Starting phenix.real_space_refine on Sun Mar 24 14:56:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdz_17627/03_2024/8pdz_17627.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdz_17627/03_2024/8pdz_17627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdz_17627/03_2024/8pdz_17627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdz_17627/03_2024/8pdz_17627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdz_17627/03_2024/8pdz_17627.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdz_17627/03_2024/8pdz_17627.pdb" } resolution = 3.32 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= 0.004 sd= 0.020 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 S 252 5.16 5 C 13804 2.51 5 N 3640 2.21 5 O 4592 1.98 5 H 20272 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 42560 Number of models: 1 Model: "" Number of chains: 28 Chain: "R" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "Q" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "P" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "O" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "U" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "T" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "S" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "V" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "W" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "X" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "Y" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "Z" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "a" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "b" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "H" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "I" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "J" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "K" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "L" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "M" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "N" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "A" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "B" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "C" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "D" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "E" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "F" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "G" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Time building chain proxies: 18.53, per 1000 atoms: 0.44 Number of scatterers: 42560 At special positions: 0 Unit cell: (87.86, 89.388, 220.032, 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 252 16.00 O 4592 8.00 N 3640 7.00 C 13804 6.00 H 20272 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=77, symmetry=0 Simple disulfide: pdb=" SG CYS R 8 " - pdb=" SG CYS L 21 " distance=2.01 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS S 15 " distance=2.18 Simple disulfide: pdb=" SG CYS R 15 " - pdb=" SG CYS Q 14 " distance=1.83 Simple disulfide: pdb=" SG CYS R 21 " - pdb=" SG CYS X 8 " distance=2.43 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS S 82 " distance=2.05 Simple disulfide: pdb=" SG CYS R 82 " - pdb=" SG CYS Q 22 " distance=2.26 Simple disulfide: pdb=" SG CYS Q 8 " - pdb=" SG CYS K 21 " distance=2.27 Simple disulfide: pdb=" SG CYS Q 15 " - pdb=" SG CYS P 14 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 21 " - pdb=" SG CYS W 8 " distance=1.86 Simple disulfide: pdb=" SG CYS Q 82 " - pdb=" SG CYS P 22 " distance=1.92 Simple disulfide: pdb=" SG CYS P 8 " - pdb=" SG CYS J 21 " distance=1.90 Simple disulfide: pdb=" SG CYS P 15 " - pdb=" SG CYS O 14 " distance=2.19 Simple disulfide: pdb=" SG CYS P 21 " - pdb=" SG CYS V 8 " distance=1.98 Simple disulfide: pdb=" SG CYS P 82 " - pdb=" SG CYS O 22 " distance=1.82 Simple disulfide: pdb=" SG CYS O 8 " - pdb=" SG CYS I 21 " distance=2.16 Simple disulfide: pdb=" SG CYS O 15 " - pdb=" SG CYS U 14 " distance=1.97 Simple disulfide: pdb=" SG CYS O 21 " - pdb=" SG CYS b 8 " distance=2.09 Simple disulfide: pdb=" SG CYS O 82 " - pdb=" SG CYS U 22 " distance=2.04 Simple disulfide: pdb=" SG CYS U 8 " - pdb=" SG CYS H 21 " distance=2.25 Simple disulfide: pdb=" SG CYS U 15 " - pdb=" SG CYS T 14 " distance=1.97 Simple disulfide: pdb=" SG CYS U 21 " - pdb=" SG CYS a 8 " distance=2.12 Simple disulfide: pdb=" SG CYS U 82 " - pdb=" SG CYS T 22 " distance=2.12 Simple disulfide: pdb=" SG CYS T 8 " - pdb=" SG CYS N 21 " distance=1.76 Simple disulfide: pdb=" SG CYS T 15 " - pdb=" SG CYS S 14 " distance=2.07 Simple disulfide: pdb=" SG CYS T 21 " - pdb=" SG CYS Z 8 " distance=2.00 Simple disulfide: pdb=" SG CYS T 82 " - pdb=" SG CYS S 22 " distance=1.84 Simple disulfide: pdb=" SG CYS S 8 " - pdb=" SG CYS M 21 " distance=2.07 Simple disulfide: pdb=" SG CYS S 21 " - pdb=" SG CYS Y 8 " distance=2.14 Simple disulfide: pdb=" SG CYS V 14 " - pdb=" SG CYS W 15 " distance=2.03 Simple disulfide: pdb=" SG CYS V 15 " - pdb=" SG CYS b 14 " distance=1.93 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS W 82 " distance=1.86 Simple disulfide: pdb=" SG CYS V 82 " - pdb=" SG CYS b 22 " distance=1.94 Simple disulfide: pdb=" SG CYS W 14 " - pdb=" SG CYS X 15 " distance=2.04 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS X 82 " distance=2.08 Simple disulfide: pdb=" SG CYS X 14 " - pdb=" SG CYS Y 15 " distance=2.18 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS Y 82 " distance=2.06 Simple disulfide: pdb=" SG CYS Y 14 " - pdb=" SG CYS Z 15 " distance=1.86 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Z 82 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 14 " - pdb=" SG CYS a 15 " distance=1.80 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS a 82 " distance=2.13 Simple disulfide: pdb=" SG CYS a 14 " - pdb=" SG CYS b 15 " distance=1.84 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS b 82 " distance=2.27 Simple disulfide: pdb=" SG CYS H 8 " - pdb=" SG CYS B 21 " distance=1.91 Simple disulfide: pdb=" SG CYS H 14 " - pdb=" SG CYS I 15 " distance=2.11 Simple disulfide: pdb=" SG CYS H 15 " - pdb=" SG CYS N 14 " distance=1.95 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS I 82 " distance=1.77 Simple disulfide: pdb=" SG CYS H 82 " - pdb=" SG CYS N 22 " distance=2.28 Simple disulfide: pdb=" SG CYS I 8 " - pdb=" SG CYS C 21 " distance=2.19 Simple disulfide: pdb=" SG CYS I 14 " - pdb=" SG CYS J 15 " distance=2.36 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS J 82 " distance=1.71 Simple disulfide: pdb=" SG CYS J 8 " - pdb=" SG CYS D 21 " distance=1.89 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS K 15 " distance=2.00 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS K 82 " distance=2.18 Simple disulfide: pdb=" SG CYS K 8 " - pdb=" SG CYS E 21 " distance=1.92 Simple disulfide: pdb=" SG CYS K 14 " - pdb=" SG CYS L 15 " distance=2.26 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS L 82 " distance=1.71 Simple disulfide: pdb=" SG CYS L 8 " - pdb=" SG CYS F 21 " distance=2.20 Simple disulfide: pdb=" SG CYS L 14 " - pdb=" SG CYS M 15 " distance=1.99 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS M 82 " distance=1.93 Simple disulfide: pdb=" SG CYS M 8 " - pdb=" SG CYS G 21 " distance=1.64 Simple disulfide: pdb=" SG CYS M 14 " - pdb=" SG CYS N 15 " distance=1.74 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS N 82 " distance=2.46 Simple disulfide: pdb=" SG CYS N 8 " - pdb=" SG CYS A 21 " distance=1.89 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 15 " distance=1.98 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS G 14 " distance=1.84 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS B 82 " distance=2.16 Simple disulfide: pdb=" SG CYS A 82 " - pdb=" SG CYS G 22 " distance=2.49 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS C 15 " distance=2.28 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS C 82 " distance=1.87 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 15 " distance=2.66 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS D 82 " distance=1.80 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS E 15 " distance=2.05 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS E 82 " distance=1.95 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 15 " distance=1.73 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS F 82 " distance=2.33 Simple disulfide: pdb=" SG CYS F 14 " - pdb=" SG CYS G 15 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS G 82 " distance=1.87 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 32.12 Conformation dependent library (CDL) restraints added in 4.8 seconds 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5544 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 28 sheets defined 0.0% alpha, 54.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'R' and resid 4 through 5 removed outlier: 3.767A pdb=" N THR L 48 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU L 81 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N LEU K 34 " --> pdb=" O CYS L 82 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N SER L 84 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE K 36 " --> pdb=" O SER L 84 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR L 86 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP K 38 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N ASN L 88 " --> pdb=" O ASP K 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE K 93 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU K 65 " --> pdb=" O PHE K 75 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE K 75 " --> pdb=" O LEU K 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL K 67 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY K 73 " --> pdb=" O VAL K 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 70 through 77 removed outlier: 8.690A pdb=" N GLY Q 73 " --> pdb=" O VAL Q 67 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL Q 67 " --> pdb=" O GLY Q 73 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE Q 75 " --> pdb=" O LEU Q 65 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU Q 65 " --> pdb=" O PHE Q 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE Q 93 " --> pdb=" O ILE Q 36 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N CYS R 82 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE Q 36 " --> pdb=" O CYS R 82 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU R 81 " --> pdb=" O ASN R 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR R 48 " --> pdb=" O SER R 110 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE X 5 " --> pdb=" O ASN R 17 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA R 19 " --> pdb=" O ILE X 5 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 70 through 77 removed outlier: 8.691A pdb=" N GLY R 73 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL R 67 " --> pdb=" O GLY R 73 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE R 75 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU R 65 " --> pdb=" O PHE R 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE R 93 " --> pdb=" O ILE R 36 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N LEU R 34 " --> pdb=" O CYS S 82 " (cutoff:3.500A) removed outlier: 9.580A pdb=" N SER S 84 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE R 36 " --> pdb=" O SER S 84 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N THR S 86 " --> pdb=" O ILE R 36 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP R 38 " --> pdb=" O THR S 86 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N ASN S 88 " --> pdb=" O ASP R 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU S 81 " --> pdb=" O ASN S 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR S 48 " --> pdb=" O SER S 110 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE Y 5 " --> pdb=" O ASN S 17 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA S 19 " --> pdb=" O ILE Y 5 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 4 through 5 removed outlier: 3.700A pdb=" N CYS K 21 " --> pdb=" O ILE Q 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR K 48 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU K 81 " --> pdb=" O ASN K 53 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N LEU J 34 " --> pdb=" O CYS K 82 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N SER K 84 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE J 36 " --> pdb=" O SER K 84 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N THR K 86 " --> pdb=" O ILE J 36 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP J 38 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N ASN K 88 " --> pdb=" O ASP J 38 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE J 93 " --> pdb=" O ILE J 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU J 65 " --> pdb=" O PHE J 75 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE J 75 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL J 67 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY J 73 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 70 through 77 removed outlier: 8.691A pdb=" N GLY P 73 " --> pdb=" O VAL P 67 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL P 67 " --> pdb=" O GLY P 73 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE P 75 " --> pdb=" O LEU P 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU P 65 " --> pdb=" O PHE P 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE P 93 " --> pdb=" O ILE P 36 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N CYS Q 82 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE P 36 " --> pdb=" O CYS Q 82 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU Q 81 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR Q 48 " --> pdb=" O SER Q 110 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE W 5 " --> pdb=" O ASN Q 17 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA Q 19 " --> pdb=" O ILE W 5 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 4 through 5 removed outlier: 3.556A pdb=" N CYS J 21 " --> pdb=" O ILE P 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR J 48 " --> pdb=" O SER J 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU J 81 " --> pdb=" O ASN J 53 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N LEU I 34 " --> pdb=" O CYS J 82 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N SER J 84 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE I 36 " --> pdb=" O SER J 84 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N THR J 86 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASP I 38 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N ASN J 88 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE I 93 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU I 65 " --> pdb=" O PHE I 75 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE I 75 " --> pdb=" O LEU I 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL I 67 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY I 73 " --> pdb=" O VAL I 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 70 through 77 removed outlier: 8.691A pdb=" N GLY O 73 " --> pdb=" O VAL O 67 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL O 67 " --> pdb=" O GLY O 73 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE O 75 " --> pdb=" O LEU O 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU O 65 " --> pdb=" O PHE O 75 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE O 93 " --> pdb=" O ILE O 36 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N CYS P 82 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE O 36 " --> pdb=" O CYS P 82 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP O 38 " --> pdb=" O SER P 84 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR P 86 " --> pdb=" O ASP O 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU P 81 " --> pdb=" O ASN P 53 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR P 48 " --> pdb=" O SER P 110 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE V 5 " --> pdb=" O ASN P 17 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA P 19 " --> pdb=" O ILE V 5 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 4 through 5 removed outlier: 3.516A pdb=" N CYS I 21 " --> pdb=" O ILE O 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR I 48 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU I 81 " --> pdb=" O ASN I 53 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N LEU H 34 " --> pdb=" O CYS I 82 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N SER I 84 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE H 36 " --> pdb=" O SER I 84 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N THR I 86 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASP H 38 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N ASN I 88 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE H 93 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 65 " --> pdb=" O PHE H 75 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE H 75 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL H 67 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY H 73 " --> pdb=" O VAL H 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 70 through 77 removed outlier: 8.691A pdb=" N GLY U 73 " --> pdb=" O VAL U 67 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL U 67 " --> pdb=" O GLY U 73 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE U 75 " --> pdb=" O LEU U 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU U 65 " --> pdb=" O PHE U 75 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE U 93 " --> pdb=" O ILE U 36 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N CYS O 82 " --> pdb=" O LEU U 34 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE U 36 " --> pdb=" O CYS O 82 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP U 38 " --> pdb=" O SER O 84 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR O 86 " --> pdb=" O ASP U 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU O 81 " --> pdb=" O ASN O 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR O 48 " --> pdb=" O SER O 110 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE b 5 " --> pdb=" O ASN O 17 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA O 19 " --> pdb=" O ILE b 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 4 through 5 removed outlier: 3.542A pdb=" N CYS H 21 " --> pdb=" O ILE U 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR H 48 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU H 81 " --> pdb=" O ASN H 53 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N CYS H 82 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE N 36 " --> pdb=" O CYS H 82 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE N 93 " --> pdb=" O ILE N 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU N 65 " --> pdb=" O PHE N 75 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE N 75 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL N 67 " --> pdb=" O GLY N 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY N 73 " --> pdb=" O VAL N 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 70 through 77 removed outlier: 8.690A pdb=" N GLY T 73 " --> pdb=" O VAL T 67 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL T 67 " --> pdb=" O GLY T 73 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE T 75 " --> pdb=" O LEU T 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU T 65 " --> pdb=" O PHE T 75 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE T 93 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N CYS U 82 " --> pdb=" O LEU T 34 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE T 36 " --> pdb=" O CYS U 82 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP T 38 " --> pdb=" O SER U 84 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR U 86 " --> pdb=" O ASP T 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU U 81 " --> pdb=" O ASN U 53 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR U 48 " --> pdb=" O SER U 110 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE a 5 " --> pdb=" O ASN U 17 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA U 19 " --> pdb=" O ILE a 5 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 4 through 5 removed outlier: 3.658A pdb=" N CYS N 21 " --> pdb=" O ILE T 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR N 48 " --> pdb=" O SER N 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU N 81 " --> pdb=" O ASN N 53 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N LEU M 34 " --> pdb=" O CYS N 82 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N SER N 84 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE M 36 " --> pdb=" O SER N 84 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N THR N 86 " --> pdb=" O ILE M 36 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP M 38 " --> pdb=" O THR N 86 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N ASN N 88 " --> pdb=" O ASP M 38 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE M 93 " --> pdb=" O ILE M 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU M 65 " --> pdb=" O PHE M 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE M 75 " --> pdb=" O LEU M 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL M 67 " --> pdb=" O GLY M 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY M 73 " --> pdb=" O VAL M 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 70 through 77 removed outlier: 8.690A pdb=" N GLY S 73 " --> pdb=" O VAL S 67 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL S 67 " --> pdb=" O GLY S 73 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE S 75 " --> pdb=" O LEU S 65 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU S 65 " --> pdb=" O PHE S 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE S 93 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N CYS T 82 " --> pdb=" O LEU S 34 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE S 36 " --> pdb=" O CYS T 82 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP S 38 " --> pdb=" O SER T 84 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR T 86 " --> pdb=" O ASP S 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU T 81 " --> pdb=" O ASN T 53 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR T 48 " --> pdb=" O SER T 110 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE Z 5 " --> pdb=" O ASN T 17 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA T 19 " --> pdb=" O ILE Z 5 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 4 through 5 removed outlier: 3.535A pdb=" N CYS M 21 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR M 48 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU M 81 " --> pdb=" O ASN M 53 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N LEU L 34 " --> pdb=" O CYS M 82 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N SER M 84 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE L 36 " --> pdb=" O SER M 84 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N THR M 86 " --> pdb=" O ILE L 36 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASP L 38 " --> pdb=" O THR M 86 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N ASN M 88 " --> pdb=" O ASP L 38 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE L 93 " --> pdb=" O ILE L 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU L 65 " --> pdb=" O PHE L 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE L 75 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL L 67 " --> pdb=" O GLY L 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY L 73 " --> pdb=" O VAL L 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'V' and resid 14 through 26 removed outlier: 3.768A pdb=" N THR V 48 " --> pdb=" O SER V 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU V 81 " --> pdb=" O ASN V 53 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N CYS V 82 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE b 36 " --> pdb=" O CYS V 82 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE b 93 " --> pdb=" O ILE b 36 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU b 65 " --> pdb=" O PHE b 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE b 75 " --> pdb=" O LEU b 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL b 67 " --> pdb=" O GLY b 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY b 73 " --> pdb=" O VAL b 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'V' and resid 70 through 77 removed outlier: 8.691A pdb=" N GLY V 73 " --> pdb=" O VAL V 67 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL V 67 " --> pdb=" O GLY V 73 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE V 75 " --> pdb=" O LEU V 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU V 65 " --> pdb=" O PHE V 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE V 93 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N LEU V 34 " --> pdb=" O CYS W 82 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N SER W 84 " --> pdb=" O LEU V 34 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE V 36 " --> pdb=" O SER W 84 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR W 86 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP V 38 " --> pdb=" O THR W 86 " (cutoff:3.500A) removed outlier: 9.382A pdb=" N ASN W 88 " --> pdb=" O ASP V 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU W 81 " --> pdb=" O ASN W 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR W 48 " --> pdb=" O SER W 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'W' and resid 70 through 77 removed outlier: 8.691A pdb=" N GLY W 73 " --> pdb=" O VAL W 67 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL W 67 " --> pdb=" O GLY W 73 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE W 75 " --> pdb=" O LEU W 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU W 65 " --> pdb=" O PHE W 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE W 93 " --> pdb=" O ILE W 36 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LEU W 34 " --> pdb=" O CYS X 82 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N SER X 84 " --> pdb=" O LEU W 34 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE W 36 " --> pdb=" O SER X 84 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR X 86 " --> pdb=" O ILE W 36 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP W 38 " --> pdb=" O THR X 86 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N ASN X 88 " --> pdb=" O ASP W 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU X 81 " --> pdb=" O ASN X 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR X 48 " --> pdb=" O SER X 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 70 through 77 removed outlier: 8.690A pdb=" N GLY X 73 " --> pdb=" O VAL X 67 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL X 67 " --> pdb=" O GLY X 73 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE X 75 " --> pdb=" O LEU X 65 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU X 65 " --> pdb=" O PHE X 75 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE X 93 " --> pdb=" O ILE X 36 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N LEU X 34 " --> pdb=" O CYS Y 82 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N SER Y 84 " --> pdb=" O LEU X 34 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE X 36 " --> pdb=" O SER Y 84 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N THR Y 86 " --> pdb=" O ILE X 36 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ASP X 38 " --> pdb=" O THR Y 86 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N ASN Y 88 " --> pdb=" O ASP X 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU Y 81 " --> pdb=" O ASN Y 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR Y 48 " --> pdb=" O SER Y 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 70 through 77 removed outlier: 8.691A pdb=" N GLY Y 73 " --> pdb=" O VAL Y 67 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL Y 67 " --> pdb=" O GLY Y 73 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE Y 75 " --> pdb=" O LEU Y 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Y 65 " --> pdb=" O PHE Y 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE Y 93 " --> pdb=" O ILE Y 36 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N LEU Y 34 " --> pdb=" O CYS Z 82 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N SER Z 84 " --> pdb=" O LEU Y 34 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE Y 36 " --> pdb=" O SER Z 84 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N THR Z 86 " --> pdb=" O ILE Y 36 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP Y 38 " --> pdb=" O THR Z 86 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N ASN Z 88 " --> pdb=" O ASP Y 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU Z 81 " --> pdb=" O ASN Z 53 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR Z 48 " --> pdb=" O SER Z 110 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Z' and resid 70 through 77 removed outlier: 8.690A pdb=" N GLY Z 73 " --> pdb=" O VAL Z 67 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL Z 67 " --> pdb=" O GLY Z 73 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE Z 75 " --> pdb=" O LEU Z 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Z 65 " --> pdb=" O PHE Z 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE Z 93 " --> pdb=" O ILE Z 36 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N LEU Z 34 " --> pdb=" O CYS a 82 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N SER a 84 " --> pdb=" O LEU Z 34 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE Z 36 " --> pdb=" O SER a 84 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N THR a 86 " --> pdb=" O ILE Z 36 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP Z 38 " --> pdb=" O THR a 86 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N ASN a 88 " --> pdb=" O ASP Z 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU a 81 " --> pdb=" O ASN a 53 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR a 48 " --> pdb=" O SER a 110 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'a' and resid 70 through 77 removed outlier: 8.690A pdb=" N GLY a 73 " --> pdb=" O VAL a 67 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL a 67 " --> pdb=" O GLY a 73 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE a 75 " --> pdb=" O LEU a 65 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU a 65 " --> pdb=" O PHE a 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE a 93 " --> pdb=" O ILE a 36 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N LEU a 34 " --> pdb=" O CYS b 82 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N SER b 84 " --> pdb=" O LEU a 34 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE a 36 " --> pdb=" O SER b 84 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N THR b 86 " --> pdb=" O ILE a 36 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASP a 38 " --> pdb=" O THR b 86 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N ASN b 88 " --> pdb=" O ASP a 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU b 81 " --> pdb=" O ASN b 53 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR b 48 " --> pdb=" O SER b 110 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.707A pdb=" N CYS B 21 " --> pdb=" O ILE H 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR B 48 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 81 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N LEU A 34 " --> pdb=" O CYS B 82 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N SER B 84 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE A 36 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N THR B 86 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP A 38 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N ASN B 88 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 93 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 65 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE A 75 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL A 67 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY A 73 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.767A pdb=" N THR C 48 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 81 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N LEU B 34 " --> pdb=" O CYS C 82 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N SER C 84 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B 36 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N THR C 86 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASP B 38 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 9.435A pdb=" N ASN C 88 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE B 93 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 65 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE B 75 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL B 67 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY B 73 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 4 through 5 removed outlier: 3.560A pdb=" N CYS D 21 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D 48 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 81 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N LEU C 34 " --> pdb=" O CYS D 82 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N SER D 84 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE C 36 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N THR D 86 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASP C 38 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N ASN D 88 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE C 93 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 65 " --> pdb=" O PHE C 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE C 75 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL C 67 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY C 73 " --> pdb=" O VAL C 67 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 4 through 5 removed outlier: 3.768A pdb=" N THR E 48 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU E 81 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N LEU D 34 " --> pdb=" O CYS E 82 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N SER E 84 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE D 36 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N THR E 86 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP D 38 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 88 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE D 93 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 65 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE D 75 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL D 67 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY D 73 " --> pdb=" O VAL D 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.571A pdb=" N CYS F 21 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR F 48 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU F 81 " --> pdb=" O ASN F 53 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N LEU E 34 " --> pdb=" O CYS F 82 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N SER F 84 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE E 36 " --> pdb=" O SER F 84 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR F 86 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASP E 38 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 9.757A pdb=" N ASN F 88 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE E 93 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 65 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE E 75 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL E 67 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY E 73 " --> pdb=" O VAL E 67 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 4 through 5 removed outlier: 3.535A pdb=" N CYS G 21 " --> pdb=" O ILE M 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR G 48 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU G 81 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N LEU F 34 " --> pdb=" O CYS G 82 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N SER G 84 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE F 36 " --> pdb=" O SER G 84 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N THR G 86 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP F 38 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N ASN G 88 " --> pdb=" O ASP F 38 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE F 93 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU F 65 " --> pdb=" O PHE F 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE F 75 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL F 67 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY F 73 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.569A pdb=" N CYS A 21 " --> pdb=" O ILE N 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 48 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 81 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N CYS A 82 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE G 36 " --> pdb=" O CYS A 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 86 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE G 93 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU G 65 " --> pdb=" O PHE G 75 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE G 75 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL G 67 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY G 73 " --> pdb=" O VAL G 67 " (cutoff:3.500A) 1127 hydrogen bonds defined for protein. 2961 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: 16.81 Time building geometry restraints manager: 33.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20244 1.03 - 1.23: 379 1.23 - 1.43: 8469 1.43 - 1.62: 13412 1.62 - 1.82: 308 Bond restraints: 42812 Sorted by residual: bond pdb=" CA CYS A 9 " pdb=" C CYS A 9 " ideal model delta sigma weight residual 1.529 1.521 0.008 9.30e-03 1.16e+04 7.10e-01 bond pdb=" CA CYS Q 9 " pdb=" C CYS Q 9 " ideal model delta sigma weight residual 1.529 1.521 0.008 9.30e-03 1.16e+04 7.01e-01 bond pdb=" CA CYS D 9 " pdb=" C CYS D 9 " ideal model delta sigma weight residual 1.529 1.521 0.008 9.30e-03 1.16e+04 7.01e-01 bond pdb=" CA CYS B 9 " pdb=" C CYS B 9 " ideal model delta sigma weight residual 1.529 1.522 0.008 9.30e-03 1.16e+04 6.85e-01 bond pdb=" CA CYS S 9 " pdb=" C CYS S 9 " ideal model delta sigma weight residual 1.529 1.522 0.008 9.30e-03 1.16e+04 6.78e-01 ... (remaining 42807 not shown) Histogram of bond angle deviations from ideal: 100.91 - 107.53: 1427 107.53 - 114.16: 52473 114.16 - 120.78: 10971 120.78 - 127.41: 11681 127.41 - 134.04: 84 Bond angle restraints: 76636 Sorted by residual: angle pdb=" C CYS P 9 " pdb=" CA CYS P 9 " pdb=" CB CYS P 9 " ideal model delta sigma weight residual 116.54 109.91 6.63 1.15e+00 7.56e-01 3.33e+01 angle pdb=" C CYS W 9 " pdb=" CA CYS W 9 " pdb=" CB CYS W 9 " ideal model delta sigma weight residual 116.54 109.93 6.61 1.15e+00 7.56e-01 3.30e+01 angle pdb=" C CYS T 9 " pdb=" CA CYS T 9 " pdb=" CB CYS T 9 " ideal model delta sigma weight residual 116.54 109.94 6.60 1.15e+00 7.56e-01 3.29e+01 angle pdb=" C CYS S 9 " pdb=" CA CYS S 9 " pdb=" CB CYS S 9 " ideal model delta sigma weight residual 116.54 109.95 6.59 1.15e+00 7.56e-01 3.29e+01 angle pdb=" C CYS X 9 " pdb=" CA CYS X 9 " pdb=" CB CYS X 9 " ideal model delta sigma weight residual 116.54 109.95 6.59 1.15e+00 7.56e-01 3.29e+01 ... (remaining 76631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 17938 16.92 - 33.84: 2067 33.84 - 50.76: 564 50.76 - 67.68: 130 67.68 - 84.60: 28 Dihedral angle restraints: 20727 sinusoidal: 11179 harmonic: 9548 Sorted by residual: dihedral pdb=" CB CYS R 8 " pdb=" SG CYS R 8 " pdb=" SG CYS L 21 " pdb=" CB CYS L 21 " ideal model delta sinusoidal sigma weight residual 93.00 134.27 -41.27 1 1.00e+01 1.00e-02 2.38e+01 dihedral pdb=" CB CYS K 8 " pdb=" SG CYS K 8 " pdb=" SG CYS E 21 " pdb=" CB CYS E 21 " ideal model delta sinusoidal sigma weight residual 93.00 134.10 -41.10 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CB CYS S 8 " pdb=" SG CYS S 8 " pdb=" SG CYS M 21 " pdb=" CB CYS M 21 " ideal model delta sinusoidal sigma weight residual 93.00 133.80 -40.80 1 1.00e+01 1.00e-02 2.33e+01 ... (remaining 20724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2347 0.031 - 0.061: 877 0.061 - 0.092: 220 0.092 - 0.122: 376 0.122 - 0.153: 128 Chirality restraints: 3948 Sorted by residual: chirality pdb=" CA ILE D 49 " pdb=" N ILE D 49 " pdb=" C ILE D 49 " pdb=" CB ILE D 49 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ILE M 49 " pdb=" N ILE M 49 " pdb=" C ILE M 49 " pdb=" CB ILE M 49 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA ILE X 49 " pdb=" N ILE X 49 " pdb=" C ILE X 49 " pdb=" CB ILE X 49 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 3945 not shown) Planarity restraints: 6832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY T 60 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO T 61 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO T 61 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO T 61 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY Z 60 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO Z 61 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO Z 61 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO Z 61 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 60 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO D 61 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 61 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 61 " -0.023 5.00e-02 4.00e+02 ... (remaining 6829 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.39: 16445 2.39 - 2.94: 93271 2.94 - 3.49: 101768 3.49 - 4.05: 148846 4.05 - 4.60: 205775 Nonbonded interactions: 566105 Sorted by model distance: nonbonded pdb="HE22 GLN X 12 " pdb=" H LEU Y 13 " model vdw 1.836 2.100 nonbonded pdb="HE22 GLN K 12 " pdb=" H LEU L 13 " model vdw 1.860 2.100 nonbonded pdb=" OD1 ASP X 39 " pdb=" H THR X 41 " model vdw 1.866 1.850 nonbonded pdb=" OD1 ASP T 39 " pdb=" H THR T 41 " model vdw 1.866 1.850 nonbonded pdb=" OD1 ASP B 39 " pdb=" H THR B 41 " model vdw 1.866 1.850 ... (remaining 566100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.670 Extract box with map and model: 8.020 Check model and map are aligned: 0.640 Set scattering table: 0.390 Process input model: 126.980 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 : 0.002 0.019 22540 Z= 0.157 Angle : 0.604 6.633 30828 Z= 0.383 Chirality : 0.051 0.153 3948 Planarity : 0.004 0.041 4004 Dihedral : 15.290 84.603 7560 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 35.59 % Favored : 64.41 % 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: 0.84 (0.16), residues: 3108 helix: None (None), residues: 0 sheet: 0.95 (0.13), residues: 1400 loop : 0.32 (0.17), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 37 PHE 0.005 0.001 PHE I 109 TYR 0.002 0.001 TYR D 113 ARG 0.001 0.000 ARG X 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 3.744 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: H 89 ASP cc_start: 0.7795 (t0) cc_final: 0.7519 (t0) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.7029 time to fit residues: 232.0013 Evaluate side-chains 187 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 20.0000 chunk 233 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 93 optimal weight: 50.0000 chunk 146 optimal weight: 9.9990 chunk 179 optimal weight: 0.0980 chunk 279 optimal weight: 20.0000 overall best weight: 6.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 12 GLN P 12 GLN O 12 GLN T 12 GLN V 12 GLN W 12 GLN X 12 GLN Y 12 GLN Z 12 GLN a 12 GLN b 12 GLN H 12 GLN I 12 GLN J 12 GLN L 12 GLN M 12 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22540 Z= 0.245 Angle : 0.545 4.772 30828 Z= 0.288 Chirality : 0.050 0.147 3948 Planarity : 0.003 0.022 4004 Dihedral : 4.033 15.187 3220 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.57 % Allowed : 32.91 % Favored : 62.52 % 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: 0.90 (0.16), residues: 3108 helix: None (None), residues: 0 sheet: 0.96 (0.14), residues: 1372 loop : 0.40 (0.16), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 37 PHE 0.024 0.001 PHE b 115 TYR 0.002 0.001 TYR b 113 ARG 0.001 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 175 time to evaluate : 3.325 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: U 11 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7652 (mp0) REVERT: S 11 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7458 (mp0) REVERT: Y 11 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7715 (mp0) REVERT: a 11 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7709 (mp0) REVERT: H 89 ASP cc_start: 0.7900 (t0) cc_final: 0.7693 (t0) REVERT: L 89 ASP cc_start: 0.8007 (t0) cc_final: 0.7762 (t0) outliers start: 114 outliers final: 64 residues processed: 285 average time/residue: 0.5597 time to fit residues: 271.7039 Evaluate side-chains 229 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 165 time to evaluate : 3.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 82 CYS Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 82 CYS Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 41 THR Chi-restraints excluded: chain a residue 82 CYS Chi-restraints excluded: chain b residue 41 THR Chi-restraints excluded: chain b residue 70 THR Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 CYS Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 82 CYS Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 232 optimal weight: 20.0000 chunk 190 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 280 optimal weight: 0.9990 chunk 302 optimal weight: 30.0000 chunk 249 optimal weight: 6.9990 chunk 277 optimal weight: 9.9990 chunk 95 optimal weight: 30.0000 chunk 224 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 12 GLN R 91 ASN Q 91 ASN P 91 ASN U 12 GLN S 12 GLN I 91 ASN J 91 ASN K 91 ASN L 91 ASN N 12 GLN N 91 ASN E 12 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22540 Z= 0.270 Angle : 0.527 4.614 30828 Z= 0.284 Chirality : 0.050 0.146 3948 Planarity : 0.002 0.018 4004 Dihedral : 4.300 27.430 3220 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.57 % Allowed : 28.85 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.15), residues: 3108 helix: None (None), residues: 0 sheet: 0.62 (0.13), residues: 1456 loop : 0.52 (0.17), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 37 PHE 0.022 0.001 PHE b 115 TYR 0.003 0.001 TYR Z 113 ARG 0.001 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 137 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 4 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.8487 (mp10) REVERT: L 89 ASP cc_start: 0.8077 (t0) cc_final: 0.7828 (t0) outliers start: 89 outliers final: 81 residues processed: 224 average time/residue: 0.5560 time to fit residues: 215.0596 Evaluate side-chains 213 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 131 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 4 GLN Chi-restraints excluded: chain R residue 21 CYS Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 82 CYS Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 82 CYS Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 82 CYS Chi-restraints excluded: chain b residue 41 THR Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 82 CYS Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain N residue 21 CYS Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 82 CYS Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 chunk 145 optimal weight: 30.0000 chunk 31 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 281 optimal weight: 20.0000 chunk 297 optimal weight: 50.0000 chunk 146 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 overall best weight: 9.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 91 ASN U 91 ASN T 91 ASN S 91 ASN V 91 ASN W 91 ASN X 91 ASN H 91 ASN K 12 GLN M 91 ASN A 12 GLN A 91 ASN B 12 GLN C 91 ASN D 12 GLN F 91 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 22540 Z= 0.347 Angle : 0.547 5.070 30828 Z= 0.299 Chirality : 0.049 0.143 3948 Planarity : 0.002 0.019 4004 Dihedral : 4.540 21.910 3220 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.42 % Allowed : 25.92 % Favored : 68.66 % 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: 0.44 (0.15), residues: 3108 helix: None (None), residues: 0 sheet: 0.41 (0.13), residues: 1456 loop : 0.34 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP M 37 PHE 0.015 0.001 PHE V 115 TYR 0.003 0.001 TYR Z 113 ARG 0.001 0.000 ARG N 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 118 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 4 GLN cc_start: 0.9337 (OUTLIER) cc_final: 0.8243 (mp10) REVERT: P 4 GLN cc_start: 0.9391 (OUTLIER) cc_final: 0.8443 (mp10) REVERT: O 4 GLN cc_start: 0.9374 (OUTLIER) cc_final: 0.8245 (mp10) REVERT: U 4 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.8275 (mp10) REVERT: T 4 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.8203 (mp10) REVERT: S 4 GLN cc_start: 0.9342 (OUTLIER) cc_final: 0.8226 (mp10) REVERT: V 4 GLN cc_start: 0.9344 (OUTLIER) cc_final: 0.8426 (mp10) REVERT: W 4 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8438 (mp10) REVERT: X 4 GLN cc_start: 0.9383 (OUTLIER) cc_final: 0.8230 (mp10) REVERT: Y 4 GLN cc_start: 0.9357 (OUTLIER) cc_final: 0.8381 (mp10) REVERT: Z 4 GLN cc_start: 0.9387 (OUTLIER) cc_final: 0.8217 (mp10) REVERT: a 4 GLN cc_start: 0.9379 (OUTLIER) cc_final: 0.8162 (mp10) REVERT: b 4 GLN cc_start: 0.9391 (OUTLIER) cc_final: 0.8223 (mp10) REVERT: I 4 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8610 (mp10) REVERT: J 4 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8451 (mp10) REVERT: K 4 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8589 (mp10) REVERT: M 4 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8818 (mp10) outliers start: 135 outliers final: 110 residues processed: 251 average time/residue: 0.5575 time to fit residues: 241.1338 Evaluate side-chains 244 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 117 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 4 GLN Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 5 ILE Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 82 CYS Chi-restraints excluded: chain U residue 4 GLN Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 4 GLN Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 82 CYS Chi-restraints excluded: chain S residue 4 GLN Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 4 GLN Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 46 ASN Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 5 ILE Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 4 GLN Chi-restraints excluded: chain X residue 5 ILE Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 4 GLN Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 46 ASN Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 4 GLN Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 46 ASN Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 4 GLN Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 82 CYS Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 70 THR Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 CYS Chi-restraints excluded: chain K residue 4 GLN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 21 CYS Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 82 CYS Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 221 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 254 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 152 optimal weight: 0.6980 chunk 267 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 22540 Z= 0.246 Angle : 0.503 4.610 30828 Z= 0.271 Chirality : 0.049 0.139 3948 Planarity : 0.002 0.016 4004 Dihedral : 4.373 22.206 3220 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.13 % Allowed : 25.04 % Favored : 70.83 % 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: 0.40 (0.15), residues: 3108 helix: None (None), residues: 0 sheet: 0.30 (0.13), residues: 1456 loop : 0.40 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 37 PHE 0.021 0.001 PHE V 115 TYR 0.003 0.000 TYR Z 113 ARG 0.001 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 121 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 4 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.8374 (mp10) REVERT: U 89 ASP cc_start: 0.8040 (t0) cc_final: 0.7834 (t0) REVERT: T 4 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8245 (mp10) REVERT: V 4 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.8440 (mp10) REVERT: X 4 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.8222 (mp10) REVERT: b 4 GLN cc_start: 0.9346 (OUTLIER) cc_final: 0.8092 (mp10) REVERT: H 4 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8310 (mp10) REVERT: I 4 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8686 (mp10) REVERT: K 4 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8479 (mp10) REVERT: L 4 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8096 (mp10) REVERT: N 4 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8130 (mp10) outliers start: 103 outliers final: 78 residues processed: 224 average time/residue: 0.5601 time to fit residues: 216.5365 Evaluate side-chains 209 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 121 time to evaluate : 3.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 4 GLN Chi-restraints excluded: chain R residue 21 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 82 CYS Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 4 GLN Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 82 CYS Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 4 GLN Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 4 GLN Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 82 CYS Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 82 CYS Chi-restraints excluded: chain K residue 4 GLN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain N residue 4 GLN Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 21 CYS Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 82 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 20.0000 chunk 268 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 298 optimal weight: 20.0000 chunk 247 optimal weight: 10.0000 chunk 137 optimal weight: 40.0000 chunk 24 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 overall best weight: 9.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 22540 Z= 0.367 Angle : 0.541 4.802 30828 Z= 0.297 Chirality : 0.049 0.135 3948 Planarity : 0.002 0.022 4004 Dihedral : 4.596 20.293 3220 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.38 % Allowed : 22.35 % Favored : 72.27 % 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: 0.28 (0.15), residues: 3108 helix: None (None), residues: 0 sheet: 0.22 (0.13), residues: 1428 loop : 0.31 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP N 37 PHE 0.029 0.001 PHE Y 115 TYR 0.003 0.001 TYR C 113 ARG 0.000 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 115 time to evaluate : 3.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 4 GLN cc_start: 0.9382 (OUTLIER) cc_final: 0.8322 (mp10) REVERT: Q 4 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.8169 (mp10) REVERT: P 4 GLN cc_start: 0.9384 (OUTLIER) cc_final: 0.8383 (mp10) REVERT: O 4 GLN cc_start: 0.9367 (OUTLIER) cc_final: 0.8256 (mp10) REVERT: U 4 GLN cc_start: 0.9345 (OUTLIER) cc_final: 0.8307 (mp10) REVERT: T 4 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.8192 (mp10) REVERT: S 4 GLN cc_start: 0.9363 (OUTLIER) cc_final: 0.8186 (mp10) REVERT: V 4 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.8376 (mp10) REVERT: W 4 GLN cc_start: 0.9359 (OUTLIER) cc_final: 0.8363 (mp10) REVERT: X 4 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.8135 (mp10) REVERT: Y 4 GLN cc_start: 0.9342 (OUTLIER) cc_final: 0.8406 (mp10) REVERT: Z 4 GLN cc_start: 0.9388 (OUTLIER) cc_final: 0.8263 (mp10) REVERT: a 4 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.8099 (mp10) REVERT: b 4 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: H 4 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8297 (mp10) REVERT: I 4 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8570 (mp10) REVERT: J 4 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8452 (mp10) REVERT: K 4 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8501 (mp10) REVERT: L 4 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8067 (mp10) REVERT: M 4 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8631 (mp10) REVERT: N 4 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8187 (mp10) outliers start: 134 outliers final: 103 residues processed: 247 average time/residue: 0.6041 time to fit residues: 258.9936 Evaluate side-chains 238 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 114 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 4 GLN Chi-restraints excluded: chain R residue 21 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 4 GLN Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 5 ILE Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 82 CYS Chi-restraints excluded: chain U residue 4 GLN Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 4 GLN Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 82 CYS Chi-restraints excluded: chain S residue 4 GLN Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 4 GLN Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 5 ILE Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 4 GLN Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 4 GLN Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 46 ASN Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 4 GLN Chi-restraints excluded: chain Z residue 46 ASN Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 4 GLN Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 82 CYS Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 CYS Chi-restraints excluded: chain K residue 4 GLN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain N residue 4 GLN Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 21 CYS Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 82 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 10.0000 chunk 33 optimal weight: 0.0060 chunk 169 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 296 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 137 optimal weight: 30.0000 overall best weight: 7.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 22540 Z= 0.270 Angle : 0.511 4.622 30828 Z= 0.276 Chirality : 0.049 0.136 3948 Planarity : 0.002 0.023 4004 Dihedral : 4.471 21.161 3220 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.06 % Allowed : 21.75 % Favored : 73.19 % 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: 0.26 (0.15), residues: 3108 helix: None (None), residues: 0 sheet: 0.16 (0.13), residues: 1428 loop : 0.34 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 37 PHE 0.023 0.001 PHE V 115 TYR 0.001 0.000 TYR T 113 ARG 0.001 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 120 time to evaluate : 3.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 4 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.8300 (mp10) REVERT: Q 4 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.8164 (mp10) REVERT: P 4 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8458 (mp10) REVERT: O 4 GLN cc_start: 0.9337 (OUTLIER) cc_final: 0.8247 (mp10) REVERT: U 4 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8261 (mp10) REVERT: T 4 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.8182 (mp10) REVERT: S 4 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.8159 (mp10) REVERT: V 4 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.8343 (mp10) REVERT: W 4 GLN cc_start: 0.9331 (OUTLIER) cc_final: 0.8336 (mp10) REVERT: X 4 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.8118 (mp10) REVERT: Y 4 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.8346 (mp10) REVERT: Z 4 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.8212 (mp10) REVERT: a 4 GLN cc_start: 0.9314 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: b 4 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.7965 (mp10) REVERT: H 4 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8285 (mp10) REVERT: I 4 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8545 (mp10) REVERT: J 4 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8418 (mp10) REVERT: K 4 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8447 (mp10) REVERT: L 4 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8076 (mp10) REVERT: M 4 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8616 (mp10) REVERT: N 4 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8164 (mp10) outliers start: 126 outliers final: 102 residues processed: 246 average time/residue: 0.5918 time to fit residues: 253.1689 Evaluate side-chains 242 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 119 time to evaluate : 3.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 4 GLN Chi-restraints excluded: chain R residue 21 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 4 GLN Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 5 ILE Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 82 CYS Chi-restraints excluded: chain U residue 4 GLN Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 4 GLN Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 82 CYS Chi-restraints excluded: chain S residue 4 GLN Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 4 GLN Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 46 ASN Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 5 ILE Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 4 GLN Chi-restraints excluded: chain X residue 21 CYS Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 4 GLN Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 21 CYS Chi-restraints excluded: chain Y residue 46 ASN Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 4 GLN Chi-restraints excluded: chain Z residue 46 ASN Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 4 GLN Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 82 CYS Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 CYS Chi-restraints excluded: chain K residue 4 GLN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain N residue 4 GLN Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 21 CYS Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 82 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 177 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 146 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 233 optimal weight: 20.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22540 Z= 0.163 Angle : 0.487 5.270 30828 Z= 0.256 Chirality : 0.051 0.139 3948 Planarity : 0.002 0.020 4004 Dihedral : 4.095 19.415 3220 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.25 % Allowed : 22.79 % Favored : 73.96 % 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: 0.41 (0.15), residues: 3108 helix: None (None), residues: 0 sheet: 0.23 (0.13), residues: 1512 loop : 0.50 (0.17), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Q 37 PHE 0.023 0.001 PHE V 115 TYR 0.003 0.000 TYR b 113 ARG 0.001 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 121 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 4 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.8620 (mp10) REVERT: O 4 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.8190 (mp10) REVERT: S 4 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.8171 (mp10) REVERT: W 4 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8357 (mp10) REVERT: Y 4 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8366 (mp10) REVERT: a 4 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8085 (mp10) REVERT: b 4 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: I 4 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8705 (mp10) REVERT: K 4 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8463 (mp10) REVERT: M 4 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8595 (mp10) REVERT: N 4 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8106 (mp10) outliers start: 81 outliers final: 43 residues processed: 202 average time/residue: 0.5868 time to fit residues: 204.3913 Evaluate side-chains 175 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 121 time to evaluate : 3.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 CYS Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain S residue 4 GLN Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 4 GLN Chi-restraints excluded: chain Y residue 21 CYS Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 4 GLN Chi-restraints excluded: chain a residue 82 CYS Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain K residue 4 GLN Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain N residue 4 GLN Chi-restraints excluded: chain N residue 21 CYS Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 20.0000 chunk 284 optimal weight: 20.0000 chunk 259 optimal weight: 20.0000 chunk 276 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 84 optimal weight: 0.0170 chunk 249 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 275 optimal weight: 30.0000 overall best weight: 5.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22540 Z= 0.228 Angle : 0.502 4.691 30828 Z= 0.267 Chirality : 0.050 0.141 3948 Planarity : 0.002 0.022 4004 Dihedral : 4.100 18.374 3220 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.29 % Allowed : 22.71 % Favored : 74.00 % 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: 0.35 (0.15), residues: 3108 helix: None (None), residues: 0 sheet: 0.13 (0.13), residues: 1512 loop : 0.52 (0.17), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Z 37 PHE 0.030 0.001 PHE Y 115 TYR 0.002 0.000 TYR b 113 ARG 0.001 0.000 ARG M 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 119 time to evaluate : 3.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 4 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.8276 (mp10) REVERT: P 4 GLN cc_start: 0.9327 (OUTLIER) cc_final: 0.8693 (mp10) REVERT: O 4 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.8255 (mp10) REVERT: S 4 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8091 (mp10) REVERT: V 4 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8243 (mp10) REVERT: W 4 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8324 (mp10) REVERT: X 4 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8099 (mp10) REVERT: Y 4 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8338 (mp10) REVERT: a 4 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.8160 (mp10) REVERT: b 4 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8044 (mp10) REVERT: H 4 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8252 (mp10) REVERT: I 4 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8680 (mp10) REVERT: J 4 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8429 (mp10) REVERT: K 4 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8491 (mp10) REVERT: M 4 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8621 (mp10) REVERT: N 4 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8074 (mp10) outliers start: 82 outliers final: 56 residues processed: 201 average time/residue: 0.5649 time to fit residues: 195.0180 Evaluate side-chains 190 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 118 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 4 GLN Chi-restraints excluded: chain R residue 21 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain S residue 4 GLN Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 4 GLN Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 4 GLN Chi-restraints excluded: chain X residue 21 CYS Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 4 GLN Chi-restraints excluded: chain Y residue 21 CYS Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 46 ASN Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 4 GLN Chi-restraints excluded: chain a residue 82 CYS Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain K residue 4 GLN Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain N residue 4 GLN Chi-restraints excluded: chain N residue 21 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 0.0030 chunk 292 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 203 optimal weight: 7.9990 chunk 306 optimal weight: 20.0000 chunk 282 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 overall best weight: 6.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 22540 Z= 0.242 Angle : 0.502 5.066 30828 Z= 0.268 Chirality : 0.049 0.137 3948 Planarity : 0.002 0.023 4004 Dihedral : 4.155 17.881 3220 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.17 % Allowed : 22.67 % Favored : 74.16 % 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: 0.47 (0.15), residues: 3108 helix: None (None), residues: 0 sheet: 0.18 (0.13), residues: 1484 loop : 0.63 (0.17), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP V 37 PHE 0.027 0.001 PHE Y 115 TYR 0.001 0.000 TYR Q 113 ARG 0.001 0.000 ARG A 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 118 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 4 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.8228 (mp10) REVERT: Q 4 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.8036 (mp10) REVERT: P 4 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.8592 (mp10) REVERT: O 4 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: U 4 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8314 (mp10) REVERT: S 4 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.8058 (mp10) REVERT: V 4 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8292 (mp10) REVERT: W 4 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8291 (mp10) REVERT: X 4 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8065 (mp10) REVERT: Y 4 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8322 (mp10) REVERT: a 4 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8124 (mp10) REVERT: b 4 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: H 4 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8288 (mp10) REVERT: I 4 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8595 (mp10) REVERT: J 4 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8442 (mp10) REVERT: K 4 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8488 (mp10) REVERT: M 4 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8651 (mp10) REVERT: N 4 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8058 (mp10) outliers start: 79 outliers final: 59 residues processed: 197 average time/residue: 0.5930 time to fit residues: 200.9940 Evaluate side-chains 195 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 118 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 4 GLN Chi-restraints excluded: chain R residue 21 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 4 GLN Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain U residue 4 GLN Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain S residue 4 GLN Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 4 GLN Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 4 GLN Chi-restraints excluded: chain X residue 21 CYS Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 4 GLN Chi-restraints excluded: chain Y residue 21 CYS Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 46 ASN Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 4 GLN Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 82 CYS Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 82 CYS Chi-restraints excluded: chain K residue 4 GLN Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain N residue 4 GLN Chi-restraints excluded: chain N residue 21 CYS Chi-restraints excluded: chain N residue 82 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 9.9990 chunk 260 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 251 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- 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 = 0.3098 r_free = 0.3098 target = 0.035172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.027526 restraints weight = 533316.896| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 5.95 r_work: 0.2579 rms_B_bonded: 5.36 restraints_weight: 2.0000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 22540 Z= 0.242 Angle : 0.502 5.185 30828 Z= 0.268 Chirality : 0.049 0.136 3948 Planarity : 0.002 0.024 4004 Dihedral : 4.145 20.357 3220 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.29 % Allowed : 22.51 % Favored : 74.20 % 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: 0.46 (0.15), residues: 3108 helix: None (None), residues: 0 sheet: 0.17 (0.13), residues: 1484 loop : 0.64 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP V 37 PHE 0.027 0.001 PHE Y 115 TYR 0.001 0.000 TYR H 113 ARG 0.000 0.000 ARG E 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6676.97 seconds wall clock time: 119 minutes 37.80 seconds (7177.80 seconds total)