 ARG cc_start: 0.9039 (mtp85) cc_final: 0.8622 (mmm160) REVERT: E 117 MET cc_start: 0.9046 (mtp) cc_final: 0.8833 (mtp) REVERT: E 163 SER cc_start: 0.9128 (m) cc_final: 0.8887 (p) REVERT: E 175 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8284 (mm-30) REVERT: E 177 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8263 (m) REVERT: E 182 LYS cc_start: 0.9382 (ptpp) cc_final: 0.9026 (pttm) REVERT: E 203 LYS cc_start: 0.9542 (mppt) cc_final: 0.9256 (pmmt) REVERT: E 213 GLU cc_start: 0.9013 (pt0) cc_final: 0.8806 (pt0) REVERT: E 214 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8827 (mpt) REVERT: G 11 ILE cc_start: 0.9551 (tt) cc_final: 0.9260 (pp) REVERT: G 50 TYR cc_start: 0.9038 (t80) cc_final: 0.8831 (t80) REVERT: G 70 ARG cc_start: 0.9144 (mmm160) cc_final: 0.8612 (mmm160) REVERT: G 76 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9155 (mp0) REVERT: G 158 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8687 (mmmt) REVERT: G 163 SER cc_start: 0.9020 (m) cc_final: 0.8738 (p) REVERT: G 214 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8910 (mpt) REVERT: I 70 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8734 (mmm160) REVERT: I 158 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8610 (mmmt) REVERT: I 163 SER cc_start: 0.9008 (m) cc_final: 0.8661 (p) REVERT: I 170 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8757 (ttmt) REVERT: I 214 MET cc_start: 0.9269 (mtp) cc_final: 0.8731 (mpp) REVERT: K 11 ILE cc_start: 0.9543 (tt) cc_final: 0.9212 (pp) REVERT: K 45 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8941 (mm-30) REVERT: K 70 ARG cc_start: 0.9126 (mmm160) cc_final: 0.8509 (mmm160) REVERT: K 76 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8718 (mp0) REVERT: K 117 MET cc_start: 0.9012 (mtp) cc_final: 0.8805 (mtp) REVERT: K 163 SER cc_start: 0.9113 (m) cc_final: 0.8878 (p) REVERT: K 175 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8268 (mm-30) REVERT: K 182 LYS cc_start: 0.9381 (ptpp) cc_final: 0.9065 (pttp) REVERT: K 213 GLU cc_start: 0.9001 (pt0) cc_final: 0.8789 (pt0) REVERT: K 214 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8738 (mpp) outliers start: 33 outliers final: 10 residues processed: 282 average time/residue: 1.6175 time to fit residues: 482.7885 Evaluate side-chains 276 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 257 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain E residue 13 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 G residue 214 MET Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 170 LYS Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 76 GLU 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: 8.9990 chunk 100 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 3 optimal weight: 0.0770 chunk 40 optimal weight: 10.0000 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 12 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.076495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.054944 restraints weight = 32955.115| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.31 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.7529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.992 11460 Z= 2.495 Angle : 4.105 99.613 15702 Z= 1.411 Chirality : 0.339 4.263 1698 Planarity : 0.005 0.107 1986 Dihedral : 29.371 179.199 1968 Min Nonbonded Distance : 1.409 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.99 % Allowed : 24.02 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1350 helix: 1.36 (0.18), residues: 870 sheet: -1.79 (0.41), residues: 54 loop : 0.60 (0.35), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 23 HIS 0.003 0.001 HIS K 84 PHE 0.011 0.002 PHE G 32 TYR 0.026 0.003 TYR I 118 ARG 0.020 0.001 ARG I 18 Details of bonding type rmsd hydrogen bonds : bond 0.04548 ( 642) hydrogen bonds : angle 4.89300 ( 1890) SS BOND : bond 0.00199 ( 6) SS BOND : angle 2.61743 ( 12) covalent geometry : bond 0.04893 (11430) covalent geometry : angle 4.10587 (15690) Misc. bond : bond 0.11350 ( 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 295 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 260 time to evaluate : 1.230 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: A 11 ILE cc_start: 0.9520 (tt) cc_final: 0.9209 (pp) REVERT: A 50 TYR cc_start: 0.9053 (t80) cc_final: 0.8850 (t80) REVERT: A 70 ARG cc_start: 0.9171 (mmm160) cc_final: 0.8599 (mmm160) REVERT: A 76 GLU cc_start: 0.9483 (mm-30) cc_final: 0.9193 (mp0) REVERT: A 158 LYS cc_start: 0.8984 (mmmt) cc_final: 0.8633 (mmmt) REVERT: A 163 SER cc_start: 0.9033 (m) cc_final: 0.8773 (p) REVERT: A 175 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8366 (mt-10) REVERT: A 182 LYS cc_start: 0.9495 (ptmt) cc_final: 0.9246 (ptpt) REVERT: A 214 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8882 (mpt) REVERT: C 70 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8683 (mtp85) REVERT: C 158 LYS cc_start: 0.8893 (mmmt) cc_final: 0.8644 (mmmt) REVERT: C 163 SER cc_start: 0.9080 (m) cc_final: 0.8745 (p) REVERT: C 170 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8733 (ttmt) REVERT: C 182 LYS cc_start: 0.9538 (ptmt) cc_final: 0.9244 (ptpp) REVERT: C 185 MET cc_start: 0.9448 (mtp) cc_final: 0.9174 (mtm) REVERT: C 203 LYS cc_start: 0.9510 (mppt) cc_final: 0.9251 (pmmt) REVERT: C 214 MET cc_start: 0.9161 (mtp) cc_final: 0.8808 (mpp) REVERT: E 11 ILE cc_start: 0.9520 (tt) cc_final: 0.9201 (pp) REVERT: E 70 ARG cc_start: 0.9058 (mtp85) cc_final: 0.8701 (mmm160) REVERT: E 163 SER cc_start: 0.9118 (m) cc_final: 0.8892 (p) REVERT: E 175 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8223 (mm-30) REVERT: E 177 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8090 (m) REVERT: E 182 LYS cc_start: 0.9369 (ptpp) cc_final: 0.9027 (pttm) REVERT: E 203 LYS cc_start: 0.9539 (mppt) cc_final: 0.9338 (pmmt) REVERT: E 214 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8732 (mpp) REVERT: G 11 ILE cc_start: 0.9527 (tt) cc_final: 0.9216 (pp) REVERT: G 50 TYR cc_start: 0.9035 (t80) cc_final: 0.8822 (t80) REVERT: G 70 ARG cc_start: 0.9173 (mmm160) cc_final: 0.8601 (mmm160) REVERT: G 76 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9187 (mp0) REVERT: G 158 LYS cc_start: 0.8997 (mmmt) cc_final: 0.8644 (mmmt) REVERT: G 163 SER cc_start: 0.9040 (m) cc_final: 0.8777 (p) REVERT: G 182 LYS cc_start: 0.9452 (ptmt) cc_final: 0.9195 (ptpt) REVERT: G 214 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8897 (mpt) REVERT: I 50 TYR cc_start: 0.8925 (t80) cc_final: 0.8694 (t80) REVERT: I 70 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8607 (mtp85) REVERT: I 158 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8640 (mmmt) REVERT: I 163 SER cc_start: 0.9069 (m) cc_final: 0.8733 (p) REVERT: I 170 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8732 (ttmt) REVERT: I 182 LYS cc_start: 0.9407 (ptpp) cc_final: 0.9131 (pttm) REVERT: I 203 LYS cc_start: 0.9542 (mppt) cc_final: 0.9257 (pmmt) REVERT: K 11 ILE cc_start: 0.9522 (tt) cc_final: 0.9202 (pp) REVERT: K 70 ARG cc_start: 0.9133 (mmm160) cc_final: 0.8491 (mmm160) REVERT: K 76 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8715 (mp0) REVERT: K 163 SER cc_start: 0.9102 (m) cc_final: 0.8879 (p) REVERT: K 175 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8264 (mm-30) REVERT: K 182 LYS cc_start: 0.9370 (ptpp) cc_final: 0.9057 (pttp) REVERT: K 203 LYS cc_start: 0.9499 (mppt) cc_final: 0.9225 (pmmt) REVERT: K 214 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8750 (mpp) outliers start: 35 outliers final: 8 residues processed: 274 average time/residue: 1.6518 time to fit residues: 478.1957 Evaluate side-chains 279 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 261 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain E residue 13 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 G residue 214 MET Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 170 LYS Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 76 GLU 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 58 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 chunk 83 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 12 HIS K 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.077187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.054874 restraints weight = 34234.347| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 4.37 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.7762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.989 11460 Z= 2.485 Angle : 4.128 98.920 15702 Z= 1.421 Chirality : 0.337 4.242 1698 Planarity : 0.005 0.050 1986 Dihedral : 29.306 179.170 1968 Min Nonbonded Distance : 1.395 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.05 % Allowed : 25.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.24), residues: 1350 helix: 1.41 (0.18), residues: 870 sheet: -1.89 (0.40), residues: 54 loop : 0.52 (0.35), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 23 HIS 0.003 0.001 HIS A 62 PHE 0.009 0.002 PHE A 32 TYR 0.025 0.003 TYR C 118 ARG 0.014 0.001 ARG I 18 Details of bonding type rmsd hydrogen bonds : bond 0.04557 ( 642) hydrogen bonds : angle 4.91794 ( 1890) SS BOND : bond 0.00185 ( 6) SS BOND : angle 2.68760 ( 12) covalent geometry : bond 0.04878 (11430) covalent geometry : angle 4.12917 (15690) Misc. bond : bond 0.11169 ( 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 284 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 1.263 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 70 ARG cc_start: 0.9155 (mmm160) cc_final: 0.8639 (mmm160) REVERT: A 76 GLU cc_start: 0.9467 (mm-30) cc_final: 0.9161 (mp0) REVERT: A 158 LYS cc_start: 0.8927 (mmmt) cc_final: 0.8584 (mmmt) REVERT: A 163 SER cc_start: 0.9148 (m) cc_final: 0.8907 (p) REVERT: A 175 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8272 (mt-10) REVERT: A 182 LYS cc_start: 0.9530 (ptmt) cc_final: 0.9260 (ptpt) REVERT: A 214 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8824 (mpt) REVERT: C 50 TYR cc_start: 0.8947 (t80) cc_final: 0.8602 (t80) REVERT: C 163 SER cc_start: 0.9182 (m) cc_final: 0.8831 (p) REVERT: C 170 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8877 (ttmt) REVERT: C 175 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8313 (tm-30) REVERT: C 182 LYS cc_start: 0.9557 (ptmt) cc_final: 0.9251 (ptpp) REVERT: C 185 MET cc_start: 0.9407 (mtp) cc_final: 0.9109 (mtm) REVERT: C 203 LYS cc_start: 0.9492 (mppt) cc_final: 0.9267 (pmmt) REVERT: C 212 GLU cc_start: 0.9332 (pm20) cc_final: 0.8965 (pm20) REVERT: C 213 GLU cc_start: 0.9023 (pt0) cc_final: 0.8734 (pm20) REVERT: C 214 MET cc_start: 0.9225 (mtp) cc_final: 0.8839 (mpp) REVERT: E 11 ILE cc_start: 0.9533 (tt) cc_final: 0.9229 (pp) REVERT: E 45 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8671 (mm-30) REVERT: E 70 ARG cc_start: 0.9075 (mtp85) cc_final: 0.8584 (mmm160) REVERT: E 163 SER cc_start: 0.9227 (m) cc_final: 0.9012 (p) REVERT: E 175 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8173 (mm-30) REVERT: E 177 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8451 (m) REVERT: E 182 LYS cc_start: 0.9406 (ptpp) cc_final: 0.9087 (pttp) REVERT: E 203 LYS cc_start: 0.9559 (mppt) cc_final: 0.9342 (pmmt) REVERT: E 212 GLU cc_start: 0.9248 (pm20) cc_final: 0.8895 (pm20) REVERT: E 213 GLU cc_start: 0.9086 (pt0) cc_final: 0.8769 (pm20) REVERT: E 214 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8843 (mpt) REVERT: G 11 ILE cc_start: 0.9550 (tt) cc_final: 0.9242 (pp) REVERT: G 70 ARG cc_start: 0.9152 (mmm160) cc_final: 0.8622 (mmm160) REVERT: G 76 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9158 (mp0) REVERT: G 158 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8597 (mmmt) REVERT: G 163 SER cc_start: 0.9149 (m) cc_final: 0.8908 (p) REVERT: G 182 LYS cc_start: 0.9428 (ptmt) cc_final: 0.9165 (ptpt) REVERT: G 214 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8887 (mpt) REVERT: I 50 TYR cc_start: 0.9029 (t80) cc_final: 0.8773 (t80) REVERT: I 70 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8610 (mtp85) REVERT: I 158 LYS cc_start: 0.8851 (mmmt) cc_final: 0.8575 (mmmt) REVERT: I 163 SER cc_start: 0.9189 (m) cc_final: 0.8839 (p) REVERT: I 170 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8850 (ttmt) REVERT: I 182 LYS cc_start: 0.9401 (ptpp) cc_final: 0.9140 (pttm) REVERT: K 11 ILE cc_start: 0.9543 (tt) cc_final: 0.9237 (pp) REVERT: K 70 ARG cc_start: 0.9159 (mmm160) cc_final: 0.8531 (mmm160) REVERT: K 154 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8562 (mmmt) REVERT: K 163 SER cc_start: 0.9221 (m) cc_final: 0.9010 (p) REVERT: K 175 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8204 (mm-30) REVERT: K 182 LYS cc_start: 0.9398 (ptpp) cc_final: 0.9079 (pttp) REVERT: K 203 LYS cc_start: 0.9547 (mppt) cc_final: 0.9270 (pmmt) REVERT: K 212 GLU cc_start: 0.9219 (pm20) cc_final: 0.8877 (pm20) REVERT: K 213 GLU cc_start: 0.9084 (pt0) cc_final: 0.8730 (pm20) REVERT: K 214 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8845 (mpt) outliers start: 24 outliers final: 10 residues processed: 274 average time/residue: 1.7501 time to fit residues: 507.2182 Evaluate side-chains 269 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 251 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain E residue 13 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 G residue 214 MET Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 170 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 108 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 42 optimal weight: 0.2980 chunk 93 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.077430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.055351 restraints weight = 32812.087| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 4.34 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.7844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.048 0.991 11460 Z= 2.462 Angle : 4.146 99.531 15702 Z= 1.426 Chirality : 0.329 4.348 1698 Planarity : 0.005 0.071 1986 Dihedral : 29.206 179.021 1968 Min Nonbonded Distance : 1.380 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.97 % Allowed : 26.32 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.24), residues: 1350 helix: 1.43 (0.18), residues: 870 sheet: -1.71 (0.39), residues: 54 loop : 0.52 (0.34), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 23 HIS 0.003 0.001 HIS A 62 PHE 0.007 0.001 PHE C 32 TYR 0.026 0.003 TYR C 118 ARG 0.018 0.001 ARG I 18 Details of bonding type rmsd hydrogen bonds : bond 0.04483 ( 642) hydrogen bonds : angle 4.82189 ( 1890) SS BOND : bond 0.00104 ( 6) SS BOND : angle 2.48472 ( 12) covalent geometry : bond 0.04829 (11430) covalent geometry : angle 4.14740 (15690) Misc. bond : bond 0.11062 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9288.03 seconds wall clock time: 159 minutes 9.03 seconds (9549.03 seconds total)