Starting phenix.real_space_refine on Tue May 13 20:05:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cnu_45760/05_2025/9cnu_45760.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cnu_45760/05_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_45760/05_2025/9cnu_45760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cnu_45760/05_2025/9cnu_45760.map" model { file = "/net/cci-nas-00/data/ceres_data/9cnu_45760/05_2025/9cnu_45760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cnu_45760/05_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-5687/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: 4.52, per 1000 atoms: 0.40 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: 6.26 Conformation dependent library (CDL) restraints added in 1.5 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: 1.11 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: 3.04 Time building geometry restraints manager: 6.68 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: 0.310 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.600 Find NCS groups from input model: 0.240 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:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.650 ------------------------------------------------------------------------------- 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 : 1.336 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: 1.4883 time to fit residues: 515.1881 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 : 1.163 ------------------------------------------------------------------------------- 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 = 65)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.067445 restraints weight = 48037.286| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 5.20 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 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 = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 91.767 15702 Z= 1.930 Chirality : 0.464 4.678 1698 Planarity : 0.008 0.086 1986 Dihedral : 22.304 138.336 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 5.36297 ( 1890) SS BOND : bond 0.00912 ( 6) SS BOND : angle 6.91128 ( 12) covalent geometry : bond 0.08364 (11430) covalent geometry : angle 5.69285 (15690) Misc. bond : bond 0.10528 ( 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 : 1.300 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: 0.9357 (OUTLIER) cc_final: 0.9136 (ptpt) REVERT: A 214 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8721 (mpt) REVERT: C 76 GLU cc_start: 0.9094 (mp0) cc_final: 0.8601 (mp0) REVERT: C 144 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8142 (mpt) REVERT: C 175 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7906 (mt-10) REVERT: C 182 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9282 (ptpp) REVERT: C 214 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.8841 (mpp) REVERT: E 175 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7816 (mm-30) REVERT: E 214 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8884 (mpt) REVERT: G 175 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8135 (mt-10) REVERT: G 182 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.9135 (ptpt) REVERT: G 214 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8711 (mpt) REVERT: I 76 GLU cc_start: 0.9100 (mp0) cc_final: 0.8611 (mp0) REVERT: I 144 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8137 (mpt) REVERT: I 175 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7908 (mt-10) REVERT: I 182 LYS cc_start: 0.9492 (OUTLIER) cc_final: 0.9287 (ptpp) REVERT: I 214 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.8825 (mpp) REVERT: K 175 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7809 (mm-30) REVERT: K 214 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8833 (mpt) outliers start: 35 outliers final: 7 residues processed: 290 average time/residue: 1.5397 time to fit residues: 473.4171 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 : 1.298 ------------------------------------------------------------------------------- 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: 0.7980 chunk 108 optimal weight: 3.9990 chunk 55 optimal weight: 0.0030 chunk 27 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.087002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.066259 restraints weight = 34204.630| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 4.55 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 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 = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.061 1.272 11460 Z= 3.082 Angle : 5.165 90.824 15702 Z= 1.750 Chirality : 0.375 4.386 1698 Planarity : 0.006 0.049 1986 Dihedral : 26.348 178.128 1972 Min Nonbonded Distance : 1.209 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.88 % Allowed : 15.47 % Favored : 82.65 % 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: 0.37 (0.23), residues: 1350 helix: 1.11 (0.17), residues: 888 sheet: -2.73 (0.55), residues: 54 loop : -1.16 (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 0.021 0.003 TYR A 10 ARG 0.071 0.002 ARG G 18 Details of bonding type rmsd hydrogen bonds : bond 0.05047 ( 642) hydrogen bonds : angle 5.02859 ( 1890) SS BOND : bond 0.00404 ( 6) SS BOND : angle 4.39705 ( 12) covalent geometry : bond 0.06079 (11430) covalent geometry : angle 5.16582 (15690) Misc. bond : bond 0.11523 ( 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 309 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 287 time to evaluate : 1.217 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: 0.9518 (m-30) cc_final: 0.9296 (m-30) REVERT: A 76 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9053 (mp0) REVERT: A 97 ASP cc_start: 0.9212 (t0) cc_final: 0.8618 (p0) REVERT: A 175 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8194 (mt-10) REVERT: A 182 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.9195 (ptpt) REVERT: A 214 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8695 (mpt) REVERT: C 76 GLU cc_start: 0.9188 (mp0) cc_final: 0.8588 (mp0) REVERT: C 182 LYS cc_start: 0.9515 (ptmt) cc_final: 0.9257 (ptpp) REVERT: C 214 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8851 (mpp) REVERT: E 75 ASP cc_start: 0.9514 (m-30) cc_final: 0.9190 (m-30) REVERT: E 76 GLU cc_start: 0.9164 (mp0) cc_final: 0.8878 (mp0) REVERT: E 175 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8079 (mt-10) REVERT: E 182 LYS cc_start: 0.9330 (ptpp) cc_final: 0.8943 (pttm) REVERT: E 214 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8905 (mpt) REVERT: G 75 ASP cc_start: 0.9522 (m-30) cc_final: 0.9298 (m-30) REVERT: G 76 GLU cc_start: 0.9423 (mm-30) cc_final: 0.9046 (mp0) REVERT: G 97 ASP cc_start: 0.9216 (t0) cc_final: 0.8624 (p0) REVERT: G 175 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8164 (mt-10) REVERT: G 182 LYS cc_start: 0.9459 (OUTLIER) cc_final: 0.9199 (ptpt) REVERT: G 214 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8690 (mpt) REVERT: I 75 ASP cc_start: 0.9560 (m-30) cc_final: 0.9287 (m-30) REVERT: I 76 GLU cc_start: 0.9185 (mp0) cc_final: 0.8581 (mp0) REVERT: I 97 ASP cc_start: 0.9132 (t0) cc_final: 0.8417 (p0) REVERT: I 182 LYS cc_start: 0.9521 (ptmt) cc_final: 0.9267 (ptpp) REVERT: I 214 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8848 (mpp) REVERT: K 75 ASP cc_start: 0.9513 (m-30) cc_final: 0.9199 (m-30) REVERT: K 76 GLU cc_start: 0.9157 (mp0) cc_final: 0.8867 (mp0) REVERT: K 118 TYR cc_start: 0.8679 (m-80) cc_final: 0.8434 (m-80) REVERT: K 175 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8062 (mt-10) REVERT: K 182 LYS cc_start: 0.9330 (ptpp) cc_final: 0.8945 (pttm) REVERT: K 214 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8849 (mpt) outliers start: 22 outliers final: 6 residues processed: 292 average time/residue: 1.5670 time to fit residues: 484.7747 Evaluate side-chains 253 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 239 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 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 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: 0.4980 chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.082933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.062575 restraints weight = 31780.141| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.30 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.052 1.071 11460 Z= 2.655 Angle : 4.631 94.976 15702 Z= 1.573 Chirality : 0.352 3.860 1698 Planarity : 0.007 0.095 1986 Dihedral : 27.500 176.082 1972 Min Nonbonded Distance : 1.417 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.22 % Allowed : 17.35 % Favored : 80.43 % 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: 0.74 (0.22), residues: 1350 helix: 1.30 (0.17), residues: 876 sheet: -2.55 (0.54), residues: 54 loop : -0.70 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 116 HIS 0.004 0.001 HIS I 84 PHE 0.009 0.002 PHE K 32 TYR 0.022 0.002 TYR I 10 ARG 0.013 0.001 ARG G 18 Details of bonding type rmsd hydrogen bonds : bond 0.04689 ( 642) hydrogen bonds : angle 4.95299 ( 1890) SS BOND : bond 0.00096 ( 6) SS BOND : angle 3.56076 ( 12) covalent geometry : bond 0.05212 (11430) covalent geometry : angle 4.63218 (15690) Misc. bond : bond 0.11731 ( 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 303 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 277 time to evaluate : 1.176 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: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9476 (mm-30) cc_final: 0.9106 (mp0) REVERT: A 118 TYR cc_start: 0.8814 (m-80) cc_final: 0.8539 (m-80) REVERT: A 175 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8369 (mt-10) REVERT: A 182 LYS cc_start: 0.9445 (ptmt) cc_final: 0.9186 (ptpp) REVERT: A 214 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8777 (mpt) REVERT: C 70 ARG cc_start: 0.8886 (ttm-80) cc_final: 0.8519 (mtp85) REVERT: C 76 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8585 (mp0) REVERT: C 175 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8070 (tm-30) REVERT: C 182 LYS cc_start: 0.9538 (ptmt) cc_final: 0.9290 (ptpp) REVERT: C 214 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8727 (mpp) REVERT: E 76 GLU cc_start: 0.9203 (mp0) cc_final: 0.8851 (mp0) REVERT: E 97 ASP cc_start: 0.9115 (t0) cc_final: 0.8736 (OUTLIER) REVERT: E 112 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8444 (pt0) REVERT: E 175 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7934 (mp0) REVERT: E 182 LYS cc_start: 0.9307 (ptpp) cc_final: 0.8974 (pttm) REVERT: E 199 LYS cc_start: 0.9458 (ttpp) cc_final: 0.9191 (mtmm) REVERT: E 212 GLU cc_start: 0.9285 (pm20) cc_final: 0.9075 (pm20) REVERT: E 214 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8878 (mpt) REVERT: G 76 GLU cc_start: 0.9470 (mm-30) cc_final: 0.9101 (mp0) REVERT: G 118 TYR cc_start: 0.8796 (m-80) cc_final: 0.8522 (m-80) REVERT: G 175 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8343 (mt-10) REVERT: G 182 LYS cc_start: 0.9448 (ptmt) cc_final: 0.9188 (ptpp) REVERT: G 214 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8783 (mpt) REVERT: I 70 ARG cc_start: 0.8898 (ttm-80) cc_final: 0.8554 (mtp85) REVERT: I 76 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8624 (mp0) REVERT: I 159 GLU cc_start: 0.8057 (tt0) cc_final: 0.7828 (tm-30) REVERT: I 175 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8058 (tm-30) REVERT: I 182 LYS cc_start: 0.9541 (ptmt) cc_final: 0.9302 (ptpp) REVERT: I 214 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8729 (mpp) REVERT: K 97 ASP cc_start: 0.9112 (t0) cc_final: 0.8734 (OUTLIER) REVERT: K 112 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8433 (pt0) REVERT: K 175 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7932 (mp0) REVERT: K 182 LYS cc_start: 0.9309 (ptpp) cc_final: 0.8973 (pttm) REVERT: K 214 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8867 (mpt) outliers start: 26 outliers final: 4 residues processed: 287 average time/residue: 1.6536 time to fit residues: 500.6365 Evaluate side-chains 249 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 239 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 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 76 GLU Chi-restraints excluded: chain I residue 214 MET 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: 5.9990 chunk 90 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 108 optimal weight: 0.1980 chunk 89 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.079813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.058622 restraints weight = 31559.111| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.27 r_work: 0.2800 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.6381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 1.042 11460 Z= 2.550 Angle : 4.361 98.011 15702 Z= 1.482 Chirality : 0.343 3.941 1698 Planarity : 0.006 0.082 1986 Dihedral : 28.307 179.986 1968 Min Nonbonded Distance : 1.436 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.22 % Allowed : 20.51 % Favored : 77.26 % 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: 1.03 (0.23), residues: 1350 helix: 1.33 (0.17), residues: 870 sheet: -2.23 (0.50), residues: 54 loop : -0.12 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 23 HIS 0.004 0.001 HIS K 84 PHE 0.008 0.001 PHE I 161 TYR 0.018 0.002 TYR K 118 ARG 0.033 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 642) hydrogen bonds : angle 4.87014 ( 1890) SS BOND : bond 0.00261 ( 6) SS BOND : angle 2.65285 ( 12) covalent geometry : bond 0.04993 (11430) covalent geometry : angle 4.36235 (15690) Misc. bond : bond 0.11903 ( 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 309 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 283 time to evaluate : 1.179 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 50 TYR cc_start: 0.9064 (t80) cc_final: 0.8784 (t80) REVERT: A 76 GLU cc_start: 0.9483 (mm-30) cc_final: 0.9113 (mp0) REVERT: A 97 ASP cc_start: 0.9345 (t0) cc_final: 0.8276 (p0) REVERT: A 118 TYR cc_start: 0.8823 (m-80) cc_final: 0.8613 (m-80) REVERT: A 175 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8360 (mp0) REVERT: A 182 LYS cc_start: 0.9484 (ptmt) cc_final: 0.9162 (ptpt) REVERT: A 214 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8896 (mpt) REVERT: C 45 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8904 (mm-30) REVERT: C 70 ARG cc_start: 0.9118 (ttm-80) cc_final: 0.8717 (mtp85) REVERT: C 76 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.8958 (mp0) REVERT: C 118 TYR cc_start: 0.8913 (m-80) cc_final: 0.8556 (m-80) REVERT: C 149 ASN cc_start: 0.8583 (t0) cc_final: 0.8117 (t0) REVERT: C 152 ASP cc_start: 0.9226 (m-30) cc_final: 0.8723 (p0) REVERT: C 153 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8713 (p) REVERT: C 175 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8372 (tm-30) REVERT: C 182 LYS cc_start: 0.9544 (ptmt) cc_final: 0.9332 (ptpp) REVERT: E 76 GLU cc_start: 0.9342 (mp0) cc_final: 0.9074 (mp0) REVERT: E 163 SER cc_start: 0.8937 (m) cc_final: 0.8694 (p) REVERT: E 175 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8334 (mp0) REVERT: E 182 LYS cc_start: 0.9327 (ptpp) cc_final: 0.9033 (pttp) REVERT: E 212 GLU cc_start: 0.9316 (pm20) cc_final: 0.9097 (pm20) REVERT: E 213 GLU cc_start: 0.9500 (tt0) cc_final: 0.9244 (mt-10) REVERT: E 214 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.8911 (mpt) REVERT: G 18 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8210 (tmm-80) REVERT: G 50 TYR cc_start: 0.9062 (t80) cc_final: 0.8816 (t80) REVERT: G 76 GLU cc_start: 0.9476 (mm-30) cc_final: 0.9109 (mp0) REVERT: G 97 ASP cc_start: 0.9344 (t0) cc_final: 0.8278 (p0) REVERT: G 118 TYR cc_start: 0.8835 (m-80) cc_final: 0.8625 (m-80) REVERT: G 175 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8387 (mp0) REVERT: G 182 LYS cc_start: 0.9487 (ptmt) cc_final: 0.9166 (ptpt) REVERT: G 214 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8873 (mpt) REVERT: I 45 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8948 (mm-30) REVERT: I 70 ARG cc_start: 0.9106 (ttm-80) cc_final: 0.8828 (mtp85) REVERT: I 76 GLU cc_start: 0.9361 (OUTLIER) cc_final: 0.9063 (mp0) REVERT: I 97 ASP cc_start: 0.9287 (t0) cc_final: 0.8963 (t0) REVERT: I 118 TYR cc_start: 0.8915 (m-80) cc_final: 0.8557 (m-80) REVERT: I 149 ASN cc_start: 0.8543 (t0) cc_final: 0.8106 (t0) REVERT: I 152 ASP cc_start: 0.9236 (m-30) cc_final: 0.8718 (p0) REVERT: I 175 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8530 (tm-30) REVERT: I 182 LYS cc_start: 0.9549 (ptmt) cc_final: 0.9293 (ptpp) REVERT: K 18 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8198 (ppp80) REVERT: K 70 ARG cc_start: 0.9255 (mmm160) cc_final: 0.8638 (mmm160) REVERT: K 76 GLU cc_start: 0.9375 (mp0) cc_final: 0.8972 (mp0) REVERT: K 163 SER cc_start: 0.8940 (m) cc_final: 0.8693 (p) REVERT: K 175 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8353 (mp0) REVERT: K 182 LYS cc_start: 0.9326 (ptpp) cc_final: 0.9030 (pttp) REVERT: K 212 GLU cc_start: 0.9262 (pm20) cc_final: 0.9022 (pm20) REVERT: K 214 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.8980 (mpt) outliers start: 26 outliers final: 4 residues processed: 291 average time/residue: 1.6196 time to fit residues: 498.7347 Evaluate side-chains 270 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 257 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 153 VAL 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 18 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 41 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 108 optimal weight: 0.0770 chunk 50 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 overall best weight: 2.3942 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.080236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.058580 restraints weight = 32332.444| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 4.38 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 1.052 11460 Z= 2.514 Angle : 4.213 99.711 15702 Z= 1.435 Chirality : 0.335 4.010 1698 Planarity : 0.007 0.197 1986 Dihedral : 29.083 178.865 1968 Min Nonbonded Distance : 1.437 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.31 % Allowed : 22.48 % Favored : 75.21 % 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: 1.15 (0.23), residues: 1350 helix: 1.36 (0.17), residues: 876 sheet: -1.99 (0.46), residues: 54 loop : 0.06 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 23 HIS 0.004 0.001 HIS A 84 PHE 0.009 0.002 PHE I 32 TYR 0.020 0.002 TYR K 118 ARG 0.015 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 642) hydrogen bonds : angle 4.69703 ( 1890) SS BOND : bond 0.00299 ( 6) SS BOND : angle 2.76637 ( 12) covalent geometry : bond 0.04930 (11430) covalent geometry : angle 4.21396 (15690) Misc. bond : bond 0.11411 ( 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 311 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 284 time to evaluate : 1.286 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 50 TYR cc_start: 0.8960 (t80) cc_final: 0.8612 (t80) REVERT: A 70 ARG cc_start: 0.8909 (mmm160) cc_final: 0.8366 (mmm160) REVERT: A 75 ASP cc_start: 0.9556 (m-30) cc_final: 0.9278 (m-30) REVERT: A 76 GLU cc_start: 0.9475 (mm-30) cc_final: 0.9154 (mp0) REVERT: A 118 TYR cc_start: 0.8829 (m-80) cc_final: 0.8598 (m-80) REVERT: A 163 SER cc_start: 0.8914 (m) cc_final: 0.8617 (p) REVERT: A 175 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8160 (mp0) REVERT: A 182 LYS cc_start: 0.9460 (ptmt) cc_final: 0.9214 (ptpt) REVERT: A 214 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8860 (mpt) REVERT: C 18 ARG cc_start: 0.8149 (ptm160) cc_final: 0.7919 (pmm-80) REVERT: C 45 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8877 (mm-30) REVERT: C 70 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8631 (mtp85) REVERT: C 76 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8896 (mp0) REVERT: C 118 TYR cc_start: 0.8903 (m-80) cc_final: 0.8486 (m-80) REVERT: C 214 MET cc_start: 0.9327 (mtp) cc_final: 0.8752 (mpp) REVERT: E 70 ARG cc_start: 0.8881 (tpt170) cc_final: 0.8676 (mmm160) REVERT: E 97 ASP cc_start: 0.9063 (t0) cc_final: 0.8724 (OUTLIER) REVERT: E 163 SER cc_start: 0.8999 (m) cc_final: 0.8771 (p) REVERT: E 175 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8089 (mp0) REVERT: E 182 LYS cc_start: 0.9316 (ptpp) cc_final: 0.8981 (pttm) REVERT: E 212 GLU cc_start: 0.9198 (pm20) cc_final: 0.8987 (pm20) REVERT: E 214 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.8873 (mpt) REVERT: G 50 TYR cc_start: 0.8963 (t80) cc_final: 0.8593 (t80) REVERT: G 70 ARG cc_start: 0.8898 (mmm160) cc_final: 0.8348 (mmm160) REVERT: G 75 ASP cc_start: 0.9546 (m-30) cc_final: 0.9273 (m-30) REVERT: G 76 GLU cc_start: 0.9480 (mm-30) cc_final: 0.9166 (mp0) REVERT: G 118 TYR cc_start: 0.8823 (m-80) cc_final: 0.8595 (m-80) REVERT: G 163 SER cc_start: 0.8926 (m) cc_final: 0.8630 (p) REVERT: G 175 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8167 (mp0) REVERT: G 182 LYS cc_start: 0.9452 (ptmt) cc_final: 0.9208 (ptpt) REVERT: G 214 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8881 (mpt) REVERT: I 45 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8875 (mm-30) REVERT: I 70 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8562 (mtp-110) REVERT: I 75 ASP cc_start: 0.9528 (m-30) cc_final: 0.9305 (m-30) REVERT: I 76 GLU cc_start: 0.9307 (OUTLIER) cc_final: 0.8887 (mp0) REVERT: I 118 TYR cc_start: 0.8923 (m-80) cc_final: 0.8515 (m-80) REVERT: I 149 ASN cc_start: 0.8423 (t0) cc_final: 0.8147 (t0) REVERT: I 152 ASP cc_start: 0.9140 (m-30) cc_final: 0.8737 (p0) REVERT: K 70 ARG cc_start: 0.9051 (mmm160) cc_final: 0.8371 (mmm160) REVERT: K 97 ASP cc_start: 0.9059 (t0) cc_final: 0.8727 (OUTLIER) REVERT: K 163 SER cc_start: 0.9000 (m) cc_final: 0.8766 (p) REVERT: K 175 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8068 (mp0) REVERT: K 182 LYS cc_start: 0.9317 (ptpp) cc_final: 0.9056 (pttp) REVERT: K 214 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8921 (mpt) outliers start: 27 outliers final: 8 residues processed: 293 average time/residue: 1.5416 time to fit residues: 478.8575 Evaluate side-chains 274 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 260 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 70 ARG Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain E residue 214 MET 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 70 ARG Chi-restraints excluded: chain I residue 76 GLU 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: 3.9990 chunk 16 optimal weight: 9.9990 chunk 86 optimal weight: 0.1980 chunk 59 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 64 optimal weight: 0.1980 chunk 92 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.078960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.057389 restraints weight = 32635.433| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 4.36 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.7067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 1.001 11460 Z= 2.499 Angle : 4.196 99.253 15702 Z= 1.432 Chirality : 0.334 4.115 1698 Planarity : 0.007 0.207 1986 Dihedral : 29.178 177.598 1968 Min Nonbonded Distance : 1.426 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.74 % Allowed : 22.39 % Favored : 74.87 % 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: 1.31 (0.24), residues: 1350 helix: 1.39 (0.17), residues: 876 sheet: -1.55 (0.44), residues: 54 loop : 0.31 (0.35), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 23 HIS 0.003 0.001 HIS I 84 PHE 0.008 0.001 PHE H 7 TYR 0.019 0.002 TYR K 118 ARG 0.019 0.001 ARG I 18 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 642) hydrogen bonds : angle 4.62841 ( 1890) SS BOND : bond 0.00153 ( 6) SS BOND : angle 2.39108 ( 12) covalent geometry : bond 0.04901 (11430) covalent geometry : angle 4.19735 (15690) Misc. bond : bond 0.11220 ( 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 311 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 1.293 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 11 ILE cc_start: 0.9530 (tt) cc_final: 0.9256 (pp) REVERT: A 50 TYR cc_start: 0.8942 (t80) cc_final: 0.8709 (t80) REVERT: A 70 ARG cc_start: 0.8885 (mmm160) cc_final: 0.8301 (mmm160) REVERT: A 76 GLU cc_start: 0.9492 (mm-30) cc_final: 0.9178 (mp0) REVERT: A 163 SER cc_start: 0.8873 (m) cc_final: 0.8587 (p) REVERT: A 175 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8174 (mp0) REVERT: A 182 LYS cc_start: 0.9473 (ptmt) cc_final: 0.9210 (ptpt) REVERT: A 214 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8823 (mpt) REVERT: C 118 TYR cc_start: 0.8782 (m-80) cc_final: 0.8575 (m-80) REVERT: C 170 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8654 (ttmt) REVERT: C 182 LYS cc_start: 0.9354 (ptpp) cc_final: 0.9032 (pttt) REVERT: E 11 ILE cc_start: 0.9517 (tt) cc_final: 0.9235 (pp) REVERT: E 45 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8760 (mm-30) REVERT: E 50 TYR cc_start: 0.9002 (t80) cc_final: 0.8788 (t80) REVERT: E 70 ARG cc_start: 0.8898 (tpt170) cc_final: 0.8691 (mmm160) REVERT: E 117 MET cc_start: 0.9012 (mtp) cc_final: 0.8771 (mtp) REVERT: E 163 SER cc_start: 0.8959 (m) cc_final: 0.8730 (p) REVERT: E 175 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8064 (mp0) REVERT: E 182 LYS cc_start: 0.9299 (ptpp) cc_final: 0.9076 (pttp) REVERT: E 213 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8784 (pt0) REVERT: E 214 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8874 (mpt) REVERT: G 11 ILE cc_start: 0.9537 (tt) cc_final: 0.9269 (pp) REVERT: G 18 ARG cc_start: 0.8728 (ppp80) cc_final: 0.8423 (ptm160) REVERT: G 50 TYR cc_start: 0.8942 (t80) cc_final: 0.8706 (t80) REVERT: G 70 ARG cc_start: 0.8884 (mmm160) cc_final: 0.8301 (mmm160) REVERT: G 76 GLU cc_start: 0.9484 (mm-30) cc_final: 0.9170 (mp0) REVERT: G 163 SER cc_start: 0.8883 (m) cc_final: 0.8589 (p) REVERT: G 175 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8192 (mp0) REVERT: G 182 LYS cc_start: 0.9475 (ptmt) cc_final: 0.9210 (ptpt) REVERT: G 214 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8826 (mpt) REVERT: I 70 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8671 (mtp-110) REVERT: I 76 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.8943 (mp0) REVERT: I 97 ASP cc_start: 0.9313 (t0) cc_final: 0.8927 (t0) REVERT: I 118 TYR cc_start: 0.8785 (m-80) cc_final: 0.8578 (m-80) REVERT: I 170 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8644 (ttmt) REVERT: I 177 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.7880 (m) REVERT: K 11 ILE cc_start: 0.9528 (tt) cc_final: 0.9236 (pp) REVERT: K 18 ARG cc_start: 0.8691 (ppp80) cc_final: 0.8321 (ptm-80) REVERT: K 50 TYR cc_start: 0.9013 (t80) cc_final: 0.8809 (t80) REVERT: K 70 ARG cc_start: 0.9047 (mmm160) cc_final: 0.8384 (mmm160) REVERT: K 163 SER cc_start: 0.8965 (m) cc_final: 0.8727 (p) REVERT: K 175 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8056 (mp0) REVERT: K 182 LYS cc_start: 0.9320 (ptpp) cc_final: 0.9081 (pttp) REVERT: K 203 LYS cc_start: 0.9503 (mppt) cc_final: 0.9287 (pmmt) REVERT: K 214 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8745 (mpp) outliers start: 32 outliers final: 11 residues processed: 295 average time/residue: 1.5953 time to fit residues: 498.2797 Evaluate side-chains 284 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 264 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 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 61 ASP Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 76 GLU Chi-restraints excluded: chain I residue 170 LYS Chi-restraints excluded: chain I residue 177 THR 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: 20.0000 chunk 23 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 54 optimal weight: 0.0370 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 overall best weight: 2.5064 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.079412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.057747 restraints weight = 32578.290| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.31 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 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 = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.7282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.995 11460 Z= 2.493 Angle : 4.160 99.810 15702 Z= 1.421 Chirality : 0.340 4.286 1698 Planarity : 0.005 0.060 1986 Dihedral : 29.486 176.764 1968 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.65 % Allowed : 24.44 % Favored : 72.91 % 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: 1.49 (0.24), residues: 1350 helix: 1.51 (0.18), residues: 876 sheet: -1.51 (0.44), residues: 54 loop : 0.42 (0.35), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 23 HIS 0.008 0.001 HIS I 62 PHE 0.008 0.002 PHE G 32 TYR 0.024 0.002 TYR G 118 ARG 0.015 0.001 ARG I 18 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 642) hydrogen bonds : angle 4.64874 ( 1890) SS BOND : bond 0.00159 ( 6) SS BOND : angle 2.65886 ( 12) covalent geometry : bond 0.04892 (11430) covalent geometry : angle 4.16071 (15690) Misc. bond : bond 0.11243 ( 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 308 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 277 time to evaluate : 1.148 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: A 11 ILE cc_start: 0.9562 (tt) cc_final: 0.9290 (pp) REVERT: A 50 TYR cc_start: 0.9005 (t80) cc_final: 0.8631 (t80) REVERT: A 70 ARG cc_start: 0.8871 (mmm160) cc_final: 0.8268 (mmm160) REVERT: A 76 GLU cc_start: 0.9461 (mm-30) cc_final: 0.9123 (mp0) REVERT: A 118 TYR cc_start: 0.8991 (m-80) cc_final: 0.8679 (m-80) REVERT: A 163 SER cc_start: 0.8987 (m) cc_final: 0.8699 (p) REVERT: A 175 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8129 (mp0) REVERT: A 213 GLU cc_start: 0.9335 (mt-10) cc_final: 0.8585 (mt-10) REVERT: A 214 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8854 (mpt) REVERT: C 76 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.8946 (mp0) REVERT: C 158 LYS cc_start: 0.8879 (mmmt) cc_final: 0.8659 (mmmt) REVERT: C 163 SER cc_start: 0.9015 (m) cc_final: 0.8662 (p) REVERT: C 170 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8781 (ttmt) REVERT: E 11 ILE cc_start: 0.9528 (tt) cc_final: 0.9240 (pp) REVERT: E 50 TYR cc_start: 0.9038 (t80) cc_final: 0.8821 (t80) REVERT: E 76 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8648 (mp0) REVERT: E 97 ASP cc_start: 0.9075 (t0) cc_final: 0.8692 (OUTLIER) REVERT: E 163 SER cc_start: 0.9102 (m) cc_final: 0.8864 (p) REVERT: E 175 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8300 (mm-30) REVERT: E 182 LYS cc_start: 0.9375 (ptpp) cc_final: 0.9138 (pttp) REVERT: E 213 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8528 (pm20) REVERT: E 214 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8815 (mpt) REVERT: G 11 ILE cc_start: 0.9570 (tt) cc_final: 0.9300 (pp) REVERT: G 50 TYR cc_start: 0.8994 (t80) cc_final: 0.8615 (t80) REVERT: G 70 ARG cc_start: 0.8857 (mmm160) cc_final: 0.8244 (mmm160) REVERT: G 76 GLU cc_start: 0.9456 (mm-30) cc_final: 0.9118 (mp0) REVERT: G 118 TYR cc_start: 0.9002 (m-80) cc_final: 0.8706 (m-80) REVERT: G 163 SER cc_start: 0.8990 (m) cc_final: 0.8701 (p) REVERT: G 175 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8139 (mp0) REVERT: G 213 GLU cc_start: 0.9331 (mt-10) cc_final: 0.8578 (mt-10) REVERT: G 214 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8861 (mpt) REVERT: I 11 ILE cc_start: 0.9537 (tt) cc_final: 0.9300 (pp) REVERT: I 163 SER cc_start: 0.8971 (m) cc_final: 0.8619 (p) REVERT: I 170 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8692 (ttmt) REVERT: I 182 LYS cc_start: 0.9385 (ptpp) cc_final: 0.9012 (pttt) REVERT: I 214 MET cc_start: 0.9356 (mtp) cc_final: 0.8889 (mpt) REVERT: K 11 ILE cc_start: 0.9546 (tt) cc_final: 0.9259 (pp) REVERT: K 50 TYR cc_start: 0.9038 (t80) cc_final: 0.8817 (t80) REVERT: K 70 ARG cc_start: 0.9013 (mmm160) cc_final: 0.8275 (mmm160) REVERT: K 76 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8632 (mp0) REVERT: K 97 ASP cc_start: 0.9080 (t0) cc_final: 0.8699 (OUTLIER) REVERT: K 163 SER cc_start: 0.9103 (m) cc_final: 0.8863 (p) REVERT: K 175 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8269 (mm-30) REVERT: K 182 LYS cc_start: 0.9375 (ptpp) cc_final: 0.9101 (pttp) REVERT: K 212 GLU cc_start: 0.9217 (pm20) cc_final: 0.8913 (pm20) REVERT: K 213 GLU cc_start: 0.9002 (pt0) cc_final: 0.8618 (pm20) REVERT: K 214 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8689 (mpp) outliers start: 31 outliers final: 14 residues processed: 293 average time/residue: 1.5450 time to fit residues: 479.7301 Evaluate side-chains 276 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 255 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 50 TYR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 ARG 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: 4.9990 chunk 100 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 3 optimal weight: 0.0010 chunk 40 optimal weight: 7.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 12 HIS K 12 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.076871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.054860 restraints weight = 33063.632| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.32 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.7446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.993 11460 Z= 2.488 Angle : 4.154 99.761 15702 Z= 1.424 Chirality : 0.341 4.313 1698 Planarity : 0.005 0.045 1986 Dihedral : 29.392 178.695 1968 Min Nonbonded Distance : 1.410 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.31 % Allowed : 25.30 % 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: 1.45 (0.24), residues: 1350 helix: 1.49 (0.18), residues: 876 sheet: -1.73 (0.40), residues: 54 loop : 0.42 (0.35), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 23 HIS 0.003 0.001 HIS I 62 PHE 0.010 0.002 PHE D 7 TYR 0.027 0.003 TYR I 118 ARG 0.014 0.001 ARG I 18 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 642) hydrogen bonds : angle 4.68189 ( 1890) SS BOND : bond 0.00165 ( 6) SS BOND : angle 2.74135 ( 12) covalent geometry : bond 0.04882 (11430) covalent geometry : angle 4.15519 (15690) Misc. bond : bond 0.11236 ( 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 293 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 266 time to evaluate : 1.201 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: A 11 ILE cc_start: 0.9528 (tt) cc_final: 0.9214 (pp) REVERT: A 50 TYR cc_start: 0.8942 (t80) cc_final: 0.8682 (t80) REVERT: A 70 ARG cc_start: 0.8899 (mmm160) cc_final: 0.8307 (mmm160) REVERT: A 76 GLU cc_start: 0.9480 (mm-30) cc_final: 0.9142 (mp0) REVERT: A 118 TYR cc_start: 0.8874 (m-80) cc_final: 0.8589 (m-80) REVERT: A 163 SER cc_start: 0.9016 (m) cc_final: 0.8764 (p) REVERT: A 175 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8085 (mp0) REVERT: A 182 LYS cc_start: 0.9491 (ptmt) cc_final: 0.9236 (ptpt) REVERT: A 214 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8854 (mpt) REVERT: C 76 GLU cc_start: 0.9295 (mp0) cc_final: 0.9064 (mp0) REVERT: C 158 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8667 (mmmt) REVERT: C 163 SER cc_start: 0.9066 (m) cc_final: 0.8736 (p) REVERT: C 170 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8749 (ttmt) REVERT: C 175 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8257 (tm-30) REVERT: C 182 LYS cc_start: 0.9425 (ptpp) cc_final: 0.9024 (pttt) REVERT: C 203 LYS cc_start: 0.9527 (mppt) cc_final: 0.9230 (pmmt) REVERT: E 11 ILE cc_start: 0.9512 (tt) cc_final: 0.9213 (pp) REVERT: E 45 GLU cc_start: 0.9252 (mm-30) cc_final: 0.9005 (mm-30) REVERT: E 50 TYR cc_start: 0.8990 (t80) cc_final: 0.8715 (t80) REVERT: E 76 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8749 (mp0) REVERT: E 154 LYS cc_start: 0.8827 (mmmt) cc_final: 0.8578 (mmmt) REVERT: E 163 SER cc_start: 0.9094 (m) cc_final: 0.8865 (p) REVERT: E 175 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8283 (mm-30) REVERT: E 182 LYS cc_start: 0.9333 (ptpp) cc_final: 0.9094 (pttp) REVERT: E 213 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8623 (pm20) REVERT: E 214 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.8845 (mpt) REVERT: G 11 ILE cc_start: 0.9521 (tt) cc_final: 0.9205 (pp) REVERT: G 50 TYR cc_start: 0.8928 (t80) cc_final: 0.8665 (t80) REVERT: G 70 ARG cc_start: 0.8893 (mmm160) cc_final: 0.8295 (mmm160) REVERT: G 76 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9140 (mp0) REVERT: G 118 TYR cc_start: 0.8902 (m-80) cc_final: 0.8577 (m-80) REVERT: G 163 SER cc_start: 0.9025 (m) cc_final: 0.8771 (p) REVERT: G 175 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8290 (mt-10) REVERT: G 182 LYS cc_start: 0.9488 (ptmt) cc_final: 0.9233 (ptpt) REVERT: G 214 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8821 (mpt) REVERT: I 50 TYR cc_start: 0.8803 (t80) cc_final: 0.8599 (t80) REVERT: I 70 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8744 (mtp85) REVERT: I 163 SER cc_start: 0.9053 (m) cc_final: 0.8731 (p) REVERT: I 170 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8788 (ttmt) REVERT: I 182 LYS cc_start: 0.9321 (ptpp) cc_final: 0.9055 (pttt) REVERT: K 11 ILE cc_start: 0.9519 (tt) cc_final: 0.9196 (pp) REVERT: K 18 ARG cc_start: 0.8880 (ppp80) cc_final: 0.8641 (ptm-80) REVERT: K 50 TYR cc_start: 0.8987 (t80) cc_final: 0.8709 (t80) REVERT: K 70 ARG cc_start: 0.9026 (mmm160) cc_final: 0.8352 (mmm160) REVERT: K 76 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8698 (mp0) REVERT: K 154 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8689 (mmmt) REVERT: K 163 SER cc_start: 0.9083 (m) cc_final: 0.8854 (p) REVERT: K 175 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8239 (mm-30) REVERT: K 182 LYS cc_start: 0.9343 (ptpp) cc_final: 0.9096 (pttp) REVERT: K 214 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8716 (mpp) outliers start: 27 outliers final: 11 residues processed: 279 average time/residue: 1.6262 time to fit residues: 479.5668 Evaluate side-chains 283 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 263 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 170 LYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 ARG 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 61 ASP 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: 4.9990 chunk 3 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN K 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.076603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.054047 restraints weight = 33710.156| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.39 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.7659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.984 11460 Z= 2.487 Angle : 4.170 99.303 15702 Z= 1.434 Chirality : 0.341 4.261 1698 Planarity : 0.005 0.055 1986 Dihedral : 29.424 178.688 1968 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.79 % Allowed : 25.64 % Favored : 72.56 % 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: 1.46 (0.24), residues: 1350 helix: 1.49 (0.18), residues: 876 sheet: -2.04 (0.38), residues: 54 loop : 0.47 (0.36), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 80 HIS 0.014 0.002 HIS I 62 PHE 0.012 0.002 PHE D 7 TYR 0.028 0.003 TYR C 118 ARG 0.013 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04591 ( 642) hydrogen bonds : angle 4.87363 ( 1890) SS BOND : bond 0.00296 ( 6) SS BOND : angle 3.11322 ( 12) covalent geometry : bond 0.04884 (11430) covalent geometry : angle 4.17067 (15690) Misc. bond : bond 0.11183 ( 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 286 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 265 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.9037 (t80) cc_final: 0.8619 (t80) REVERT: A 70 ARG cc_start: 0.8890 (mmm160) cc_final: 0.8265 (mmm160) REVERT: A 76 GLU cc_start: 0.9480 (mm-30) cc_final: 0.9149 (mp0) REVERT: A 163 SER cc_start: 0.9139 (m) cc_final: 0.8933 (p) REVERT: A 175 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8268 (mt-10) REVERT: A 182 LYS cc_start: 0.9534 (ptmt) cc_final: 0.9258 (ptpt) REVERT: A 203 LYS cc_start: 0.9538 (mppt) cc_final: 0.9272 (pmmt) REVERT: A 213 GLU cc_start: 0.9327 (mt-10) cc_final: 0.8575 (mt-10) REVERT: A 214 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8694 (mpt) REVERT: C 45 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8723 (mm-30) REVERT: C 50 TYR cc_start: 0.8885 (t80) cc_final: 0.8656 (t80) REVERT: C 158 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8599 (mmmt) REVERT: C 163 SER cc_start: 0.9251 (m) cc_final: 0.8907 (p) REVERT: C 170 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8862 (ttmt) REVERT: C 182 LYS cc_start: 0.9429 (ptpp) cc_final: 0.9085 (pttt) REVERT: C 203 LYS cc_start: 0.9541 (mppt) cc_final: 0.9253 (pmmt) REVERT: E 11 ILE cc_start: 0.9527 (tt) cc_final: 0.9232 (pp) REVERT: E 50 TYR cc_start: 0.9045 (t80) cc_final: 0.8803 (t80) REVERT: E 76 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8646 (mp0) REVERT: E 97 ASP cc_start: 0.9116 (t0) cc_final: 0.8729 (OUTLIER) REVERT: E 154 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8498 (mmmt) REVERT: E 163 SER cc_start: 0.9227 (m) cc_final: 0.9012 (p) REVERT: E 175 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8242 (mm-30) REVERT: E 182 LYS cc_start: 0.9371 (ptpp) cc_final: 0.9100 (pttp) REVERT: E 212 GLU cc_start: 0.9275 (pm20) cc_final: 0.8949 (pm20) REVERT: E 213 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8568 (pm20) REVERT: E 214 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8879 (mpt) REVERT: G 18 ARG cc_start: 0.8909 (ppp80) cc_final: 0.8577 (ptm160) REVERT: G 50 TYR cc_start: 0.9033 (t80) cc_final: 0.8614 (t80) REVERT: G 70 ARG cc_start: 0.8891 (mmm160) cc_final: 0.8335 (mmm160) REVERT: G 76 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9148 (mp0) REVERT: G 163 SER cc_start: 0.9139 (m) cc_final: 0.8933 (p) REVERT: G 175 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8490 (tm-30) REVERT: G 182 LYS cc_start: 0.9529 (ptmt) cc_final: 0.9259 (ptpt) REVERT: G 203 LYS cc_start: 0.9542 (mppt) cc_final: 0.9277 (pmmt) REVERT: G 213 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8560 (mt-10) REVERT: G 214 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8702 (mpt) REVERT: I 45 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8717 (mm-30) REVERT: I 70 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8639 (mtp85) REVERT: I 152 ASP cc_start: 0.9144 (m-30) cc_final: 0.8735 (p0) REVERT: I 163 SER cc_start: 0.9199 (m) cc_final: 0.8859 (p) REVERT: I 170 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8852 (ttmt) REVERT: I 182 LYS cc_start: 0.9309 (ptpp) cc_final: 0.9077 (pttm) REVERT: I 214 MET cc_start: 0.9270 (mtt) cc_final: 0.8867 (mpt) REVERT: K 11 ILE cc_start: 0.9543 (tt) cc_final: 0.9236 (pp) REVERT: K 18 ARG cc_start: 0.9047 (ppp80) cc_final: 0.8822 (ptm160) REVERT: K 70 ARG cc_start: 0.9025 (mmm160) cc_final: 0.8298 (mmm160) REVERT: K 76 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8615 (mp0) REVERT: K 97 ASP cc_start: 0.9113 (t0) cc_final: 0.8728 (OUTLIER) REVERT: K 152 ASP cc_start: 0.9110 (m-30) cc_final: 0.8741 (p0) REVERT: K 163 SER cc_start: 0.9233 (m) cc_final: 0.9022 (p) REVERT: K 175 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8269 (mm-30) REVERT: K 182 LYS cc_start: 0.9376 (ptpp) cc_final: 0.9118 (pttp) REVERT: K 212 GLU cc_start: 0.9239 (pm20) cc_final: 0.9015 (pm20) REVERT: K 213 GLU cc_start: 0.9070 (pt0) cc_final: 0.8724 (pm20) REVERT: K 214 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8725 (mpp) outliers start: 21 outliers final: 11 residues processed: 274 average time/residue: 1.7182 time to fit residues: 496.5397 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 : 1.195 ------------------------------------------------------------------------------- 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 170 LYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 76 GLU 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 61 ASP 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 108 optimal weight: 0.0270 chunk 117 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.076567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.054413 restraints weight = 32750.065| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 4.32 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 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 = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.7755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.981 11460 Z= 2.467 Angle : 4.199 98.660 15702 Z= 1.444 Chirality : 0.329 4.194 1698 Planarity : 0.005 0.062 1986 Dihedral : 29.224 178.527 1968 Min Nonbonded Distance : 1.383 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.62 % Allowed : 26.24 % 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: 1.49 (0.24), residues: 1350 helix: 1.49 (0.18), residues: 876 sheet: -1.84 (0.37), residues: 54 loop : 0.52 (0.36), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 23 HIS 0.005 0.001 HIS I 62 PHE 0.008 0.001 PHE A 161 TYR 0.031 0.003 TYR I 50 ARG 0.012 0.001 ARG I 18 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 642) hydrogen bonds : angle 4.75431 ( 1890) SS BOND : bond 0.00131 ( 6) SS BOND : angle 2.70300 ( 12) covalent geometry : bond 0.04842 (11430) covalent geometry : angle 4.19980 (15690) Misc. bond : bond 0.11033 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8760.17 seconds wall clock time: 151 minutes 15.35 seconds (9075.35 seconds total)