Starting phenix.real_space_refine on Mon Sep 23 16:21:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb3_25791/09_2024/7tb3_25791.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb3_25791/09_2024/7tb3_25791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb3_25791/09_2024/7tb3_25791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb3_25791/09_2024/7tb3_25791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb3_25791/09_2024/7tb3_25791.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb3_25791/09_2024/7tb3_25791.cif" } resolution = 2.57 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= 0.008 sd= 0.050 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: 4 Type Number sf(0) Gaussians S 312 5.16 5 C 30168 2.51 5 N 8448 2.21 5 O 9072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 48000 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "B" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "C" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "D" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "E" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "F" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "G" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "H" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "I" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "J" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "K" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "L" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "M" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "N" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "O" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "P" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "Q" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "R" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "S" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "T" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "U" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "V" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "W" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "X" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Time building chain proxies: 38.29, per 1000 atoms: 0.80 Number of scatterers: 48000 At special positions: 0 Unit cell: (164, 164, 164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 312 16.00 O 9072 8.00 N 8448 7.00 C 30168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS J 169 " distance=2.02 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS J 237 " distance=2.02 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS J 27 " distance=2.09 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS J 31 " distance=2.10 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS I 169 " distance=2.07 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS I 237 " distance=2.19 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS I 27 " distance=2.00 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS I 31 " distance=2.06 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS L 169 " distance=2.14 Simple disulfide: pdb=" SG CYS C 31 " - pdb=" SG CYS L 237 " distance=2.11 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS L 27 " distance=2.25 Simple disulfide: pdb=" SG CYS C 237 " - pdb=" SG CYS L 31 " distance=2.24 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS K 169 " distance=2.09 Simple disulfide: pdb=" SG CYS D 31 " - pdb=" SG CYS K 237 " distance=1.97 Simple disulfide: pdb=" SG CYS D 169 " - pdb=" SG CYS K 27 " distance=2.12 Simple disulfide: pdb=" SG CYS D 237 " - pdb=" SG CYS K 31 " distance=2.01 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS N 169 " distance=2.03 Simple disulfide: pdb=" SG CYS E 31 " - pdb=" SG CYS N 237 " distance=2.10 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS N 27 " distance=1.98 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS N 31 " distance=2.07 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS M 169 " distance=2.08 Simple disulfide: pdb=" SG CYS F 31 " - pdb=" SG CYS M 237 " distance=1.99 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS M 27 " distance=2.06 Simple disulfide: pdb=" SG CYS F 237 " - pdb=" SG CYS M 31 " distance=1.96 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS P 169 " distance=1.95 Simple disulfide: pdb=" SG CYS G 31 " - pdb=" SG CYS P 237 " distance=2.00 Simple disulfide: pdb=" SG CYS G 169 " - pdb=" SG CYS P 27 " distance=2.08 Simple disulfide: pdb=" SG CYS G 237 " - pdb=" SG CYS P 31 " distance=2.15 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS O 169 " distance=2.02 Simple disulfide: pdb=" SG CYS H 31 " - pdb=" SG CYS O 237 " distance=1.92 Simple disulfide: pdb=" SG CYS H 169 " - pdb=" SG CYS O 27 " distance=2.04 Simple disulfide: pdb=" SG CYS H 237 " - pdb=" SG CYS O 31 " distance=1.97 Simple disulfide: pdb=" SG CYS Q 27 " - pdb=" SG CYS X 169 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 31 " - pdb=" SG CYS X 237 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 169 " - pdb=" SG CYS X 27 " distance=1.95 Simple disulfide: pdb=" SG CYS Q 237 " - pdb=" SG CYS X 31 " distance=1.99 Simple disulfide: pdb=" SG CYS R 27 " - pdb=" SG CYS W 169 " distance=1.96 Simple disulfide: pdb=" SG CYS R 31 " - pdb=" SG CYS W 237 " distance=1.92 Simple disulfide: pdb=" SG CYS R 169 " - pdb=" SG CYS W 27 " distance=1.96 Simple disulfide: pdb=" SG CYS R 237 " - pdb=" SG CYS W 31 " distance=1.96 Simple disulfide: pdb=" SG CYS S 27 " - pdb=" SG CYS V 169 " distance=1.97 Simple disulfide: pdb=" SG CYS S 31 " - pdb=" SG CYS V 237 " distance=1.99 Simple disulfide: pdb=" SG CYS S 169 " - pdb=" SG CYS V 27 " distance=2.00 Simple disulfide: pdb=" SG CYS S 237 " - pdb=" SG CYS V 31 " distance=2.01 Simple disulfide: pdb=" SG CYS T 27 " - pdb=" SG CYS U 169 " distance=1.96 Simple disulfide: pdb=" SG CYS T 31 " - pdb=" SG CYS U 237 " distance=2.07 Simple disulfide: pdb=" SG CYS T 169 " - pdb=" SG CYS U 27 " distance=1.91 Simple disulfide: pdb=" SG CYS T 237 " - pdb=" SG CYS U 31 " distance=1.90 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.24 Conformation dependent library (CDL) restraints added in 8.7 seconds 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11328 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 0 sheets defined 76.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 9 through 25 removed outlier: 3.988A pdb=" N LYS A 19 " --> pdb=" O HIS A 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 22 " --> pdb=" O HIS A 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 55 removed outlier: 3.677A pdb=" N GLU A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 74 Processing helix chain 'A' and resid 88 through 117 Processing helix chain 'A' and resid 123 through 151 Processing helix chain 'A' and resid 171 through 199 Processing helix chain 'A' and resid 201 through 211 Processing helix chain 'A' and resid 212 through 234 removed outlier: 3.917A pdb=" N LYS A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.987A pdb=" N LYS B 19 " --> pdb=" O HIS B 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN B 22 " --> pdb=" O HIS B 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B 25 " --> pdb=" O VAL B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 55 removed outlier: 3.693A pdb=" N GLU B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 74 Processing helix chain 'B' and resid 88 through 117 Processing helix chain 'B' and resid 123 through 151 Processing helix chain 'B' and resid 171 through 199 Processing helix chain 'B' and resid 201 through 211 Processing helix chain 'B' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 25 removed outlier: 3.988A pdb=" N LYS C 19 " --> pdb=" O HIS C 15 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 21 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN C 22 " --> pdb=" O HIS C 18 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 55 removed outlier: 3.598A pdb=" N GLU C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 74 Processing helix chain 'C' and resid 88 through 117 Processing helix chain 'C' and resid 123 through 151 Processing helix chain 'C' and resid 171 through 199 Processing helix chain 'C' and resid 201 through 211 Processing helix chain 'C' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR C 243 " --> pdb=" O GLY C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 25 removed outlier: 3.974A pdb=" N LYS D 19 " --> pdb=" O HIS D 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 21 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN D 22 " --> pdb=" O HIS D 18 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE D 25 " --> pdb=" O VAL D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 55 removed outlier: 3.599A pdb=" N GLU D 39 " --> pdb=" O ASP D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 74 Processing helix chain 'D' and resid 88 through 117 Processing helix chain 'D' and resid 123 through 151 Processing helix chain 'D' and resid 171 through 199 Processing helix chain 'D' and resid 201 through 211 Processing helix chain 'D' and resid 212 through 234 removed outlier: 3.919A pdb=" N LYS D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS D 232 " --> pdb=" O THR D 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 25 removed outlier: 4.002A pdb=" N LYS E 19 " --> pdb=" O HIS E 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 21 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN E 22 " --> pdb=" O HIS E 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 55 removed outlier: 3.692A pdb=" N GLU E 39 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 74 Processing helix chain 'E' and resid 88 through 117 Processing helix chain 'E' and resid 123 through 151 Processing helix chain 'E' and resid 171 through 199 Processing helix chain 'E' and resid 201 through 211 Processing helix chain 'E' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS E 218 " --> pdb=" O SER E 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR E 243 " --> pdb=" O GLY E 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 25 removed outlier: 3.997A pdb=" N LYS F 19 " --> pdb=" O HIS F 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL F 21 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN F 22 " --> pdb=" O HIS F 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 55 removed outlier: 3.671A pdb=" N GLU F 39 " --> pdb=" O ASP F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 74 Processing helix chain 'F' and resid 88 through 117 Processing helix chain 'F' and resid 123 through 151 Processing helix chain 'F' and resid 171 through 199 Processing helix chain 'F' and resid 201 through 211 Processing helix chain 'F' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS F 218 " --> pdb=" O SER F 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS F 232 " --> pdb=" O THR F 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY F 234 " --> pdb=" O LEU F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR F 243 " --> pdb=" O GLY F 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 25 removed outlier: 3.987A pdb=" N LYS G 19 " --> pdb=" O HIS G 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU G 20 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL G 21 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN G 22 " --> pdb=" O HIS G 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE G 25 " --> pdb=" O VAL G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 55 removed outlier: 3.599A pdb=" N GLU G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 74 Processing helix chain 'G' and resid 88 through 117 Processing helix chain 'G' and resid 123 through 151 Processing helix chain 'G' and resid 171 through 199 Processing helix chain 'G' and resid 201 through 211 Processing helix chain 'G' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS G 218 " --> pdb=" O SER G 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS G 232 " --> pdb=" O THR G 228 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY G 234 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR G 243 " --> pdb=" O GLY G 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 25 removed outlier: 4.037A pdb=" N LYS H 19 " --> pdb=" O HIS H 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU H 20 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN H 22 " --> pdb=" O HIS H 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE H 25 " --> pdb=" O VAL H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 55 removed outlier: 3.671A pdb=" N GLU H 39 " --> pdb=" O ASP H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 74 Processing helix chain 'H' and resid 88 through 117 Processing helix chain 'H' and resid 123 through 151 Processing helix chain 'H' and resid 171 through 199 Processing helix chain 'H' and resid 201 through 211 Processing helix chain 'H' and resid 212 through 234 removed outlier: 3.919A pdb=" N LYS H 218 " --> pdb=" O SER H 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS H 232 " --> pdb=" O THR H 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY H 234 " --> pdb=" O LEU H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR H 243 " --> pdb=" O GLY H 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 25 removed outlier: 3.995A pdb=" N LYS I 19 " --> pdb=" O HIS I 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU I 20 " --> pdb=" O LEU I 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL I 21 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN I 22 " --> pdb=" O HIS I 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE I 25 " --> pdb=" O VAL I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 55 removed outlier: 3.675A pdb=" N GLU I 39 " --> pdb=" O ASP I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 74 Processing helix chain 'I' and resid 88 through 117 Processing helix chain 'I' and resid 123 through 151 Processing helix chain 'I' and resid 171 through 199 Processing helix chain 'I' and resid 201 through 211 Processing helix chain 'I' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS I 218 " --> pdb=" O SER I 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS I 232 " --> pdb=" O THR I 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY I 234 " --> pdb=" O LEU I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU I 242 " --> pdb=" O ALA I 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR I 243 " --> pdb=" O GLY I 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 25 removed outlier: 3.976A pdb=" N LYS J 19 " --> pdb=" O HIS J 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU J 20 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL J 21 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN J 22 " --> pdb=" O HIS J 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE J 25 " --> pdb=" O VAL J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 55 removed outlier: 3.694A pdb=" N GLU J 39 " --> pdb=" O ASP J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 74 Processing helix chain 'J' and resid 88 through 117 Processing helix chain 'J' and resid 123 through 151 Processing helix chain 'J' and resid 171 through 199 Processing helix chain 'J' and resid 201 through 211 Processing helix chain 'J' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS J 218 " --> pdb=" O SER J 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS J 232 " --> pdb=" O THR J 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU J 242 " --> pdb=" O ALA J 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR J 243 " --> pdb=" O GLY J 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 25 removed outlier: 4.010A pdb=" N LYS K 19 " --> pdb=" O HIS K 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU K 20 " --> pdb=" O LEU K 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL K 21 " --> pdb=" O VAL K 17 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN K 22 " --> pdb=" O HIS K 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE K 25 " --> pdb=" O VAL K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 55 removed outlier: 3.550A pdb=" N GLU K 39 " --> pdb=" O ASP K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 74 Processing helix chain 'K' and resid 88 through 117 Processing helix chain 'K' and resid 123 through 151 Processing helix chain 'K' and resid 171 through 199 Processing helix chain 'K' and resid 201 through 211 Processing helix chain 'K' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS K 218 " --> pdb=" O SER K 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS K 232 " --> pdb=" O THR K 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY K 234 " --> pdb=" O LEU K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR K 243 " --> pdb=" O GLY K 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 25 removed outlier: 3.984A pdb=" N LYS L 19 " --> pdb=" O HIS L 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU L 20 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL L 21 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN L 22 " --> pdb=" O HIS L 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE L 25 " --> pdb=" O VAL L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 55 removed outlier: 3.662A pdb=" N GLU L 39 " --> pdb=" O ASP L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 74 Processing helix chain 'L' and resid 88 through 117 Processing helix chain 'L' and resid 123 through 151 Processing helix chain 'L' and resid 171 through 199 Processing helix chain 'L' and resid 201 through 211 Processing helix chain 'L' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS L 218 " --> pdb=" O SER L 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS L 232 " --> pdb=" O THR L 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY L 234 " --> pdb=" O LEU L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR L 243 " --> pdb=" O GLY L 239 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 25 removed outlier: 3.987A pdb=" N LYS M 19 " --> pdb=" O HIS M 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU M 20 " --> pdb=" O LEU M 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN M 22 " --> pdb=" O HIS M 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE M 25 " --> pdb=" O VAL M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 55 removed outlier: 3.696A pdb=" N GLU M 39 " --> pdb=" O ASP M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 74 Processing helix chain 'M' and resid 88 through 117 Processing helix chain 'M' and resid 123 through 151 Processing helix chain 'M' and resid 171 through 199 Processing helix chain 'M' and resid 201 through 211 Processing helix chain 'M' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS M 218 " --> pdb=" O SER M 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS M 232 " --> pdb=" O THR M 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY M 234 " --> pdb=" O LEU M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU M 242 " --> pdb=" O ALA M 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR M 243 " --> pdb=" O GLY M 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 25 removed outlier: 4.021A pdb=" N LYS N 19 " --> pdb=" O HIS N 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL N 21 " --> pdb=" O VAL N 17 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN N 22 " --> pdb=" O HIS N 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE N 25 " --> pdb=" O VAL N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 55 removed outlier: 3.698A pdb=" N GLU N 39 " --> pdb=" O ASP N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 74 Processing helix chain 'N' and resid 88 through 117 Processing helix chain 'N' and resid 123 through 151 Processing helix chain 'N' and resid 171 through 199 Processing helix chain 'N' and resid 201 through 211 Processing helix chain 'N' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS N 218 " --> pdb=" O SER N 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS N 232 " --> pdb=" O THR N 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU N 242 " --> pdb=" O ALA N 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR N 243 " --> pdb=" O GLY N 239 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 25 removed outlier: 3.984A pdb=" N LYS O 19 " --> pdb=" O HIS O 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU O 20 " --> pdb=" O LEU O 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL O 21 " --> pdb=" O VAL O 17 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN O 22 " --> pdb=" O HIS O 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE O 25 " --> pdb=" O VAL O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 55 removed outlier: 3.671A pdb=" N GLU O 39 " --> pdb=" O ASP O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 74 Processing helix chain 'O' and resid 88 through 117 Processing helix chain 'O' and resid 123 through 151 Processing helix chain 'O' and resid 171 through 199 Processing helix chain 'O' and resid 201 through 211 Processing helix chain 'O' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS O 218 " --> pdb=" O SER O 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS O 232 " --> pdb=" O THR O 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY O 234 " --> pdb=" O LEU O 230 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU O 242 " --> pdb=" O ALA O 238 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR O 243 " --> pdb=" O GLY O 239 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 25 removed outlier: 3.980A pdb=" N LYS P 19 " --> pdb=" O HIS P 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU P 20 " --> pdb=" O LEU P 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL P 21 " --> pdb=" O VAL P 17 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN P 22 " --> pdb=" O HIS P 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE P 25 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 35 through 55 removed outlier: 3.696A pdb=" N GLU P 39 " --> pdb=" O ASP P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 74 Processing helix chain 'P' and resid 88 through 117 Processing helix chain 'P' and resid 123 through 151 Processing helix chain 'P' and resid 171 through 199 Processing helix chain 'P' and resid 201 through 211 Processing helix chain 'P' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS P 218 " --> pdb=" O SER P 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS P 232 " --> pdb=" O THR P 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY P 234 " --> pdb=" O LEU P 230 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR P 243 " --> pdb=" O GLY P 239 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 25 removed outlier: 3.988A pdb=" N LYS Q 19 " --> pdb=" O HIS Q 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU Q 20 " --> pdb=" O LEU Q 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN Q 22 " --> pdb=" O HIS Q 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE Q 25 " --> pdb=" O VAL Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 35 through 55 removed outlier: 3.669A pdb=" N GLU Q 39 " --> pdb=" O ASP Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 74 Processing helix chain 'Q' and resid 88 through 117 Processing helix chain 'Q' and resid 123 through 151 Processing helix chain 'Q' and resid 171 through 199 Processing helix chain 'Q' and resid 201 through 211 Processing helix chain 'Q' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS Q 218 " --> pdb=" O SER Q 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS Q 232 " --> pdb=" O THR Q 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY Q 234 " --> pdb=" O LEU Q 230 " (cutoff:3.500A) Processing helix chain 'Q' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU Q 242 " --> pdb=" O ALA Q 238 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR Q 243 " --> pdb=" O GLY Q 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 25 removed outlier: 4.016A pdb=" N LYS R 19 " --> pdb=" O HIS R 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU R 20 " --> pdb=" O LEU R 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL R 21 " --> pdb=" O VAL R 17 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN R 22 " --> pdb=" O HIS R 18 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE R 25 " --> pdb=" O VAL R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 removed outlier: 3.689A pdb=" N GLU R 39 " --> pdb=" O ASP R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 74 Processing helix chain 'R' and resid 88 through 117 Processing helix chain 'R' and resid 123 through 151 Processing helix chain 'R' and resid 171 through 199 Processing helix chain 'R' and resid 201 through 211 Processing helix chain 'R' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS R 218 " --> pdb=" O SER R 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS R 232 " --> pdb=" O THR R 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU R 242 " --> pdb=" O ALA R 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR R 243 " --> pdb=" O GLY R 239 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 25 removed outlier: 3.996A pdb=" N LYS S 19 " --> pdb=" O HIS S 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU S 20 " --> pdb=" O LEU S 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL S 21 " --> pdb=" O VAL S 17 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN S 22 " --> pdb=" O HIS S 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE S 25 " --> pdb=" O VAL S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 35 through 55 removed outlier: 3.668A pdb=" N GLU S 39 " --> pdb=" O ASP S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 59 through 74 Processing helix chain 'S' and resid 88 through 117 Processing helix chain 'S' and resid 123 through 151 Processing helix chain 'S' and resid 171 through 199 Processing helix chain 'S' and resid 201 through 211 Processing helix chain 'S' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS S 218 " --> pdb=" O SER S 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS S 232 " --> pdb=" O THR S 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY S 234 " --> pdb=" O LEU S 230 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU S 242 " --> pdb=" O ALA S 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR S 243 " --> pdb=" O GLY S 239 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 25 removed outlier: 4.021A pdb=" N LYS T 19 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU T 20 " --> pdb=" O LEU T 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL T 21 " --> pdb=" O VAL T 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN T 22 " --> pdb=" O HIS T 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE T 25 " --> pdb=" O VAL T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 55 removed outlier: 3.692A pdb=" N GLU T 39 " --> pdb=" O ASP T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 59 through 74 Processing helix chain 'T' and resid 88 through 117 Processing helix chain 'T' and resid 123 through 151 Processing helix chain 'T' and resid 171 through 199 Processing helix chain 'T' and resid 201 through 211 Processing helix chain 'T' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS T 218 " --> pdb=" O SER T 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS T 232 " --> pdb=" O THR T 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY T 234 " --> pdb=" O LEU T 230 " (cutoff:3.500A) Processing helix chain 'T' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR T 243 " --> pdb=" O GLY T 239 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 25 removed outlier: 3.999A pdb=" N LYS U 19 " --> pdb=" O HIS U 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU U 20 " --> pdb=" O LEU U 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL U 21 " --> pdb=" O VAL U 17 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN U 22 " --> pdb=" O HIS U 18 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE U 25 " --> pdb=" O VAL U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 55 removed outlier: 3.598A pdb=" N GLU U 39 " --> pdb=" O ASP U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 74 Processing helix chain 'U' and resid 88 through 117 Processing helix chain 'U' and resid 123 through 151 Processing helix chain 'U' and resid 171 through 199 Processing helix chain 'U' and resid 201 through 211 Processing helix chain 'U' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS U 218 " --> pdb=" O SER U 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS U 232 " --> pdb=" O THR U 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY U 234 " --> pdb=" O LEU U 230 " (cutoff:3.500A) Processing helix chain 'U' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU U 242 " --> pdb=" O ALA U 238 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR U 243 " --> pdb=" O GLY U 239 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 25 removed outlier: 3.969A pdb=" N LYS V 19 " --> pdb=" O HIS V 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU V 20 " --> pdb=" O LEU V 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL V 21 " --> pdb=" O VAL V 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN V 22 " --> pdb=" O HIS V 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE V 25 " --> pdb=" O VAL V 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 55 removed outlier: 3.690A pdb=" N GLU V 39 " --> pdb=" O ASP V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 74 Processing helix chain 'V' and resid 88 through 117 Processing helix chain 'V' and resid 123 through 151 Processing helix chain 'V' and resid 171 through 199 Processing helix chain 'V' and resid 201 through 211 Processing helix chain 'V' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS V 218 " --> pdb=" O SER V 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS V 232 " --> pdb=" O THR V 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY V 234 " --> pdb=" O LEU V 230 " (cutoff:3.500A) Processing helix chain 'V' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR V 243 " --> pdb=" O GLY V 239 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 25 removed outlier: 3.982A pdb=" N LYS W 19 " --> pdb=" O HIS W 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU W 20 " --> pdb=" O LEU W 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL W 21 " --> pdb=" O VAL W 17 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN W 22 " --> pdb=" O HIS W 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE W 25 " --> pdb=" O VAL W 21 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 55 removed outlier: 3.597A pdb=" N GLU W 39 " --> pdb=" O ASP W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 74 Processing helix chain 'W' and resid 88 through 117 Processing helix chain 'W' and resid 123 through 151 Processing helix chain 'W' and resid 171 through 199 Processing helix chain 'W' and resid 201 through 211 Processing helix chain 'W' and resid 212 through 234 removed outlier: 3.919A pdb=" N LYS W 218 " --> pdb=" O SER W 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS W 232 " --> pdb=" O THR W 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY W 234 " --> pdb=" O LEU W 230 " (cutoff:3.500A) Processing helix chain 'W' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU W 242 " --> pdb=" O ALA W 238 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR W 243 " --> pdb=" O GLY W 239 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 25 removed outlier: 3.963A pdb=" N LYS X 19 " --> pdb=" O HIS X 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU X 20 " --> pdb=" O LEU X 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL X 21 " --> pdb=" O VAL X 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN X 22 " --> pdb=" O HIS X 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE X 25 " --> pdb=" O VAL X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 35 through 55 removed outlier: 3.678A pdb=" N GLU X 39 " --> pdb=" O ASP X 35 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 74 Processing helix chain 'X' and resid 88 through 117 Processing helix chain 'X' and resid 123 through 151 Processing helix chain 'X' and resid 171 through 199 Processing helix chain 'X' and resid 201 through 211 Processing helix chain 'X' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS X 218 " --> pdb=" O SER X 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS X 232 " --> pdb=" O THR X 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY X 234 " --> pdb=" O LEU X 230 " (cutoff:3.500A) Processing helix chain 'X' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU X 242 " --> pdb=" O ALA X 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR X 243 " --> pdb=" O GLY X 239 " (cutoff:3.500A) 3313 hydrogen bonds defined for protein. 9915 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: 13.45 Time building geometry restraints manager: 11.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 16176 1.34 - 1.46: 10603 1.46 - 1.58: 21725 1.58 - 1.69: 0 1.69 - 1.81: 480 Bond restraints: 48984 Sorted by residual: bond pdb=" CA GLU A 76 " pdb=" C GLU A 76 " ideal model delta sigma weight residual 1.517 1.532 -0.014 6.30e-03 2.52e+04 5.22e+00 bond pdb=" CA GLU M 76 " pdb=" C GLU M 76 " ideal model delta sigma weight residual 1.517 1.532 -0.014 6.30e-03 2.52e+04 5.22e+00 bond pdb=" CA GLU I 76 " pdb=" C GLU I 76 " ideal model delta sigma weight residual 1.517 1.531 -0.014 6.30e-03 2.52e+04 4.88e+00 bond pdb=" CA GLU L 76 " pdb=" C GLU L 76 " ideal model delta sigma weight residual 1.517 1.531 -0.014 6.30e-03 2.52e+04 4.87e+00 bond pdb=" CA GLU P 76 " pdb=" C GLU P 76 " ideal model delta sigma weight residual 1.517 1.531 -0.014 6.30e-03 2.52e+04 4.86e+00 ... (remaining 48979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 64342 1.23 - 2.46: 1300 2.46 - 3.69: 199 3.69 - 4.92: 15 4.92 - 6.15: 48 Bond angle restraints: 65904 Sorted by residual: angle pdb=" N LYS R 232 " pdb=" CA LYS R 232 " pdb=" C LYS R 232 " ideal model delta sigma weight residual 114.62 110.96 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N LYS I 232 " pdb=" CA LYS I 232 " pdb=" C LYS I 232 " ideal model delta sigma weight residual 114.62 110.96 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N LYS N 232 " pdb=" CA LYS N 232 " pdb=" C LYS N 232 " ideal model delta sigma weight residual 114.62 110.97 3.65 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N LYS E 232 " pdb=" CA LYS E 232 " pdb=" C LYS E 232 " ideal model delta sigma weight residual 114.62 110.97 3.65 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N LYS M 232 " pdb=" CA LYS M 232 " pdb=" C LYS M 232 " ideal model delta sigma weight residual 114.62 110.97 3.65 1.14e+00 7.69e-01 1.03e+01 ... (remaining 65899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 29122 17.92 - 35.83: 942 35.83 - 53.75: 151 53.75 - 71.67: 53 71.67 - 89.59: 44 Dihedral angle restraints: 30312 sinusoidal: 12792 harmonic: 17520 Sorted by residual: dihedral pdb=" CB GLU G 49 " pdb=" CG GLU G 49 " pdb=" CD GLU G 49 " pdb=" OE1 GLU G 49 " ideal model delta sinusoidal sigma weight residual 0.00 86.44 -86.44 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB GLU C 79 " pdb=" CG GLU C 79 " pdb=" CD GLU C 79 " pdb=" OE1 GLU C 79 " ideal model delta sinusoidal sigma weight residual 0.00 -85.32 85.32 1 3.00e+01 1.11e-03 9.80e+00 dihedral pdb=" CB GLU J 79 " pdb=" CG GLU J 79 " pdb=" CD GLU J 79 " pdb=" OE1 GLU J 79 " ideal model delta sinusoidal sigma weight residual 0.00 -84.91 84.91 1 3.00e+01 1.11e-03 9.72e+00 ... (remaining 30309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 4999 0.028 - 0.057: 1454 0.057 - 0.085: 386 0.085 - 0.114: 73 0.114 - 0.142: 24 Chirality restraints: 6936 Sorted by residual: chirality pdb=" CG LEU O 77 " pdb=" CB LEU O 77 " pdb=" CD1 LEU O 77 " pdb=" CD2 LEU O 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CG LEU Q 77 " pdb=" CB LEU Q 77 " pdb=" CD1 LEU Q 77 " pdb=" CD2 LEU Q 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CG LEU H 77 " pdb=" CB LEU H 77 " pdb=" CD1 LEU H 77 " pdb=" CD2 LEU H 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 6933 not shown) Planarity restraints: 8616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 70 " 0.004 2.00e-02 2.50e+03 8.74e-03 7.64e-01 pdb=" C ILE G 70 " -0.015 2.00e-02 2.50e+03 pdb=" O ILE G 70 " 0.006 2.00e-02 2.50e+03 pdb=" N TYR G 71 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 49 " -0.004 2.00e-02 2.50e+03 8.44e-03 7.12e-01 pdb=" C GLU F 49 " 0.015 2.00e-02 2.50e+03 pdb=" O GLU F 49 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY F 50 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU K 49 " -0.004 2.00e-02 2.50e+03 8.42e-03 7.10e-01 pdb=" C GLU K 49 " 0.015 2.00e-02 2.50e+03 pdb=" O GLU K 49 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY K 50 " -0.005 2.00e-02 2.50e+03 ... (remaining 8613 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5593 2.75 - 3.29: 48106 3.29 - 3.82: 82314 3.82 - 4.36: 88539 4.36 - 4.90: 156758 Nonbonded interactions: 381310 Sorted by model distance: nonbonded pdb=" OG1 THR H 249 " pdb=" OH TYR L 243 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR L 249 " pdb=" OH TYR P 243 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR K 243 " pdb=" OG1 THR Q 249 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR C 243 " pdb=" OG1 THR S 249 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR J 243 " pdb=" OG1 THR N 249 " model vdw 2.258 3.040 ... (remaining 381305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'B' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'C' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'D' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'E' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'F' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'G' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'H' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'I' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'J' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'K' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'L' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'M' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'N' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'O' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'P' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'Q' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'R' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'S' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'T' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'U' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'V' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'W' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'X' and (resid 9 through 137 or resid 139 through 251)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.070 Extract box with map and model: 1.590 Check model and map are aligned: 0.290 Set scattering table: 0.370 Process input model: 102.990 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.260 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: 0.020 Load rotamer database and sin/cos tables:9.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 48984 Z= 0.100 Angle : 0.414 6.147 65904 Z= 0.254 Chirality : 0.031 0.142 6936 Planarity : 0.002 0.021 8616 Dihedral : 9.420 89.586 18840 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.46 % Favored : 90.13 % Rotamer: Outliers : 1.06 % Allowed : 4.07 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.76 (0.11), residues: 5808 helix: 1.73 (0.08), residues: 4440 sheet: None (None), residues: 0 loop : -3.90 (0.13), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 168 HIS 0.002 0.000 HIS K 193 PHE 0.003 0.000 PHE Q 25 TYR 0.004 0.000 TYR O 62 ARG 0.001 0.000 ARG K 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1680 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1625 time to evaluate : 4.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 TYR cc_start: 0.8135 (t80) cc_final: 0.7630 (t80) REVERT: B 22 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7441 (mp10) REVERT: B 129 TYR cc_start: 0.8077 (t80) cc_final: 0.7705 (t80) REVERT: C 22 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7475 (mp10) REVERT: C 129 TYR cc_start: 0.8085 (t80) cc_final: 0.7375 (t80) REVERT: D 22 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7420 (mp10) REVERT: D 129 TYR cc_start: 0.8024 (t80) cc_final: 0.7293 (t80) REVERT: E 22 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: E 129 TYR cc_start: 0.8067 (t80) cc_final: 0.7359 (t80) REVERT: F 10 GLN cc_start: 0.4098 (OUTLIER) cc_final: 0.2464 (mt0) REVERT: F 22 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7541 (mp10) REVERT: F 129 TYR cc_start: 0.8084 (t80) cc_final: 0.7414 (t80) REVERT: G 22 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7495 (mp10) REVERT: G 129 TYR cc_start: 0.8096 (t80) cc_final: 0.7484 (t80) REVERT: H 22 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7335 (mp10) REVERT: H 129 TYR cc_start: 0.8010 (t80) cc_final: 0.7342 (t80) REVERT: I 22 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7590 (mp10) REVERT: I 49 GLU cc_start: 0.5417 (OUTLIER) cc_final: 0.5127 (tp30) REVERT: I 129 TYR cc_start: 0.8125 (t80) cc_final: 0.7392 (t80) REVERT: J 49 GLU cc_start: 0.5538 (OUTLIER) cc_final: 0.5338 (tp30) REVERT: J 129 TYR cc_start: 0.8037 (t80) cc_final: 0.7576 (t80) REVERT: K 10 GLN cc_start: 0.3430 (OUTLIER) cc_final: 0.1896 (mp10) REVERT: K 22 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7384 (mp10) REVERT: K 129 TYR cc_start: 0.8069 (t80) cc_final: 0.7523 (t80) REVERT: L 22 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7576 (mp10) REVERT: M 129 TYR cc_start: 0.8060 (t80) cc_final: 0.7206 (t80) REVERT: N 22 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: N 129 TYR cc_start: 0.8010 (t80) cc_final: 0.7392 (t80) REVERT: O 129 TYR cc_start: 0.8030 (t80) cc_final: 0.7260 (t80) REVERT: P 11 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.6928 (p0) REVERT: P 49 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.5270 (tp30) REVERT: P 129 TYR cc_start: 0.8040 (t80) cc_final: 0.7260 (t80) REVERT: Q 22 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7622 (mp10) REVERT: Q 129 TYR cc_start: 0.8073 (t80) cc_final: 0.7370 (t80) REVERT: R 22 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7502 (mp10) REVERT: R 129 TYR cc_start: 0.8079 (t80) cc_final: 0.7427 (t80) REVERT: S 22 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7578 (mp10) REVERT: S 49 GLU cc_start: 0.5210 (OUTLIER) cc_final: 0.4969 (tp30) REVERT: S 129 TYR cc_start: 0.8028 (t80) cc_final: 0.7430 (t80) REVERT: T 22 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7427 (mp10) REVERT: T 129 TYR cc_start: 0.8062 (t80) cc_final: 0.7662 (t80) REVERT: U 22 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: U 129 TYR cc_start: 0.8146 (t80) cc_final: 0.7714 (t80) REVERT: V 22 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7469 (mp10) REVERT: V 129 TYR cc_start: 0.8017 (t80) cc_final: 0.7226 (t80) REVERT: W 129 TYR cc_start: 0.8030 (t80) cc_final: 0.7455 (t80) REVERT: X 22 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: X 129 TYR cc_start: 0.8015 (t80) cc_final: 0.7397 (t80) outliers start: 55 outliers final: 10 residues processed: 1679 average time/residue: 1.3288 time to fit residues: 2751.9138 Evaluate side-chains 925 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 890 time to evaluate : 4.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain F residue 10 GLN Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain H residue 22 GLN Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain K residue 10 GLN Chi-restraints excluded: chain K residue 22 GLN Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 164 ASP Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain P residue 11 ASP Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 54 GLU Chi-restraints excluded: chain R residue 22 GLN Chi-restraints excluded: chain R residue 54 GLU Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain X residue 22 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 486 optimal weight: 30.0000 chunk 436 optimal weight: 7.9990 chunk 242 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 294 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 chunk 451 optimal weight: 1.9990 chunk 174 optimal weight: 0.1980 chunk 274 optimal weight: 3.9990 chunk 336 optimal weight: 50.0000 chunk 523 optimal weight: 0.6980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 74 GLN A 86 ASN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 150 GLN B 74 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 150 GLN C 86 ASN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 150 GLN D 86 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 150 GLN E 86 ASN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN E 150 GLN F 10 GLN F 86 ASN F 88 HIS F 125 ASN F 150 GLN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN H 74 GLN H 125 ASN H 150 GLN I 74 GLN I 86 ASN I 88 HIS ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 ASN I 150 GLN J 86 ASN ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 125 ASN J 150 GLN K 10 GLN K 86 ASN K 88 HIS ** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 ASN K 150 GLN L 86 ASN L 125 ASN L 150 GLN M 22 GLN M 74 GLN M 86 ASN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 ASN M 150 GLN N 86 ASN ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN ** O 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 ASN O 150 GLN ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 125 ASN P 150 GLN Q 86 ASN ** Q 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 ASN Q 150 GLN R 86 ASN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 GLN S 74 GLN ** S 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 150 GLN U 86 ASN U 125 ASN U 150 GLN V 86 ASN ** V 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 125 ASN V 150 GLN W 86 ASN W 88 HIS W 100 ASN W 125 ASN W 150 GLN ** X 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 48984 Z= 0.276 Angle : 0.698 9.326 65904 Z= 0.355 Chirality : 0.041 0.189 6936 Planarity : 0.006 0.064 8616 Dihedral : 5.786 79.489 6607 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.89 % Favored : 95.06 % Rotamer: Outliers : 2.34 % Allowed : 17.07 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.12), residues: 5808 helix: 2.29 (0.08), residues: 4488 sheet: None (None), residues: 0 loop : -3.08 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 168 HIS 0.005 0.001 HIS L 203 PHE 0.022 0.003 PHE H 207 TYR 0.024 0.002 TYR X 212 ARG 0.006 0.001 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 904 time to evaluate : 4.306 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: A 52 MET cc_start: 0.1875 (tmm) cc_final: 0.0044 (pmt) REVERT: B 22 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7437 (mp10) REVERT: B 52 MET cc_start: 0.1686 (tmm) cc_final: -0.0131 (pmt) REVERT: C 22 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7393 (mp10) REVERT: D 22 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7291 (mp10) REVERT: D 52 MET cc_start: 0.1060 (tmt) cc_final: -0.0660 (pmm) REVERT: E 22 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7430 (mp10) REVERT: E 52 MET cc_start: 0.1941 (tmm) cc_final: 0.0080 (pmt) REVERT: F 22 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7363 (mp10) REVERT: F 52 MET cc_start: 0.1741 (tmm) cc_final: 0.0098 (ppp) REVERT: G 22 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7394 (mp10) REVERT: G 52 MET cc_start: 0.1365 (tmm) cc_final: -0.0538 (pmm) REVERT: H 22 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7338 (mp10) REVERT: I 22 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7402 (mp10) REVERT: K 22 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: K 52 MET cc_start: 0.1657 (tmm) cc_final: 0.0040 (ppp) REVERT: L 22 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7452 (mp10) REVERT: N 22 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7406 (mp10) REVERT: O 52 MET cc_start: 0.1195 (tmt) cc_final: -0.0490 (pmm) REVERT: Q 22 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7396 (mp10) REVERT: R 22 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: R 52 MET cc_start: 0.1596 (tmm) cc_final: -0.0120 (pmt) REVERT: S 22 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7502 (mp10) REVERT: S 52 MET cc_start: 0.1651 (tmm) cc_final: -0.0165 (pmm) REVERT: T 22 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7375 (mp10) REVERT: T 52 MET cc_start: 0.1557 (tmm) cc_final: -0.0120 (ptp) REVERT: U 22 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7495 (mp10) REVERT: U 52 MET cc_start: 0.1681 (tmm) cc_final: -0.0199 (pmt) REVERT: V 22 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7395 (mp10) REVERT: W 52 MET cc_start: 0.0797 (tmm) cc_final: -0.1169 (ptm) REVERT: X 22 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7458 (mp10) REVERT: X 52 MET cc_start: 0.1563 (tmm) cc_final: -0.0176 (pmm) outliers start: 122 outliers final: 35 residues processed: 994 average time/residue: 1.2086 time to fit residues: 1509.9969 Evaluate side-chains 762 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 709 time to evaluate : 4.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain H residue 22 GLN Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 54 GLU Chi-restraints excluded: chain I residue 164 ASP Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain J residue 164 ASP Chi-restraints excluded: chain K residue 22 GLN Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 164 ASP Chi-restraints excluded: chain M residue 164 ASP Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 197 THR Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 54 GLU Chi-restraints excluded: chain Q residue 164 ASP Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain R residue 22 GLN Chi-restraints excluded: chain R residue 54 GLU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain T residue 197 THR Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 86 ASN Chi-restraints excluded: chain U residue 164 ASP Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain X residue 22 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 290 optimal weight: 30.0000 chunk 162 optimal weight: 3.9990 chunk 435 optimal weight: 10.0000 chunk 356 optimal weight: 0.9990 chunk 144 optimal weight: 50.0000 chunk 524 optimal weight: 3.9990 chunk 566 optimal weight: 6.9990 chunk 466 optimal weight: 0.6980 chunk 519 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 420 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 148 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 148 GLN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 148 GLN D 187 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN E 187 GLN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN F 148 GLN G 82 GLN G 86 ASN ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN G 187 GLN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN H 148 GLN H 187 GLN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN I 148 GLN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN J 148 GLN K 82 GLN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 GLN L 148 GLN ** M 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 GLN M 187 GLN ** N 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 148 GLN N 187 GLN ** O 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 148 GLN ** P 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 148 GLN P 187 GLN ** Q 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 148 GLN Q 187 GLN ** R 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 GLN R 148 GLN R 187 GLN S 86 ASN S 98 GLN S 148 GLN S 187 GLN ** T 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 GLN T 148 GLN T 187 GLN U 88 HIS U 98 GLN U 148 GLN ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 98 GLN V 148 GLN V 187 GLN W 82 GLN ** W 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 98 GLN W 148 GLN W 187 GLN X 86 ASN X 148 GLN X 187 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 48984 Z= 0.299 Angle : 0.687 10.549 65904 Z= 0.352 Chirality : 0.042 0.206 6936 Planarity : 0.005 0.056 8616 Dihedral : 5.391 68.330 6584 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.60 % Favored : 95.37 % Rotamer: Outliers : 2.65 % Allowed : 18.99 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.12), residues: 5808 helix: 2.38 (0.08), residues: 4488 sheet: None (None), residues: 0 loop : -2.69 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 168 HIS 0.007 0.001 HIS U 88 PHE 0.019 0.002 PHE W 207 TYR 0.046 0.002 TYR L 62 ARG 0.006 0.001 ARG U 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 574 time to evaluate : 4.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7795 (mpp) cc_final: 0.6568 (tpt) REVERT: B 22 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7312 (mp10) REVERT: B 38 MET cc_start: 0.7973 (mpp) cc_final: 0.6719 (tpt) REVERT: C 22 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7293 (mp10) REVERT: C 38 MET cc_start: 0.7848 (mpp) cc_final: 0.6635 (tpt) REVERT: D 22 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7178 (mp10) REVERT: D 38 MET cc_start: 0.7921 (mpp) cc_final: 0.6902 (tpt) REVERT: E 22 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: E 38 MET cc_start: 0.7933 (mpp) cc_final: 0.6645 (tpt) REVERT: F 22 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: F 38 MET cc_start: 0.7756 (mpp) cc_final: 0.6711 (tpt) REVERT: G 22 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7289 (mp10) REVERT: H 22 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: I 22 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7347 (mp10) REVERT: I 38 MET cc_start: 0.7927 (mpp) cc_final: 0.6547 (tpt) REVERT: J 38 MET cc_start: 0.7788 (mpp) cc_final: 0.6562 (tpt) REVERT: K 22 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7156 (mp10) REVERT: L 22 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7314 (mp10) REVERT: M 38 MET cc_start: 0.7961 (mpp) cc_final: 0.6733 (tpt) REVERT: N 22 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7348 (mp10) REVERT: N 38 MET cc_start: 0.7923 (mpp) cc_final: 0.6636 (tpt) REVERT: O 38 MET cc_start: 0.7926 (mpp) cc_final: 0.6824 (tpt) REVERT: P 38 MET cc_start: 0.7896 (mpp) cc_final: 0.6669 (tpt) REVERT: Q 22 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7321 (mp10) REVERT: Q 38 MET cc_start: 0.7920 (mpp) cc_final: 0.6774 (tpt) REVERT: Q 52 MET cc_start: 0.0932 (tmt) cc_final: -0.0698 (pmm) REVERT: R 22 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7253 (mp10) REVERT: R 38 MET cc_start: 0.7931 (mpp) cc_final: 0.6594 (tpt) REVERT: S 22 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7388 (mp10) REVERT: S 38 MET cc_start: 0.7911 (mpp) cc_final: 0.6631 (tpt) REVERT: T 22 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7266 (mp10) REVERT: T 38 MET cc_start: 0.7895 (mpp) cc_final: 0.6763 (tpt) REVERT: U 22 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7424 (mp10) REVERT: V 22 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7259 (mp10) REVERT: V 38 MET cc_start: 0.7819 (mpp) cc_final: 0.6654 (tpt) REVERT: W 38 MET cc_start: 0.7769 (mpp) cc_final: 0.6737 (tpt) REVERT: X 22 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: X 38 MET cc_start: 0.7854 (mpp) cc_final: 0.6605 (tpt) outliers start: 138 outliers final: 75 residues processed: 695 average time/residue: 1.3943 time to fit residues: 1189.3822 Evaluate side-chains 562 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 469 time to evaluate : 4.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 LYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain H residue 22 GLN Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 22 GLN Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 208 ILE Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 197 THR Chi-restraints excluded: chain P residue 208 ILE Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain Q residue 199 LYS Chi-restraints excluded: chain Q residue 208 ILE Chi-restraints excluded: chain R residue 22 GLN Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 208 ILE Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 197 THR Chi-restraints excluded: chain T residue 208 ILE Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain U residue 197 THR Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 172 LEU Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain W residue 172 LEU Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain X residue 22 GLN Chi-restraints excluded: chain X residue 208 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 517 optimal weight: 2.9990 chunk 393 optimal weight: 1.9990 chunk 271 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 250 optimal weight: 4.9990 chunk 351 optimal weight: 10.0000 chunk 525 optimal weight: 4.9990 chunk 556 optimal weight: 40.0000 chunk 274 optimal weight: 3.9990 chunk 498 optimal weight: 4.9990 chunk 150 optimal weight: 30.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN B 187 GLN C 86 ASN D 86 ASN D 187 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 GLN I 86 ASN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 GLN J 86 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 GLN K 86 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 187 GLN L 86 ASN M 86 ASN ** M 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 187 GLN ** N 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN Q 86 ASN R 86 ASN ** R 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 187 GLN S 86 ASN ** S 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 187 GLN U 187 GLN V 82 GLN V 86 ASN ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 187 GLN W 86 ASN W 187 GLN X 86 ASN ** X 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.6538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 48984 Z= 0.361 Angle : 0.690 8.835 65904 Z= 0.348 Chirality : 0.044 0.188 6936 Planarity : 0.004 0.052 8616 Dihedral : 5.300 58.944 6564 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.53 % Allowed : 18.93 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.11), residues: 5808 helix: 2.38 (0.08), residues: 4488 sheet: None (None), residues: 0 loop : -2.48 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 168 HIS 0.006 0.001 HIS U 88 PHE 0.023 0.003 PHE P 116 TYR 0.020 0.002 TYR D 212 ARG 0.007 0.001 ARG S 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 460 time to evaluate : 4.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7271 (mp10) REVERT: B 52 MET cc_start: 0.0926 (tmt) cc_final: -0.0875 (pmm) REVERT: B 199 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9079 (mptp) REVERT: C 22 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7240 (mp10) REVERT: C 38 MET cc_start: 0.7670 (mpp) cc_final: 0.6692 (tpt) REVERT: C 52 MET cc_start: 0.0863 (tmt) cc_final: -0.0982 (pmm) REVERT: D 22 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7107 (mp10) REVERT: D 38 MET cc_start: 0.7704 (mpp) cc_final: 0.6837 (tpt) REVERT: D 52 MET cc_start: 0.1205 (tmt) cc_final: -0.0564 (pmm) REVERT: D 199 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9063 (mptp) REVERT: E 22 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7320 (mp10) REVERT: E 52 MET cc_start: 0.1123 (tmt) cc_final: -0.0651 (pmm) REVERT: F 22 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7156 (mp10) REVERT: F 38 MET cc_start: 0.7652 (mpp) cc_final: 0.6690 (tpt) REVERT: F 52 MET cc_start: 0.1611 (tmm) cc_final: -0.0065 (ppp) REVERT: F 199 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.9066 (mptp) REVERT: G 22 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: I 22 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: I 52 MET cc_start: 0.0838 (tmt) cc_final: -0.1063 (pmm) REVERT: J 38 MET cc_start: 0.7637 (mpp) cc_final: 0.6591 (tpt) REVERT: J 199 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.9062 (mptp) REVERT: K 38 MET cc_start: 0.7874 (mpp) cc_final: 0.6885 (tpt) REVERT: K 52 MET cc_start: 0.1643 (tmm) cc_final: -0.0073 (ppp) REVERT: L 22 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7210 (mp10) REVERT: L 38 MET cc_start: 0.7469 (mpp) cc_final: 0.6540 (tpt) REVERT: L 52 MET cc_start: 0.1582 (ppp) cc_final: 0.0061 (pmt) REVERT: O 52 MET cc_start: 0.1097 (tmt) cc_final: -0.0643 (pmm) REVERT: P 38 MET cc_start: 0.7637 (mpp) cc_final: 0.6584 (tpt) REVERT: P 199 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.9072 (mptp) REVERT: Q 22 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: R 22 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7269 (mp10) REVERT: R 38 MET cc_start: 0.7659 (mpp) cc_final: 0.6490 (tpt) REVERT: R 52 MET cc_start: 0.0946 (tmt) cc_final: -0.0836 (pmm) REVERT: S 22 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7229 (mp10) REVERT: U 22 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7289 (mp10) REVERT: V 22 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7134 (mp10) REVERT: W 52 MET cc_start: 0.1048 (tmm) cc_final: -0.0847 (ppp) REVERT: W 199 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.9052 (mptp) REVERT: X 22 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7193 (mp10) REVERT: X 52 MET cc_start: 0.1489 (tmm) cc_final: -0.0404 (pmm) outliers start: 132 outliers final: 56 residues processed: 589 average time/residue: 1.2888 time to fit residues: 946.4101 Evaluate side-chains 506 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 430 time to evaluate : 4.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 LYS Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 199 LYS Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 197 THR Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain R residue 22 GLN Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 86 ASN Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 197 THR Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain U residue 197 THR Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 199 LYS Chi-restraints excluded: chain X residue 22 GLN Chi-restraints excluded: chain X residue 86 ASN Chi-restraints excluded: chain X residue 197 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 463 optimal weight: 2.9990 chunk 316 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 414 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 475 optimal weight: 0.9980 chunk 384 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 284 optimal weight: 5.9990 chunk 499 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN C 86 ASN D 86 ASN E 86 ASN F 82 GLN F 86 ASN G 86 ASN H 187 GLN I 86 ASN J 86 ASN K 86 ASN L 98 GLN M 86 ASN N 86 ASN O 86 ASN Q 82 GLN Q 86 ASN Q 88 HIS Q 98 GLN R 86 ASN ** S 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 GLN T 88 HIS U 86 ASN V 86 ASN W 86 ASN X 82 GLN ** X 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 48984 Z= 0.233 Angle : 0.630 8.325 65904 Z= 0.315 Chirality : 0.040 0.199 6936 Planarity : 0.004 0.050 8616 Dihedral : 4.842 57.716 6552 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.80 % Allowed : 19.74 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.12), residues: 5808 helix: 2.54 (0.08), residues: 4536 sheet: None (None), residues: 0 loop : -2.20 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 168 HIS 0.006 0.001 HIS V 88 PHE 0.013 0.002 PHE H 207 TYR 0.015 0.001 TYR U 212 ARG 0.004 0.000 ARG T 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 471 time to evaluate : 4.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.1564 (tmm) cc_final: -0.0490 (pmm) REVERT: B 22 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7227 (mp10) REVERT: B 199 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.9028 (mmtp) REVERT: C 22 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7260 (mp10) REVERT: D 22 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7120 (mp10) REVERT: D 38 MET cc_start: 0.7663 (mpp) cc_final: 0.6843 (tpt) REVERT: D 199 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9047 (mptp) REVERT: E 22 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: F 22 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7144 (mp10) REVERT: F 199 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.9051 (mptp) REVERT: G 22 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7171 (mp10) REVERT: G 52 MET cc_start: 0.1149 (tmm) cc_final: -0.0961 (pmm) REVERT: I 22 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7272 (mp10) REVERT: K 38 MET cc_start: 0.7843 (mpp) cc_final: 0.6895 (tpt) REVERT: L 22 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7216 (mp10) REVERT: L 38 MET cc_start: 0.7411 (mpp) cc_final: 0.6577 (tpt) REVERT: L 52 MET cc_start: 0.1334 (ppp) cc_final: -0.0222 (pmt) REVERT: Q 22 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: Q 52 MET cc_start: 0.1596 (tmm) cc_final: -0.0327 (pmm) REVERT: R 22 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7242 (mp10) REVERT: S 22 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: S 52 MET cc_start: 0.1135 (tmm) cc_final: -0.0968 (pmt) REVERT: T 52 MET cc_start: 0.0756 (tmm) cc_final: -0.1124 (pmm) REVERT: U 22 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: U 52 MET cc_start: 0.1443 (tmm) cc_final: -0.0674 (pmm) REVERT: V 22 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7145 (mp10) REVERT: W 199 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.9023 (mptp) REVERT: X 22 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7173 (mp10) REVERT: X 52 MET cc_start: 0.1476 (tmm) cc_final: -0.0552 (pmm) outliers start: 94 outliers final: 57 residues processed: 563 average time/residue: 1.3915 time to fit residues: 964.8229 Evaluate side-chains 499 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 424 time to evaluate : 4.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 LYS Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 86 ASN Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain K residue 86 ASN Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 86 ASN Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 199 LYS Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain N residue 199 LYS Chi-restraints excluded: chain O residue 86 ASN Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 86 ASN Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain R residue 22 GLN Chi-restraints excluded: chain R residue 86 ASN Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 199 LYS Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain V residue 86 ASN Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 199 LYS Chi-restraints excluded: chain W residue 86 ASN Chi-restraints excluded: chain W residue 199 LYS Chi-restraints excluded: chain X residue 22 GLN Chi-restraints excluded: chain X residue 197 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 187 optimal weight: 3.9990 chunk 501 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 326 optimal weight: 8.9990 chunk 137 optimal weight: 0.7980 chunk 557 optimal weight: 30.0000 chunk 462 optimal weight: 8.9990 chunk 258 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 184 optimal weight: 5.9990 chunk 292 optimal weight: 30.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN B 86 ASN C 86 ASN D 82 GLN D 86 ASN E 86 ASN F 86 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN I 86 ASN J 86 ASN J 88 HIS K 86 ASN L 86 ASN M 86 ASN M 140 HIS N 86 ASN N 140 HIS O 86 ASN P 86 ASN Q 86 ASN R 86 ASN S 86 ASN ** S 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 140 HIS T 86 ASN T 140 HIS U 86 ASN ** U 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 140 HIS V 82 GLN V 86 ASN W 86 ASN X 86 ASN ** X 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 140 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.6696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 48984 Z= 0.263 Angle : 0.630 8.964 65904 Z= 0.314 Chirality : 0.041 0.160 6936 Planarity : 0.004 0.048 8616 Dihedral : 4.812 57.799 6552 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.09 % Allowed : 19.05 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.12), residues: 5808 helix: 2.60 (0.08), residues: 4536 sheet: None (None), residues: 0 loop : -2.07 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 168 HIS 0.008 0.001 HIS R 88 PHE 0.016 0.002 PHE F 116 TYR 0.016 0.001 TYR O 212 ARG 0.005 0.000 ARG Q 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 441 time to evaluate : 4.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.1588 (tmm) cc_final: -0.0449 (pmm) REVERT: B 22 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7234 (mp10) REVERT: B 52 MET cc_start: 0.1549 (tmm) cc_final: -0.0460 (pmt) REVERT: B 199 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.9052 (mptp) REVERT: C 22 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: C 52 MET cc_start: 0.0803 (tmt) cc_final: -0.1073 (pmm) REVERT: D 22 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7086 (mp10) REVERT: D 52 MET cc_start: 0.1174 (tmt) cc_final: -0.0654 (pmm) REVERT: D 199 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.9066 (mptp) REVERT: E 22 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7302 (mp10) REVERT: E 52 MET cc_start: 0.0968 (tmt) cc_final: -0.0953 (pmm) REVERT: F 22 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7106 (mp10) REVERT: F 52 MET cc_start: 0.1639 (tmm) cc_final: 0.0005 (pmm) REVERT: F 199 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.9066 (mptp) REVERT: G 52 MET cc_start: 0.1092 (tmm) cc_final: -0.1008 (pmm) REVERT: I 22 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: K 38 MET cc_start: 0.7822 (mpp) cc_final: 0.6848 (tpt) REVERT: K 52 MET cc_start: 0.1511 (tmm) cc_final: -0.0286 (pmm) REVERT: L 22 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7203 (mp10) REVERT: L 38 MET cc_start: 0.7419 (mpp) cc_final: 0.6571 (tpt) REVERT: L 52 MET cc_start: 0.1225 (ppp) cc_final: -0.0326 (pmm) REVERT: O 52 MET cc_start: 0.1579 (tmm) cc_final: -0.0473 (pmm) REVERT: P 52 MET cc_start: 0.0971 (tmm) cc_final: -0.1095 (pmm) REVERT: Q 22 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7185 (mp10) REVERT: Q 52 MET cc_start: 0.1507 (tmm) cc_final: -0.0432 (pmm) REVERT: R 22 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: R 52 MET cc_start: 0.1094 (tmm) cc_final: -0.0736 (pmm) REVERT: S 22 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7214 (mp10) REVERT: S 52 MET cc_start: 0.1374 (tmm) cc_final: -0.0782 (pmt) REVERT: T 52 MET cc_start: 0.0667 (tmm) cc_final: -0.1196 (pmm) REVERT: U 52 MET cc_start: 0.1555 (tmm) cc_final: -0.0603 (pmm) REVERT: W 38 MET cc_start: 0.7831 (mpp) cc_final: 0.6767 (tpt) REVERT: W 52 MET cc_start: 0.0825 (tmm) cc_final: -0.0924 (pmm) REVERT: W 199 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.9036 (mptp) REVERT: X 22 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7151 (mp10) outliers start: 109 outliers final: 81 residues processed: 545 average time/residue: 1.3365 time to fit residues: 904.2542 Evaluate side-chains 522 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 426 time to evaluate : 4.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 LYS Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 86 ASN Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain K residue 86 ASN Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain K residue 240 MET Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 86 ASN Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 199 LYS Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 199 LYS Chi-restraints excluded: chain O residue 86 ASN Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 86 ASN Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain R residue 22 GLN Chi-restraints excluded: chain R residue 86 ASN Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 199 LYS Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 86 ASN Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain T residue 86 ASN Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain U residue 86 ASN Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain U residue 197 THR Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain V residue 86 ASN Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 199 LYS Chi-restraints excluded: chain W residue 86 ASN Chi-restraints excluded: chain W residue 199 LYS Chi-restraints excluded: chain X residue 22 GLN Chi-restraints excluded: chain X residue 86 ASN Chi-restraints excluded: chain X residue 197 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 537 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 317 optimal weight: 40.0000 chunk 406 optimal weight: 0.0980 chunk 315 optimal weight: 9.9990 chunk 469 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 chunk 555 optimal weight: 30.0000 chunk 347 optimal weight: 4.9990 chunk 338 optimal weight: 0.0020 chunk 256 optimal weight: 0.8980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN B 82 GLN B 86 ASN B 140 HIS C 86 ASN C 140 HIS D 86 ASN D 140 HIS E 86 ASN F 86 ASN F 140 HIS G 86 ASN G 140 HIS H 86 ASN I 86 ASN J 86 ASN K 86 ASN K 140 HIS L 86 ASN M 86 ASN ** N 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN O 140 HIS P 86 ASN P 98 GLN Q 86 ASN Q 140 HIS R 86 ASN R 140 HIS S 86 ASN T 86 ASN U 86 ASN V 86 ASN W 86 ASN ** X 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.6665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 48984 Z= 0.174 Angle : 0.589 9.315 65904 Z= 0.292 Chirality : 0.038 0.136 6936 Planarity : 0.003 0.047 8616 Dihedral : 4.491 57.287 6543 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.63 % Allowed : 19.78 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.12), residues: 5808 helix: 2.79 (0.08), residues: 4536 sheet: None (None), residues: 0 loop : -2.05 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP L 168 HIS 0.006 0.001 HIS U 88 PHE 0.014 0.002 PHE H 207 TYR 0.014 0.001 TYR S 212 ARG 0.004 0.000 ARG Q 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 474 time to evaluate : 4.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.1623 (tmm) cc_final: -0.0389 (pmm) REVERT: B 22 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7219 (mp10) REVERT: B 52 MET cc_start: 0.1601 (tmm) cc_final: -0.0428 (pmm) REVERT: C 22 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: D 22 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7082 (mp10) REVERT: D 38 MET cc_start: 0.8377 (mpm) cc_final: 0.7314 (tpt) REVERT: E 22 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: E 52 MET cc_start: 0.0989 (tmt) cc_final: -0.0905 (pmm) REVERT: F 22 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7114 (mp10) REVERT: F 52 MET cc_start: 0.1439 (tmm) cc_final: -0.0203 (pmm) REVERT: F 199 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.9046 (mptp) REVERT: I 22 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7284 (mp10) REVERT: K 38 MET cc_start: 0.7838 (mpp) cc_final: 0.6909 (tpt) REVERT: K 52 MET cc_start: 0.1292 (tmm) cc_final: -0.0448 (pmm) REVERT: L 22 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7236 (mp10) REVERT: L 38 MET cc_start: 0.7435 (mpp) cc_final: 0.6653 (tpt) REVERT: L 52 MET cc_start: 0.1338 (ppp) cc_final: -0.0255 (pmm) REVERT: M 52 MET cc_start: 0.1548 (tmm) cc_final: -0.0493 (pmm) REVERT: O 52 MET cc_start: 0.1547 (tmm) cc_final: -0.0431 (pmm) REVERT: P 52 MET cc_start: 0.0958 (tmm) cc_final: -0.1079 (pmm) REVERT: Q 22 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7132 (mp10) REVERT: Q 52 MET cc_start: 0.1560 (tmm) cc_final: -0.0381 (pmm) REVERT: R 22 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: R 52 MET cc_start: 0.1210 (tmm) cc_final: -0.0664 (pmm) REVERT: S 22 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7209 (mp10) REVERT: U 52 MET cc_start: 0.1663 (tmm) cc_final: -0.0510 (pmm) REVERT: W 38 MET cc_start: 0.7862 (mpp) cc_final: 0.6818 (tpt) REVERT: X 22 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7134 (mp10) outliers start: 85 outliers final: 61 residues processed: 557 average time/residue: 1.3249 time to fit residues: 917.4315 Evaluate side-chains 514 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 441 time to evaluate : 4.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 199 LYS Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 86 ASN Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 86 ASN Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 86 ASN Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 199 LYS Chi-restraints excluded: chain N residue 199 LYS Chi-restraints excluded: chain O residue 86 ASN Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 86 ASN Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain R residue 22 GLN Chi-restraints excluded: chain R residue 86 ASN Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 199 LYS Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 86 ASN Chi-restraints excluded: chain T residue 86 ASN Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 86 ASN Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 199 LYS Chi-restraints excluded: chain W residue 86 ASN Chi-restraints excluded: chain X residue 22 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 343 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 331 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 352 optimal weight: 3.9990 chunk 378 optimal weight: 0.9980 chunk 274 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 436 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN B 86 ASN B 88 HIS C 86 ASN D 86 ASN D 88 HIS E 86 ASN E 140 HIS F 86 ASN G 86 ASN H 86 ASN I 86 ASN I 140 HIS J 86 ASN J 140 HIS K 86 ASN L 86 ASN L 140 HIS M 86 ASN N 86 ASN O 86 ASN P 86 ASN P 140 HIS Q 86 ASN R 86 ASN S 86 ASN T 86 ASN ** U 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 86 ASN W 86 ASN W 88 HIS ** X 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.6904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 48984 Z= 0.388 Angle : 0.671 10.688 65904 Z= 0.334 Chirality : 0.043 0.185 6936 Planarity : 0.004 0.043 8616 Dihedral : 4.667 57.240 6543 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.13 % Allowed : 19.68 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.12), residues: 5808 helix: 2.66 (0.08), residues: 4536 sheet: None (None), residues: 0 loop : -1.97 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 168 HIS 0.010 0.001 HIS P 88 PHE 0.022 0.003 PHE W 116 TYR 0.019 0.001 TYR U 212 ARG 0.006 0.001 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 441 time to evaluate : 4.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.1750 (tmm) cc_final: -0.0272 (pmm) REVERT: B 22 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7185 (mp10) REVERT: B 52 MET cc_start: 0.1634 (tmm) cc_final: -0.0379 (pmm) REVERT: C 22 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: C 52 MET cc_start: 0.0886 (tmt) cc_final: -0.1019 (pmm) REVERT: D 22 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7121 (mp10) REVERT: E 22 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7257 (mp10) REVERT: F 22 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7083 (mp10) REVERT: F 52 MET cc_start: 0.1642 (tmm) cc_final: -0.0069 (pmm) REVERT: H 52 MET cc_start: 0.0552 (tmm) cc_final: -0.1521 (pmm) REVERT: I 22 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7226 (mp10) REVERT: K 38 MET cc_start: 0.7891 (mpp) cc_final: 0.6935 (tpt) REVERT: L 22 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7178 (mp10) REVERT: L 38 MET cc_start: 0.7430 (mpp) cc_final: 0.6616 (tpt) REVERT: L 52 MET cc_start: 0.1371 (ppp) cc_final: -0.0216 (pmm) REVERT: M 52 MET cc_start: 0.1690 (tmm) cc_final: -0.0406 (pmm) REVERT: O 52 MET cc_start: 0.1602 (tmm) cc_final: -0.0364 (pmm) REVERT: P 52 MET cc_start: 0.0851 (tmm) cc_final: -0.1183 (pmm) REVERT: Q 52 MET cc_start: 0.1692 (tmm) cc_final: -0.0295 (pmm) REVERT: R 52 MET cc_start: 0.1258 (tmm) cc_final: -0.0624 (pmm) REVERT: S 22 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: U 52 MET cc_start: 0.1737 (tmm) cc_final: -0.0444 (pmm) REVERT: V 52 MET cc_start: 0.0663 (tmm) cc_final: -0.1335 (pmm) REVERT: W 38 MET cc_start: 0.7867 (mpp) cc_final: 0.6827 (tpt) REVERT: W 52 MET cc_start: 0.0852 (tmm) cc_final: -0.0982 (pmm) REVERT: X 52 MET cc_start: 0.0974 (tmm) cc_final: -0.0916 (pmm) REVERT: X 89 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7436 (pm20) outliers start: 111 outliers final: 75 residues processed: 539 average time/residue: 1.3301 time to fit residues: 891.3409 Evaluate side-chains 512 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 428 time to evaluate : 4.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 86 ASN Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 86 ASN Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 86 ASN Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 199 LYS Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 199 LYS Chi-restraints excluded: chain O residue 86 ASN Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 92 GLU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 197 THR Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain Q residue 86 ASN Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain R residue 86 ASN Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 199 LYS Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 86 ASN Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain T residue 86 ASN Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 197 THR Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain V residue 86 ASN Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain V residue 199 LYS Chi-restraints excluded: chain W residue 86 ASN Chi-restraints excluded: chain X residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 505 optimal weight: 3.9990 chunk 531 optimal weight: 20.0000 chunk 485 optimal weight: 7.9990 chunk 517 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 chunk 406 optimal weight: 0.0570 chunk 158 optimal weight: 1.9990 chunk 467 optimal weight: 0.6980 chunk 489 optimal weight: 0.8980 chunk 515 optimal weight: 0.8980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN B 86 ASN C 86 ASN D 86 ASN E 86 ASN F 74 GLN F 86 ASN F 88 HIS G 86 ASN H 86 ASN I 86 ASN J 86 ASN K 86 ASN M 86 ASN N 86 ASN O 82 GLN O 86 ASN P 86 ASN Q 86 ASN R 86 ASN S 88 HIS V 86 ASN W 86 ASN W 140 HIS W 158 GLN X 82 GLN ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.6843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 48984 Z= 0.182 Angle : 0.606 11.104 65904 Z= 0.299 Chirality : 0.038 0.175 6936 Planarity : 0.003 0.044 8616 Dihedral : 4.323 56.918 6534 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.69 % Allowed : 19.91 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.12), residues: 5808 helix: 2.86 (0.08), residues: 4536 sheet: None (None), residues: 0 loop : -1.88 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 168 HIS 0.007 0.001 HIS N 88 PHE 0.013 0.002 PHE T 207 TYR 0.014 0.001 TYR S 212 ARG 0.003 0.000 ARG N 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 447 time to evaluate : 4.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.1740 (tmm) cc_final: -0.0285 (pmm) REVERT: B 22 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7176 (mp10) REVERT: B 52 MET cc_start: 0.1617 (tmm) cc_final: -0.0370 (pmm) REVERT: C 22 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: C 52 MET cc_start: 0.0903 (tmt) cc_final: -0.0983 (pmm) REVERT: C 117 ASP cc_start: 0.7773 (t70) cc_final: 0.7555 (t0) REVERT: D 22 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7107 (mp10) REVERT: D 52 MET cc_start: 0.1097 (tmt) cc_final: -0.0764 (pmm) REVERT: E 22 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7283 (mp10) REVERT: F 52 MET cc_start: 0.1644 (tmm) cc_final: -0.0026 (pmm) REVERT: G 52 MET cc_start: 0.0797 (tmm) cc_final: -0.1279 (pmm) REVERT: I 22 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7264 (mp10) REVERT: J 52 MET cc_start: 0.0716 (tmt) cc_final: -0.1159 (pmm) REVERT: K 38 MET cc_start: 0.7828 (mpp) cc_final: 0.6894 (tpt) REVERT: K 52 MET cc_start: 0.1705 (tmm) cc_final: -0.0333 (pmm) REVERT: L 22 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7175 (mp10) REVERT: L 52 MET cc_start: 0.1281 (ppp) cc_final: -0.0179 (pmm) REVERT: M 52 MET cc_start: 0.1662 (tmm) cc_final: -0.0403 (pmm) REVERT: M 117 ASP cc_start: 0.7810 (t70) cc_final: 0.7579 (t0) REVERT: N 52 MET cc_start: 0.0543 (tmm) cc_final: -0.1580 (pmm) REVERT: O 52 MET cc_start: 0.1558 (tmm) cc_final: -0.0315 (pmm) REVERT: P 52 MET cc_start: 0.0826 (tmm) cc_final: -0.1191 (pmm) REVERT: Q 52 MET cc_start: 0.1671 (tmm) cc_final: -0.0211 (pmm) REVERT: Q 117 ASP cc_start: 0.7795 (t70) cc_final: 0.7577 (t0) REVERT: R 52 MET cc_start: 0.1282 (tmm) cc_final: -0.0599 (pmm) REVERT: S 22 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7218 (mp10) REVERT: S 52 MET cc_start: 0.1034 (tmm) cc_final: -0.1104 (pmm) REVERT: T 22 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: T 52 MET cc_start: 0.0724 (tmm) cc_final: -0.1298 (pmm) REVERT: U 22 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: U 52 MET cc_start: 0.1732 (tmm) cc_final: -0.0419 (pmm) REVERT: V 52 MET cc_start: 0.0738 (tmm) cc_final: -0.1267 (pmm) REVERT: W 38 MET cc_start: 0.7815 (mpp) cc_final: 0.6765 (tpt) REVERT: W 52 MET cc_start: 0.0816 (tmm) cc_final: -0.0914 (pmm) REVERT: X 52 MET cc_start: 0.0976 (tmm) cc_final: -0.0943 (pmm) outliers start: 88 outliers final: 58 residues processed: 529 average time/residue: 1.2832 time to fit residues: 849.9527 Evaluate side-chains 493 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 426 time to evaluate : 4.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 86 ASN Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 86 ASN Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 86 ASN Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 199 LYS Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 199 LYS Chi-restraints excluded: chain O residue 86 ASN Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain Q residue 86 ASN Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain R residue 86 ASN Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 199 LYS Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 86 ASN Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 199 LYS Chi-restraints excluded: chain W residue 86 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 339 optimal weight: 10.0000 chunk 547 optimal weight: 3.9990 chunk 333 optimal weight: 3.9990 chunk 259 optimal weight: 0.0010 chunk 380 optimal weight: 2.9990 chunk 573 optimal weight: 3.9990 chunk 528 optimal weight: 50.0000 chunk 456 optimal weight: 50.0000 chunk 47 optimal weight: 3.9990 chunk 352 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN C 86 ASN D 86 ASN E 86 ASN F 86 ASN G 86 ASN H 86 ASN I 86 ASN J 86 ASN K 86 ASN M 86 ASN N 86 ASN O 86 ASN P 86 ASN Q 86 ASN R 86 ASN T 86 ASN ** U 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 86 ASN W 86 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.6917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 48984 Z= 0.296 Angle : 0.644 11.190 65904 Z= 0.317 Chirality : 0.041 0.190 6936 Planarity : 0.004 0.042 8616 Dihedral : 4.361 56.709 6534 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.56 % Allowed : 20.07 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.12), residues: 5808 helix: 2.80 (0.08), residues: 4536 sheet: None (None), residues: 0 loop : -1.86 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP U 168 HIS 0.006 0.001 HIS L 88 PHE 0.017 0.002 PHE F 116 TYR 0.016 0.001 TYR L 212 ARG 0.006 0.001 ARG N 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 435 time to evaluate : 4.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.1763 (tmm) cc_final: -0.0264 (pmm) REVERT: B 22 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7175 (mp10) REVERT: B 52 MET cc_start: 0.1634 (tmm) cc_final: -0.0342 (pmm) REVERT: C 22 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: C 52 MET cc_start: 0.0852 (tmt) cc_final: -0.1021 (pmm) REVERT: E 22 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7227 (mp10) REVERT: E 52 MET cc_start: 0.0947 (tmt) cc_final: -0.1007 (pmm) REVERT: F 52 MET cc_start: 0.1622 (tmm) cc_final: 0.0012 (pmm) REVERT: G 52 MET cc_start: 0.0694 (tmm) cc_final: -0.1354 (pmm) REVERT: I 22 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7254 (mp10) REVERT: K 38 MET cc_start: 0.7822 (mpp) cc_final: 0.6950 (tpt) REVERT: K 52 MET cc_start: 0.1756 (tmm) cc_final: -0.0277 (pmm) REVERT: L 22 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: L 38 MET cc_start: 0.8344 (mpm) cc_final: 0.7146 (tpt) REVERT: L 52 MET cc_start: 0.1324 (ppp) cc_final: -0.0137 (pmm) REVERT: M 52 MET cc_start: 0.1680 (tmm) cc_final: -0.0406 (pmm) REVERT: N 52 MET cc_start: 0.0688 (tmm) cc_final: -0.1409 (pmm) REVERT: O 52 MET cc_start: 0.1655 (tmm) cc_final: -0.0281 (pmm) REVERT: P 52 MET cc_start: 0.0830 (tmm) cc_final: -0.1200 (pmm) REVERT: Q 52 MET cc_start: 0.1668 (tmm) cc_final: -0.0215 (pmm) REVERT: R 52 MET cc_start: 0.1274 (tmm) cc_final: -0.0622 (pmm) REVERT: S 22 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: S 52 MET cc_start: 0.1087 (tmm) cc_final: -0.1032 (pmm) REVERT: T 52 MET cc_start: 0.0753 (tmm) cc_final: -0.1259 (pmm) REVERT: U 22 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: U 52 MET cc_start: 0.1825 (tmm) cc_final: -0.0313 (pmm) REVERT: V 52 MET cc_start: 0.0732 (tmm) cc_final: -0.1267 (pmm) REVERT: W 38 MET cc_start: 0.7823 (mpp) cc_final: 0.6768 (tpt) REVERT: W 52 MET cc_start: 0.0956 (tmm) cc_final: -0.0811 (pmm) REVERT: X 52 MET cc_start: 0.0969 (tmm) cc_final: -0.0963 (pmm) outliers start: 81 outliers final: 68 residues processed: 510 average time/residue: 1.3260 time to fit residues: 842.1892 Evaluate side-chains 496 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 421 time to evaluate : 4.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 86 ASN Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain K residue 86 ASN Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 86 ASN Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 199 LYS Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 199 LYS Chi-restraints excluded: chain O residue 86 ASN Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain Q residue 86 ASN Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain R residue 86 ASN Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 199 LYS Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain T residue 86 ASN Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 197 THR Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain U residue 197 THR Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 199 LYS Chi-restraints excluded: chain W residue 86 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 362 optimal weight: 8.9990 chunk 486 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 421 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 126 optimal weight: 0.2980 chunk 457 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 469 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS C 86 ASN K 86 ASN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN R 86 ASN ** T 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 140 HIS X 88 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.156332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.098059 restraints weight = 156623.960| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.63 r_work: 0.3057 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.6877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 48984 Z= 0.182 Angle : 0.606 11.053 65904 Z= 0.300 Chirality : 0.038 0.179 6936 Planarity : 0.003 0.043 8616 Dihedral : 4.291 56.659 6534 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.59 % Allowed : 20.10 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.01 (0.12), residues: 5808 helix: 2.92 (0.08), residues: 4536 sheet: None (None), residues: 0 loop : -1.75 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP J 168 HIS 0.007 0.001 HIS T 88 PHE 0.014 0.002 PHE T 207 TYR 0.014 0.001 TYR N 212 ARG 0.006 0.000 ARG T 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17565.37 seconds wall clock time: 301 minutes 11.58 seconds (18071.58 seconds total)