Starting phenix.real_space_refine on Sun Mar 24 11:21:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bjc_7101/03_2024/6bjc_7101_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bjc_7101/03_2024/6bjc_7101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bjc_7101/03_2024/6bjc_7101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bjc_7101/03_2024/6bjc_7101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bjc_7101/03_2024/6bjc_7101_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bjc_7101/03_2024/6bjc_7101_updated.pdb" } resolution = 3.3 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= -0.016 sd= 0.932 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 284 5.16 5 C 25854 2.51 5 N 7020 2.21 5 O 7930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C ARG 320": "NH1" <-> "NH2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C GLU 415": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C GLU 433": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E ARG 320": "NH1" <-> "NH2" Residue "E PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 414": "OE1" <-> "OE2" Residue "E GLU 415": "OE1" <-> "OE2" Residue "E GLU 429": "OE1" <-> "OE2" Residue "E GLU 433": "OE1" <-> "OE2" Residue "F GLU 160": "OE1" <-> "OE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J GLU 168": "OE1" <-> "OE2" Residue "J GLU 279": "OE1" <-> "OE2" Residue "J ARG 320": "NH1" <-> "NH2" Residue "J PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 414": "OE1" <-> "OE2" Residue "J GLU 415": "OE1" <-> "OE2" Residue "J GLU 429": "OE1" <-> "OE2" Residue "J GLU 433": "OE1" <-> "OE2" Residue "H GLU 160": "OE1" <-> "OE2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L GLU 168": "OE1" <-> "OE2" Residue "L GLU 279": "OE1" <-> "OE2" Residue "L ARG 320": "NH1" <-> "NH2" Residue "L PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 414": "OE1" <-> "OE2" Residue "L GLU 415": "OE1" <-> "OE2" Residue "L GLU 429": "OE1" <-> "OE2" Residue "L GLU 433": "OE1" <-> "OE2" Residue "G GLU 160": "OE1" <-> "OE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 84": "NH1" <-> "NH2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "K GLU 168": "OE1" <-> "OE2" Residue "K GLU 279": "OE1" <-> "OE2" Residue "K ARG 320": "NH1" <-> "NH2" Residue "K PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 414": "OE1" <-> "OE2" Residue "K GLU 415": "OE1" <-> "OE2" Residue "K GLU 429": "OE1" <-> "OE2" Residue "K GLU 433": "OE1" <-> "OE2" Residue "I GLU 160": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41136 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 27} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 27} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.92, per 1000 atoms: 0.51 Number of scatterers: 41136 At special positions: 0 Unit cell: (172.9, 89.11, 214.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 284 16.00 P 36 15.00 Mg 12 11.99 O 7930 8.00 N 7020 7.00 C 25854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.95 Conformation dependent library (CDL) restraints added in 7.0 seconds 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9648 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 254 helices and 30 sheets defined 50.1% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.48 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.613A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.589A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.100A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.565A pdb=" N THR A 190 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 195 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS A 197 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.440A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.725A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 283' Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.702A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.549A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 41 through 47 removed outlier: 3.555A pdb=" N GLU B 47 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 110 through 128 removed outlier: 4.382A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.562A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 224 through 243 removed outlier: 3.801A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 338 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.637A pdb=" N ARG B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG B 400 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 Processing helix chain 'B' and resid 415 through 436 Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 48 through 51 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.613A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 115 through 128 removed outlier: 3.589A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.100A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.564A pdb=" N THR C 190 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 195 " --> pdb=" O HIS C 192 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS C 197 " --> pdb=" O THR C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 224 through 243 removed outlier: 4.440A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.725A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N HIS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 283' Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.702A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 325 through 337 Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.548A pdb=" N TYR C 399 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 415 through 436 Processing helix chain 'D' and resid 10 through 27 Processing helix chain 'D' and resid 41 through 47 removed outlier: 3.555A pdb=" N GLU D 47 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 110 through 128 removed outlier: 4.383A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 160 Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.562A pdb=" N GLN D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 224 through 243 removed outlier: 3.801A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 325 through 338 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 382 through 401 removed outlier: 3.638A pdb=" N ARG D 390 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG D 400 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 411 Processing helix chain 'D' and resid 415 through 436 Processing helix chain 'T' and resid 327 through 336 removed outlier: 3.509A pdb=" N HIS T 335 " --> pdb=" O VAL T 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 48 through 51 Processing helix chain 'E' and resid 73 through 80 removed outlier: 3.613A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 115 through 128 removed outlier: 3.588A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.100A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.565A pdb=" N THR E 190 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 195 " --> pdb=" O HIS E 192 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS E 197 " --> pdb=" O THR E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 217 Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.441A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 278 through 283 removed outlier: 3.724A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N HIS E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 278 through 283' Processing helix chain 'E' and resid 288 through 296 removed outlier: 3.702A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 307 through 309 No H-bonds generated for 'chain 'E' and resid 307 through 309' Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'E' and resid 382 through 401 removed outlier: 3.548A pdb=" N TYR E 399 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 415 through 436 Processing helix chain 'F' and resid 10 through 27 Processing helix chain 'F' and resid 41 through 47 removed outlier: 3.556A pdb=" N GLU F 47 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 110 through 128 removed outlier: 4.381A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 160 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.562A pdb=" N GLN F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 Processing helix chain 'F' and resid 224 through 243 removed outlier: 3.801A pdb=" N THR F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 259 Processing helix chain 'F' and resid 279 through 281 No H-bonds generated for 'chain 'F' and resid 279 through 281' Processing helix chain 'F' and resid 288 through 296 Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 307 through 309 No H-bonds generated for 'chain 'F' and resid 307 through 309' Processing helix chain 'F' and resid 325 through 338 Processing helix chain 'F' and resid 340 through 342 No H-bonds generated for 'chain 'F' and resid 340 through 342' Processing helix chain 'F' and resid 382 through 401 removed outlier: 3.636A pdb=" N ARG F 390 " --> pdb=" O LEU F 387 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG F 400 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 Processing helix chain 'F' and resid 415 through 436 Processing helix chain 'J' and resid 10 through 28 Processing helix chain 'J' and resid 48 through 51 Processing helix chain 'J' and resid 73 through 80 removed outlier: 3.613A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 91 No H-bonds generated for 'chain 'J' and resid 89 through 91' Processing helix chain 'J' and resid 103 through 107 Processing helix chain 'J' and resid 111 through 113 No H-bonds generated for 'chain 'J' and resid 111 through 113' Processing helix chain 'J' and resid 115 through 128 removed outlier: 3.588A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 161 removed outlier: 4.099A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 197 removed outlier: 3.565A pdb=" N THR J 190 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU J 195 " --> pdb=" O HIS J 192 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS J 197 " --> pdb=" O THR J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 217 Processing helix chain 'J' and resid 224 through 243 removed outlier: 4.442A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 259 Processing helix chain 'J' and resid 278 through 283 removed outlier: 3.725A pdb=" N TYR J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 278 through 283' Processing helix chain 'J' and resid 288 through 296 removed outlier: 3.702A pdb=" N PHE J 296 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 300 No H-bonds generated for 'chain 'J' and resid 298 through 300' Processing helix chain 'J' and resid 307 through 309 No H-bonds generated for 'chain 'J' and resid 307 through 309' Processing helix chain 'J' and resid 325 through 337 Processing helix chain 'J' and resid 382 through 401 removed outlier: 3.549A pdb=" N TYR J 399 " --> pdb=" O ASP J 396 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 410 Processing helix chain 'J' and resid 415 through 436 Processing helix chain 'H' and resid 10 through 27 Processing helix chain 'H' and resid 41 through 47 removed outlier: 3.556A pdb=" N GLU H 47 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 110 through 128 removed outlier: 4.383A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 160 Processing helix chain 'H' and resid 183 through 197 removed outlier: 3.561A pdb=" N GLN H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 215 Processing helix chain 'H' and resid 224 through 243 removed outlier: 3.799A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 259 Processing helix chain 'H' and resid 279 through 281 No H-bonds generated for 'chain 'H' and resid 279 through 281' Processing helix chain 'H' and resid 288 through 296 Processing helix chain 'H' and resid 298 through 300 No H-bonds generated for 'chain 'H' and resid 298 through 300' Processing helix chain 'H' and resid 307 through 309 No H-bonds generated for 'chain 'H' and resid 307 through 309' Processing helix chain 'H' and resid 325 through 338 Processing helix chain 'H' and resid 340 through 342 No H-bonds generated for 'chain 'H' and resid 340 through 342' Processing helix chain 'H' and resid 382 through 401 removed outlier: 3.636A pdb=" N ARG H 390 " --> pdb=" O LEU H 387 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG H 400 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 411 Processing helix chain 'H' and resid 415 through 436 Processing helix chain 'L' and resid 10 through 28 Processing helix chain 'L' and resid 48 through 51 Processing helix chain 'L' and resid 73 through 80 removed outlier: 3.613A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 91 No H-bonds generated for 'chain 'L' and resid 89 through 91' Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'L' and resid 111 through 113 No H-bonds generated for 'chain 'L' and resid 111 through 113' Processing helix chain 'L' and resid 115 through 128 removed outlier: 3.589A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 161 removed outlier: 4.101A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 197 removed outlier: 3.565A pdb=" N THR L 190 " --> pdb=" O SER L 187 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU L 195 " --> pdb=" O HIS L 192 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS L 197 " --> pdb=" O THR L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 217 Processing helix chain 'L' and resid 224 through 243 removed outlier: 4.441A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 259 Processing helix chain 'L' and resid 278 through 283 removed outlier: 3.725A pdb=" N TYR L 282 " --> pdb=" O ALA L 278 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HIS L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 278 through 283' Processing helix chain 'L' and resid 288 through 296 removed outlier: 3.702A pdb=" N PHE L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 300 No H-bonds generated for 'chain 'L' and resid 298 through 300' Processing helix chain 'L' and resid 307 through 309 No H-bonds generated for 'chain 'L' and resid 307 through 309' Processing helix chain 'L' and resid 325 through 337 Processing helix chain 'L' and resid 382 through 401 removed outlier: 3.550A pdb=" N TYR L 399 " --> pdb=" O ASP L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 410 Processing helix chain 'L' and resid 415 through 436 Processing helix chain 'G' and resid 10 through 27 Processing helix chain 'G' and resid 41 through 47 removed outlier: 3.555A pdb=" N GLU G 47 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 103 through 108 Processing helix chain 'G' and resid 110 through 128 removed outlier: 4.383A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 160 Processing helix chain 'G' and resid 183 through 197 removed outlier: 3.560A pdb=" N GLN G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 215 Processing helix chain 'G' and resid 224 through 243 removed outlier: 3.799A pdb=" N THR G 239 " --> pdb=" O MET G 235 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU G 242 " --> pdb=" O VAL G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 279 through 281 No H-bonds generated for 'chain 'G' and resid 279 through 281' Processing helix chain 'G' and resid 288 through 296 Processing helix chain 'G' and resid 298 through 300 No H-bonds generated for 'chain 'G' and resid 298 through 300' Processing helix chain 'G' and resid 307 through 309 No H-bonds generated for 'chain 'G' and resid 307 through 309' Processing helix chain 'G' and resid 325 through 338 Processing helix chain 'G' and resid 340 through 342 No H-bonds generated for 'chain 'G' and resid 340 through 342' Processing helix chain 'G' and resid 382 through 401 removed outlier: 3.635A pdb=" N ARG G 390 " --> pdb=" O LEU G 387 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG G 400 " --> pdb=" O ALA G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 411 Processing helix chain 'G' and resid 415 through 436 Processing helix chain 'K' and resid 10 through 28 Processing helix chain 'K' and resid 48 through 51 Processing helix chain 'K' and resid 73 through 80 removed outlier: 3.613A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 91 No H-bonds generated for 'chain 'K' and resid 89 through 91' Processing helix chain 'K' and resid 103 through 107 Processing helix chain 'K' and resid 111 through 113 No H-bonds generated for 'chain 'K' and resid 111 through 113' Processing helix chain 'K' and resid 115 through 128 removed outlier: 3.589A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 161 removed outlier: 4.100A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 197 removed outlier: 3.565A pdb=" N THR K 190 " --> pdb=" O SER K 187 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU K 195 " --> pdb=" O HIS K 192 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS K 197 " --> pdb=" O THR K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 217 Processing helix chain 'K' and resid 224 through 243 removed outlier: 4.442A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 259 Processing helix chain 'K' and resid 278 through 283 removed outlier: 3.725A pdb=" N TYR K 282 " --> pdb=" O ALA K 278 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 278 through 283' Processing helix chain 'K' and resid 288 through 296 removed outlier: 3.701A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 307 through 309 No H-bonds generated for 'chain 'K' and resid 307 through 309' Processing helix chain 'K' and resid 325 through 337 Processing helix chain 'K' and resid 382 through 401 removed outlier: 3.550A pdb=" N TYR K 399 " --> pdb=" O ASP K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 Processing helix chain 'K' and resid 415 through 436 Processing helix chain 'I' and resid 10 through 27 Processing helix chain 'I' and resid 41 through 47 removed outlier: 3.555A pdb=" N GLU I 47 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 72 through 80 Processing helix chain 'I' and resid 84 through 86 No H-bonds generated for 'chain 'I' and resid 84 through 86' Processing helix chain 'I' and resid 89 through 91 No H-bonds generated for 'chain 'I' and resid 89 through 91' Processing helix chain 'I' and resid 103 through 108 Processing helix chain 'I' and resid 110 through 128 removed outlier: 4.383A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N SER I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 160 Processing helix chain 'I' and resid 183 through 197 removed outlier: 3.560A pdb=" N GLN I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU I 196 " --> pdb=" O HIS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 215 Processing helix chain 'I' and resid 224 through 243 removed outlier: 3.799A pdb=" N THR I 239 " --> pdb=" O MET I 235 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU I 242 " --> pdb=" O VAL I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 259 Processing helix chain 'I' and resid 279 through 281 No H-bonds generated for 'chain 'I' and resid 279 through 281' Processing helix chain 'I' and resid 288 through 296 Processing helix chain 'I' and resid 298 through 300 No H-bonds generated for 'chain 'I' and resid 298 through 300' Processing helix chain 'I' and resid 307 through 309 No H-bonds generated for 'chain 'I' and resid 307 through 309' Processing helix chain 'I' and resid 325 through 338 Processing helix chain 'I' and resid 340 through 342 No H-bonds generated for 'chain 'I' and resid 340 through 342' Processing helix chain 'I' and resid 382 through 401 removed outlier: 3.636A pdb=" N ARG I 390 " --> pdb=" O LEU I 387 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG I 400 " --> pdb=" O ALA I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 411 Processing helix chain 'I' and resid 415 through 436 Processing helix chain 'P' and resid 327 through 336 removed outlier: 3.505A pdb=" N HIS P 335 " --> pdb=" O VAL P 331 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.057A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY A 134 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE A 7 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 136 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL A 9 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE A 138 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.624A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.888A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL B 5 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE B 7 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA B 9 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N HIS B 139 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU B 137 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N HIS B 139 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU B 200 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N SER B 170 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR B 202 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 172 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE B 204 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ASP B 205 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 11.556A pdb=" N PHE B 272 " --> pdb=" O ASP B 205 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.985A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.058A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY C 134 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE C 7 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU C 136 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL C 9 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE C 138 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N SER C 165 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL C 137 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU C 167 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N HIS C 139 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE C 169 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER C 170 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE C 202 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR C 172 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL C 204 " --> pdb=" O TYR C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= H, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.623A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.887A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL D 5 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE D 7 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA D 9 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N HIS D 139 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE D 165 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU D 137 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN D 167 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N HIS D 139 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE D 169 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU D 200 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N SER D 170 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR D 202 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL D 172 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE D 204 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ASP D 205 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 11.555A pdb=" N PHE D 272 " --> pdb=" O ASP D 205 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 53 through 56 removed outlier: 3.985A pdb=" N LYS D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.057A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY E 134 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE E 7 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU E 136 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL E 9 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE E 138 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VAL E 137 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N HIS E 139 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE E 169 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER E 170 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR E 172 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VAL E 204 " --> pdb=" O TYR E 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= M, first strand: chain 'E' and resid 269 through 273 removed outlier: 3.622A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.887A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL F 5 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE F 7 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA F 9 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N HIS F 139 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE F 165 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU F 137 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN F 167 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N HIS F 139 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE F 169 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU F 200 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N SER F 170 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR F 202 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL F 172 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE F 204 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASP F 205 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 11.555A pdb=" N PHE F 272 " --> pdb=" O ASP F 205 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.986A pdb=" N LYS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.056A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY J 134 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE J 7 " --> pdb=" O GLY J 134 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU J 136 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL J 9 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE J 138 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N SER J 165 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL J 137 " --> pdb=" O SER J 165 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU J 167 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N HIS J 139 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE J 169 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS J 200 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N SER J 170 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE J 202 " --> pdb=" O SER J 170 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR J 172 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL J 204 " --> pdb=" O TYR J 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'J' and resid 53 through 55 Processing sheet with id= R, first strand: chain 'J' and resid 269 through 273 removed outlier: 3.623A pdb=" N ALA J 314 " --> pdb=" O ASN J 380 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.886A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL H 5 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE H 7 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA H 9 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N HIS H 139 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE H 165 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU H 137 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN H 167 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N HIS H 139 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE H 169 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU H 200 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N SER H 170 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR H 202 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL H 172 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE H 204 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASP H 205 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N PHE H 272 " --> pdb=" O ASP H 205 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.986A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.058A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY L 134 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE L 7 " --> pdb=" O GLY L 134 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU L 136 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL L 9 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE L 138 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER L 165 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VAL L 137 " --> pdb=" O SER L 165 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU L 167 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N HIS L 139 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE L 169 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N CYS L 200 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER L 170 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE L 202 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR L 172 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL L 204 " --> pdb=" O TYR L 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'L' and resid 53 through 55 Processing sheet with id= W, first strand: chain 'L' and resid 269 through 273 removed outlier: 3.623A pdb=" N ALA L 314 " --> pdb=" O ASN L 380 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.887A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL G 5 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE G 7 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA G 9 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N HIS G 139 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE G 165 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU G 137 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN G 167 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N HIS G 139 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE G 169 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU G 200 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N SER G 170 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR G 202 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL G 172 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE G 204 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP G 205 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N PHE G 272 " --> pdb=" O ASP G 205 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE G 267 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER G 381 " --> pdb=" O PHE G 267 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.985A pdb=" N LYS G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.057A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY K 134 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE K 7 " --> pdb=" O GLY K 134 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU K 136 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL K 9 " --> pdb=" O LEU K 136 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE K 138 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER K 165 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VAL K 137 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU K 167 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N HIS K 139 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE K 169 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N CYS K 200 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER K 170 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE K 202 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR K 172 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL K 204 " --> pdb=" O TYR K 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'K' and resid 53 through 55 Processing sheet with id= AB, first strand: chain 'K' and resid 269 through 273 removed outlier: 3.624A pdb=" N ALA K 314 " --> pdb=" O ASN K 380 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.886A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL I 68 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL I 5 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE I 7 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA I 9 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N HIS I 139 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE I 165 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU I 137 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN I 167 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N HIS I 139 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE I 169 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU I 200 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N SER I 170 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR I 202 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL I 172 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE I 204 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASP I 205 " --> pdb=" O PRO I 270 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N PHE I 272 " --> pdb=" O ASP I 205 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE I 267 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER I 381 " --> pdb=" O PHE I 267 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 53 through 56 removed outlier: 3.986A pdb=" N LYS I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) 1828 hydrogen bonds defined for protein. 4692 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: 15.84 Time building geometry restraints manager: 16.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6979 1.32 - 1.44: 11347 1.44 - 1.56: 23219 1.56 - 1.69: 67 1.69 - 1.81: 458 Bond restraints: 42070 Sorted by residual: bond pdb=" O3B G2P F 501 " pdb=" PG G2P F 501 " ideal model delta sigma weight residual 1.716 1.607 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" O3B G2P H 501 " pdb=" PG G2P H 501 " ideal model delta sigma weight residual 1.716 1.608 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" O3B G2P D 501 " pdb=" PG G2P D 501 " ideal model delta sigma weight residual 1.716 1.608 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" O3B G2P B 501 " pdb=" PG G2P B 501 " ideal model delta sigma weight residual 1.716 1.608 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" O3B G2P G 501 " pdb=" PG G2P G 501 " ideal model delta sigma weight residual 1.716 1.608 0.108 2.00e-02 2.50e+03 2.90e+01 ... (remaining 42065 not shown) Histogram of bond angle deviations from ideal: 94.98 - 103.48: 566 103.48 - 111.97: 17529 111.97 - 120.47: 22361 120.47 - 128.96: 16392 128.96 - 137.45: 314 Bond angle restraints: 57162 Sorted by residual: angle pdb=" CA THR I 109 " pdb=" C THR I 109 " pdb=" N GLU I 110 " ideal model delta sigma weight residual 119.46 116.25 3.21 6.10e-01 2.69e+00 2.77e+01 angle pdb=" C ILE A 110 " pdb=" N GLY A 111 " pdb=" CA GLY A 111 " ideal model delta sigma weight residual 119.98 125.81 -5.83 1.11e+00 8.12e-01 2.76e+01 angle pdb=" N SER D 97 " pdb=" CA SER D 97 " pdb=" C SER D 97 " ideal model delta sigma weight residual 111.40 117.80 -6.40 1.22e+00 6.72e-01 2.75e+01 angle pdb=" N SER F 97 " pdb=" CA SER F 97 " pdb=" C SER F 97 " ideal model delta sigma weight residual 111.40 117.78 -6.38 1.22e+00 6.72e-01 2.74e+01 angle pdb=" C ILE C 110 " pdb=" N GLY C 111 " pdb=" CA GLY C 111 " ideal model delta sigma weight residual 119.98 125.78 -5.80 1.11e+00 8.12e-01 2.73e+01 ... (remaining 57157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 24208 33.64 - 67.28: 842 67.28 - 100.92: 54 100.92 - 134.56: 0 134.56 - 168.20: 18 Dihedral angle restraints: 25122 sinusoidal: 10086 harmonic: 15036 Sorted by residual: dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.53 -168.20 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.64 -168.09 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.92 -167.81 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 25119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4525 0.086 - 0.171: 1341 0.171 - 0.257: 307 0.257 - 0.342: 75 0.342 - 0.428: 4 Chirality restraints: 6252 Sorted by residual: chirality pdb=" C3' G2P F 501 " pdb=" C2' G2P F 501 " pdb=" C4' G2P F 501 " pdb=" O3' G2P F 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" C3' G2P B 501 " pdb=" C2' G2P B 501 " pdb=" C4' G2P B 501 " pdb=" O3' G2P B 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" C3' G2P I 501 " pdb=" C2' G2P I 501 " pdb=" C4' G2P I 501 " pdb=" O3' G2P I 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.42 2.00e-01 2.50e+01 4.50e+00 ... (remaining 6249 not shown) Planarity restraints: 7436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP L 501 " 0.029 2.00e-02 2.50e+03 1.33e-02 5.27e+00 pdb=" C2 GTP L 501 " -0.006 2.00e-02 2.50e+03 pdb=" C4 GTP L 501 " -0.004 2.00e-02 2.50e+03 pdb=" C5 GTP L 501 " -0.002 2.00e-02 2.50e+03 pdb=" C6 GTP L 501 " 0.005 2.00e-02 2.50e+03 pdb=" C8 GTP L 501 " 0.005 2.00e-02 2.50e+03 pdb=" N1 GTP L 501 " 0.008 2.00e-02 2.50e+03 pdb=" N2 GTP L 501 " 0.001 2.00e-02 2.50e+03 pdb=" N3 GTP L 501 " -0.007 2.00e-02 2.50e+03 pdb=" N7 GTP L 501 " -0.002 2.00e-02 2.50e+03 pdb=" N9 GTP L 501 " -0.032 2.00e-02 2.50e+03 pdb=" O6 GTP L 501 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP C 501 " 0.027 2.00e-02 2.50e+03 1.25e-02 4.71e+00 pdb=" C2 GTP C 501 " -0.007 2.00e-02 2.50e+03 pdb=" C4 GTP C 501 " -0.002 2.00e-02 2.50e+03 pdb=" C5 GTP C 501 " -0.002 2.00e-02 2.50e+03 pdb=" C6 GTP C 501 " 0.005 2.00e-02 2.50e+03 pdb=" C8 GTP C 501 " 0.003 2.00e-02 2.50e+03 pdb=" N1 GTP C 501 " 0.008 2.00e-02 2.50e+03 pdb=" N2 GTP C 501 " 0.001 2.00e-02 2.50e+03 pdb=" N3 GTP C 501 " -0.005 2.00e-02 2.50e+03 pdb=" N7 GTP C 501 " -0.000 2.00e-02 2.50e+03 pdb=" N9 GTP C 501 " -0.031 2.00e-02 2.50e+03 pdb=" O6 GTP C 501 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP K 501 " -0.026 2.00e-02 2.50e+03 1.24e-02 4.61e+00 pdb=" C2 GTP K 501 " 0.007 2.00e-02 2.50e+03 pdb=" C4 GTP K 501 " 0.001 2.00e-02 2.50e+03 pdb=" C5 GTP K 501 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GTP K 501 " -0.005 2.00e-02 2.50e+03 pdb=" C8 GTP K 501 " -0.004 2.00e-02 2.50e+03 pdb=" N1 GTP K 501 " -0.008 2.00e-02 2.50e+03 pdb=" N2 GTP K 501 " -0.001 2.00e-02 2.50e+03 pdb=" N3 GTP K 501 " 0.006 2.00e-02 2.50e+03 pdb=" N7 GTP K 501 " 0.002 2.00e-02 2.50e+03 pdb=" N9 GTP K 501 " 0.031 2.00e-02 2.50e+03 pdb=" O6 GTP K 501 " -0.004 2.00e-02 2.50e+03 ... (remaining 7433 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 105 2.58 - 3.16: 33183 3.16 - 3.74: 66313 3.74 - 4.32: 93191 4.32 - 4.90: 155678 Nonbonded interactions: 348470 Sorted by model distance: nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 1.999 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 2.021 2.170 nonbonded pdb=" O1B GTP K 501 " pdb="MG MG K 502 " model vdw 2.068 2.170 nonbonded pdb=" O1B GTP L 501 " pdb="MG MG L 502 " model vdw 2.070 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.093 2.170 ... (remaining 348465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'P' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.900 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: 0.030 Extract box with map and model: 28.840 Check model and map are aligned: 0.640 Set scattering table: 0.400 Process input model: 102.400 Find NCS groups from input model: 3.360 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.009 0.109 42070 Z= 0.607 Angle : 1.541 15.626 57162 Z= 1.040 Chirality : 0.087 0.428 6252 Planarity : 0.007 0.054 7436 Dihedral : 16.534 168.196 15474 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 2.99 % Allowed : 8.25 % Favored : 88.75 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 4.88 % 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: -0.11 (0.11), residues: 5160 helix: 0.69 (0.09), residues: 2356 sheet: 0.57 (0.19), residues: 792 loop : -1.21 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP L 21 HIS 0.009 0.002 HIS L 88 PHE 0.022 0.003 PHE B 92 TYR 0.025 0.003 TYR J 224 ARG 0.026 0.001 ARG B 2 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1967 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1835 time to evaluate : 3.890 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: A 47 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.5307 (t0) REVERT: A 178 SER cc_start: 0.8077 (p) cc_final: 0.7611 (t) REVERT: B 55 GLU cc_start: 0.6885 (tm-30) cc_final: 0.6351 (tm-30) REVERT: B 116 ASP cc_start: 0.6632 (p0) cc_final: 0.6186 (p0) REVERT: B 325 MET cc_start: 0.6467 (mmm) cc_final: 0.6114 (mmm) REVERT: B 335 VAL cc_start: 0.8989 (t) cc_final: 0.8752 (t) REVERT: B 425 MET cc_start: 0.7631 (ttp) cc_final: 0.7404 (ttp) REVERT: C 178 SER cc_start: 0.7946 (p) cc_final: 0.7639 (p) REVERT: C 209 ILE cc_start: 0.8792 (mm) cc_final: 0.8292 (mm) REVERT: C 259 LEU cc_start: 0.8684 (tp) cc_final: 0.8478 (tp) REVERT: D 199 ASP cc_start: 0.7172 (m-30) cc_final: 0.6957 (m-30) REVERT: D 300 ASN cc_start: 0.8131 (OUTLIER) cc_final: 0.7662 (t0) REVERT: D 398 MET cc_start: 0.7232 (mtt) cc_final: 0.6700 (mtt) REVERT: E 47 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.5523 (t0) REVERT: E 118 VAL cc_start: 0.8816 (m) cc_final: 0.8420 (p) REVERT: E 122 ILE cc_start: 0.8746 (mt) cc_final: 0.8510 (mt) REVERT: E 285 GLN cc_start: 0.7285 (tt0) cc_final: 0.6496 (tt0) REVERT: F 1 MET cc_start: 0.7597 (mmt) cc_final: 0.7283 (tpp) REVERT: F 163 ASP cc_start: 0.7103 (p0) cc_final: 0.6542 (p0) REVERT: F 209 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8148 (mt) REVERT: F 257 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.8006 (p) REVERT: J 209 ILE cc_start: 0.8801 (mm) cc_final: 0.8323 (mm) REVERT: H 55 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6735 (tm-30) REVERT: H 180 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8178 (m) REVERT: H 252 LEU cc_start: 0.8455 (mt) cc_final: 0.8245 (mt) REVERT: H 428 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9035 (tp) REVERT: L 328 VAL cc_start: 0.8542 (t) cc_final: 0.8324 (t) REVERT: G 114 LEU cc_start: 0.8669 (tp) cc_final: 0.8275 (tp) REVERT: G 170 SER cc_start: 0.8755 (m) cc_final: 0.8518 (p) REVERT: G 300 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7741 (t0) REVERT: G 389 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8357 (mtmm) REVERT: G 428 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8715 (tt) REVERT: K 189 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8626 (mt) REVERT: K 295 CYS cc_start: 0.7782 (m) cc_final: 0.7518 (m) REVERT: K 304 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7659 (ttmm) REVERT: I 24 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8682 (tt) REVERT: I 176 LYS cc_start: 0.8454 (mttt) cc_final: 0.8059 (mtmt) REVERT: I 346 TRP cc_start: 0.7896 (p-90) cc_final: 0.7660 (p-90) outliers start: 132 outliers final: 25 residues processed: 1906 average time/residue: 0.5338 time to fit residues: 1629.9921 Evaluate side-chains 1157 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1121 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 300 ASN Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 428 LEU Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 315 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 435 optimal weight: 2.9990 chunk 391 optimal weight: 0.8980 chunk 217 optimal weight: 0.9990 chunk 133 optimal weight: 0.2980 chunk 263 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 404 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 301 optimal weight: 0.9990 chunk 468 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN A 101 ASN A 107 HIS A 228 ASN A 300 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 28 HIS B 101 ASN B 133 GLN B 350 ASN B 385 GLN B 424 ASN B 436 GLN C 8 HIS C 35 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS C 228 ASN C 256 GLN C 300 ASN ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN D 133 GLN D 136 GLN D 309 HIS D 350 ASN D 385 GLN D 436 GLN T 311 GLN T 329 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS E 228 ASN ** E 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN F 133 GLN F 309 HIS F 334 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 GLN F 424 ASN F 436 GLN J 8 HIS ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 ASN J 107 HIS J 228 ASN J 300 ASN J 309 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 37 HIS H 133 GLN H 385 GLN H 424 ASN H 436 GLN ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 ASN L 101 ASN L 107 HIS L 128 GLN L 228 ASN L 285 GLN L 300 ASN G 133 GLN G 136 GLN G 258 ASN G 385 GLN G 424 ASN G 436 GLN ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 GLN K 101 ASN K 107 HIS K 128 GLN K 228 ASN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN I 136 GLN I 385 GLN I 436 GLN P 329 GLN Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 42070 Z= 0.197 Angle : 0.625 8.908 57162 Z= 0.325 Chirality : 0.044 0.154 6252 Planarity : 0.005 0.087 7436 Dihedral : 12.447 173.149 5979 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.90 % Allowed : 17.10 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.92 (0.12), residues: 5160 helix: 1.71 (0.11), residues: 2374 sheet: 0.84 (0.17), residues: 780 loop : -0.82 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 346 HIS 0.011 0.001 HIS C 88 PHE 0.024 0.002 PHE K 255 TYR 0.019 0.001 TYR K 357 ARG 0.013 0.001 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1403 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1231 time to evaluate : 4.203 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: A 47 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.6704 (m-30) REVERT: A 275 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8292 (m) REVERT: A 285 GLN cc_start: 0.7736 (tt0) cc_final: 0.7502 (tt0) REVERT: B 309 HIS cc_start: 0.7520 (m90) cc_final: 0.7145 (m-70) REVERT: B 415 GLU cc_start: 0.6462 (pp20) cc_final: 0.5217 (pp20) REVERT: C 47 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.5897 (t0) REVERT: C 71 GLU cc_start: 0.7138 (pt0) cc_final: 0.6835 (pt0) REVERT: C 313 MET cc_start: 0.7544 (mtm) cc_final: 0.7162 (mtt) REVERT: D 1 MET cc_start: 0.7677 (mmm) cc_final: 0.7464 (tpp) REVERT: D 205 ASP cc_start: 0.6566 (t0) cc_final: 0.6281 (t0) REVERT: D 398 MET cc_start: 0.7440 (mtp) cc_final: 0.6824 (mtt) REVERT: E 47 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.6411 (m-30) REVERT: E 176 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8113 (mm-40) REVERT: E 285 GLN cc_start: 0.6901 (tt0) cc_final: 0.6218 (tt0) REVERT: F 212 ILE cc_start: 0.9173 (mm) cc_final: 0.8870 (mm) REVERT: F 415 GLU cc_start: 0.6310 (pp20) cc_final: 0.5304 (pp20) REVERT: J 357 TYR cc_start: 0.7422 (m-10) cc_final: 0.7182 (m-10) REVERT: H 205 ASP cc_start: 0.6410 (t0) cc_final: 0.6045 (t0) REVERT: H 428 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8564 (tt) REVERT: L 47 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6581 (m-30) REVERT: K 293 ASN cc_start: 0.7023 (m-40) cc_final: 0.6734 (m110) REVERT: K 304 LYS cc_start: 0.8299 (mtpp) cc_final: 0.7947 (ttmm) REVERT: I 24 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8806 (tt) outliers start: 172 outliers final: 91 residues processed: 1327 average time/residue: 0.5398 time to fit residues: 1192.1569 Evaluate side-chains 1054 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 956 time to evaluate : 3.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 341 ILE Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 428 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 260 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 389 optimal weight: 3.9990 chunk 319 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 469 optimal weight: 7.9990 chunk 507 optimal weight: 4.9990 chunk 418 optimal weight: 1.9990 chunk 465 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 376 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 6 HIS B 133 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN D 6 HIS D 50 ASN D 293 GLN ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN D 424 ASN E 50 ASN E 256 GLN ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 ASN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 GLN F 334 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN L 128 GLN L 192 HIS L 342 GLN G 37 HIS G 136 GLN G 293 GLN K 91 GLN K 128 GLN K 300 ASN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 42070 Z= 0.324 Angle : 0.606 9.443 57162 Z= 0.315 Chirality : 0.044 0.144 6252 Planarity : 0.005 0.067 7436 Dihedral : 11.947 174.784 5960 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.74 % Allowed : 17.48 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.12), residues: 5160 helix: 1.67 (0.11), residues: 2368 sheet: 0.79 (0.19), residues: 762 loop : -0.76 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 346 HIS 0.031 0.002 HIS H 37 PHE 0.035 0.002 PHE E 255 TYR 0.015 0.001 TYR E 357 ARG 0.022 0.001 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 949 time to evaluate : 5.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: A 269 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8604 (pp) REVERT: B 309 HIS cc_start: 0.7536 (m90) cc_final: 0.7032 (m90) REVERT: B 325 MET cc_start: 0.7796 (tpp) cc_final: 0.7366 (mmm) REVERT: C 47 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8061 (m-30) REVERT: C 71 GLU cc_start: 0.7122 (pt0) cc_final: 0.6798 (pt0) REVERT: C 285 GLN cc_start: 0.4449 (mm-40) cc_final: 0.4117 (mm110) REVERT: D 1 MET cc_start: 0.7650 (mmm) cc_final: 0.7414 (tpp) REVERT: D 398 MET cc_start: 0.7594 (mtp) cc_final: 0.7273 (mtm) REVERT: T 307 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8333 (p90) REVERT: E 47 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.6889 (m-30) REVERT: E 391 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8868 (mm) REVERT: J 172 TYR cc_start: 0.8325 (t80) cc_final: 0.8048 (t80) REVERT: J 230 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8405 (mp) REVERT: H 116 ASP cc_start: 0.7143 (m-30) cc_final: 0.6775 (m-30) REVERT: H 205 ASP cc_start: 0.6672 (t0) cc_final: 0.6279 (t0) REVERT: H 428 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8780 (tt) REVERT: L 47 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7383 (m-30) REVERT: L 55 GLU cc_start: 0.6819 (tp30) cc_final: 0.6475 (tp30) REVERT: G 205 ASP cc_start: 0.7185 (t0) cc_final: 0.6922 (t0) REVERT: G 252 LEU cc_start: 0.8605 (mt) cc_final: 0.8306 (mt) REVERT: G 431 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6972 (mm-30) REVERT: K 112 LYS cc_start: 0.7738 (pttm) cc_final: 0.7528 (pttm) REVERT: K 293 ASN cc_start: 0.7057 (m-40) cc_final: 0.6760 (m110) outliers start: 209 outliers final: 130 residues processed: 1081 average time/residue: 0.5056 time to fit residues: 904.6166 Evaluate side-chains 1001 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 862 time to evaluate : 4.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 278 ARG Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 307 PHE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain J residue 50 ASN Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 335 VAL Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain P residue 307 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 463 optimal weight: 2.9990 chunk 352 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 315 optimal weight: 2.9990 chunk 471 optimal weight: 9.9990 chunk 498 optimal weight: 8.9990 chunk 246 optimal weight: 3.9990 chunk 446 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 311 GLN E 258 ASN E 285 GLN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS L 342 GLN G 293 GLN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN K 192 HIS ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 42070 Z= 0.269 Angle : 0.567 9.556 57162 Z= 0.291 Chirality : 0.042 0.138 6252 Planarity : 0.004 0.050 7436 Dihedral : 11.647 171.658 5947 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.24 % Allowed : 18.39 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.00 (0.12), residues: 5160 helix: 1.60 (0.11), residues: 2404 sheet: 1.19 (0.20), residues: 702 loop : -0.64 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP I 346 HIS 0.022 0.001 HIS I 37 PHE 0.028 0.001 PHE E 255 TYR 0.013 0.001 TYR L 185 ARG 0.009 0.000 ARG D 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 928 time to evaluate : 4.742 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: A 47 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7336 (m-30) REVERT: A 269 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8633 (pp) REVERT: B 259 MET cc_start: 0.7373 (mmp) cc_final: 0.7145 (mmt) REVERT: B 309 HIS cc_start: 0.7637 (m90) cc_final: 0.7296 (m-70) REVERT: C 47 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8393 (m-30) REVERT: C 71 GLU cc_start: 0.7113 (pt0) cc_final: 0.6826 (pt0) REVERT: E 47 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.6522 (t70) REVERT: E 411 GLU cc_start: 0.7282 (mm-30) cc_final: 0.7078 (mm-30) REVERT: F 415 GLU cc_start: 0.6842 (pm20) cc_final: 0.6515 (pm20) REVERT: H 205 ASP cc_start: 0.6694 (t0) cc_final: 0.6278 (t0) REVERT: L 47 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7737 (m-30) REVERT: G 205 ASP cc_start: 0.7217 (t0) cc_final: 0.6984 (t0) REVERT: G 252 LEU cc_start: 0.8640 (mt) cc_final: 0.8350 (mt) REVERT: G 431 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6881 (mm-30) REVERT: K 254 GLU cc_start: 0.4638 (mm-30) cc_final: 0.4277 (mm-30) REVERT: K 293 ASN cc_start: 0.6934 (m-40) cc_final: 0.6687 (m110) outliers start: 187 outliers final: 132 residues processed: 1039 average time/residue: 0.5203 time to fit residues: 895.3300 Evaluate side-chains 988 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 851 time to evaluate : 4.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 308 ASN Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain J residue 50 ASN Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 413 MET Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 192 HIS Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 302 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain P residue 307 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 415 optimal weight: 0.8980 chunk 283 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 371 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 425 optimal weight: 8.9990 chunk 344 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 254 optimal weight: 1.9990 chunk 447 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS T 311 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS L 342 GLN G 50 ASN G 229 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN K 192 HIS K 342 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 42070 Z= 0.186 Angle : 0.547 9.789 57162 Z= 0.279 Chirality : 0.041 0.204 6252 Planarity : 0.004 0.049 7436 Dihedral : 11.317 169.456 5942 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.51 % Allowed : 19.64 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.07 (0.12), residues: 5160 helix: 1.59 (0.11), residues: 2404 sheet: 1.47 (0.19), residues: 714 loop : -0.63 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 346 HIS 0.019 0.001 HIS L 192 PHE 0.023 0.001 PHE E 255 TYR 0.021 0.001 TYR G 161 ARG 0.010 0.000 ARG D 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 948 time to evaluate : 4.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: B 308 ARG cc_start: 0.7899 (mpp80) cc_final: 0.7400 (mtm-85) REVERT: B 309 HIS cc_start: 0.7696 (m90) cc_final: 0.7466 (m-70) REVERT: C 251 ASP cc_start: 0.6254 (m-30) cc_final: 0.5897 (m-30) REVERT: C 254 GLU cc_start: 0.5898 (mt-10) cc_final: 0.5573 (mt-10) REVERT: D 192 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7741 (t70) REVERT: E 47 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7056 (m-30) REVERT: E 411 GLU cc_start: 0.7267 (mm-30) cc_final: 0.7066 (mm-30) REVERT: H 205 ASP cc_start: 0.6630 (t0) cc_final: 0.6222 (t0) REVERT: L 47 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: G 205 ASP cc_start: 0.7163 (t0) cc_final: 0.6944 (t0) REVERT: G 252 LEU cc_start: 0.8600 (mt) cc_final: 0.8322 (mt) REVERT: G 431 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6829 (mm-30) REVERT: K 254 GLU cc_start: 0.4908 (mm-30) cc_final: 0.4463 (mm-30) REVERT: K 293 ASN cc_start: 0.6883 (m-40) cc_final: 0.6640 (m-40) outliers start: 155 outliers final: 115 residues processed: 1040 average time/residue: 0.5055 time to fit residues: 869.2608 Evaluate side-chains 991 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 872 time to evaluate : 5.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 307 PHE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 413 MET Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 192 HIS Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 302 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain P residue 307 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 167 optimal weight: 5.9990 chunk 449 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 292 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 chunk 499 optimal weight: 0.9980 chunk 414 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 262 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 311 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS G 229 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN K 192 HIS K 197 HIS K 342 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 42070 Z= 0.253 Angle : 0.561 9.351 57162 Z= 0.285 Chirality : 0.042 0.182 6252 Planarity : 0.004 0.051 7436 Dihedral : 11.124 166.487 5933 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.97 % Allowed : 19.86 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.04 (0.12), residues: 5160 helix: 1.56 (0.11), residues: 2398 sheet: 1.47 (0.20), residues: 714 loop : -0.63 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 346 HIS 0.018 0.001 HIS K 192 PHE 0.024 0.001 PHE G 377 TYR 0.031 0.001 TYR L 24 ARG 0.011 0.000 ARG D 400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 895 time to evaluate : 4.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7940 (m-30) REVERT: C 251 ASP cc_start: 0.6248 (m-30) cc_final: 0.5751 (m-30) REVERT: D 192 HIS cc_start: 0.8072 (OUTLIER) cc_final: 0.7713 (t70) REVERT: E 47 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7221 (m-30) REVERT: E 411 GLU cc_start: 0.7268 (mm-30) cc_final: 0.7062 (mm-30) REVERT: H 1 MET cc_start: 0.7335 (mmp) cc_final: 0.6957 (tpt) REVERT: H 116 ASP cc_start: 0.7280 (m-30) cc_final: 0.7039 (m-30) REVERT: H 205 ASP cc_start: 0.6695 (t0) cc_final: 0.6256 (t0) REVERT: L 47 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8029 (m-30) REVERT: G 200 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6909 (pt0) REVERT: G 205 ASP cc_start: 0.7227 (t0) cc_final: 0.7003 (t0) REVERT: K 254 GLU cc_start: 0.4562 (mm-30) cc_final: 0.4041 (mm-30) REVERT: K 293 ASN cc_start: 0.6936 (m-40) cc_final: 0.6688 (m-40) outliers start: 175 outliers final: 132 residues processed: 1004 average time/residue: 0.5127 time to fit residues: 840.8341 Evaluate side-chains 991 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 854 time to evaluate : 4.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 317 LEU Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 413 MET Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 200 GLU Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 192 HIS Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 342 GLN Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 302 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain P residue 307 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 481 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 364 optimal weight: 6.9990 chunk 282 optimal weight: 0.1980 chunk 420 optimal weight: 0.9980 chunk 278 optimal weight: 0.8980 chunk 497 optimal weight: 8.9990 chunk 311 optimal weight: 0.0970 chunk 303 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 HIS C 206 ASN T 311 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN K 88 HIS K 128 GLN K 192 HIS ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 42070 Z= 0.178 Angle : 0.554 9.046 57162 Z= 0.281 Chirality : 0.041 0.259 6252 Planarity : 0.004 0.049 7436 Dihedral : 10.904 163.431 5933 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.27 % Allowed : 20.70 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.05 (0.12), residues: 5160 helix: 1.59 (0.11), residues: 2368 sheet: 1.55 (0.20), residues: 714 loop : -0.66 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 346 HIS 0.010 0.001 HIS K 192 PHE 0.022 0.001 PHE K 255 TYR 0.026 0.001 TYR L 24 ARG 0.010 0.000 ARG D 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 922 time to evaluate : 5.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.7912 (m-30) REVERT: A 168 GLU cc_start: 0.6226 (pt0) cc_final: 0.5945 (pt0) REVERT: E 47 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7136 (m-30) REVERT: E 411 GLU cc_start: 0.7231 (mm-30) cc_final: 0.7029 (mm-30) REVERT: J 432 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.7680 (t80) REVERT: H 179 ASP cc_start: 0.5220 (t0) cc_final: 0.4980 (t0) REVERT: H 205 ASP cc_start: 0.6640 (t0) cc_final: 0.6210 (t0) REVERT: L 47 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: L 425 MET cc_start: 0.8158 (tpp) cc_final: 0.7936 (tpt) REVERT: G 205 ASP cc_start: 0.7161 (t0) cc_final: 0.6916 (t0) REVERT: K 254 GLU cc_start: 0.4605 (mm-30) cc_final: 0.3800 (mm-30) REVERT: K 293 ASN cc_start: 0.6952 (m-40) cc_final: 0.6655 (m-40) outliers start: 144 outliers final: 118 residues processed: 1002 average time/residue: 0.5259 time to fit residues: 864.7480 Evaluate side-chains 987 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 865 time to evaluate : 4.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 307 PHE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain H residue 160 GLU Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 413 MET Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 192 HIS Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 302 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain P residue 307 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 307 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 chunk 149 optimal weight: 0.3980 chunk 97 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 316 optimal weight: 0.7980 chunk 338 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 390 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN T 311 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 HIS ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 ASN ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN K 192 HIS K 342 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 42070 Z= 0.219 Angle : 0.566 9.394 57162 Z= 0.287 Chirality : 0.042 0.221 6252 Planarity : 0.004 0.048 7436 Dihedral : 10.712 159.770 5931 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.38 % Allowed : 21.16 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.00 (0.12), residues: 5160 helix: 1.57 (0.11), residues: 2356 sheet: 1.54 (0.20), residues: 714 loop : -0.70 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 346 HIS 0.015 0.001 HIS K 192 PHE 0.023 0.001 PHE J 255 TYR 0.023 0.001 TYR L 24 ARG 0.010 0.000 ARG D 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 900 time to evaluate : 5.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 127 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7270 (mp0) REVERT: E 47 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7865 (m-30) REVERT: F 205 ASP cc_start: 0.6795 (t70) cc_final: 0.6479 (t70) REVERT: J 254 GLU cc_start: 0.4615 (mm-30) cc_final: 0.3953 (mm-30) REVERT: J 377 MET cc_start: 0.7104 (ttp) cc_final: 0.6801 (ttp) REVERT: J 432 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.7675 (t80) REVERT: H 205 ASP cc_start: 0.6655 (t0) cc_final: 0.6221 (t0) REVERT: L 47 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8151 (m-30) REVERT: L 425 MET cc_start: 0.8190 (tpp) cc_final: 0.7938 (tpt) REVERT: G 205 ASP cc_start: 0.7183 (t0) cc_final: 0.6948 (t0) REVERT: K 254 GLU cc_start: 0.4508 (mm-30) cc_final: 0.3882 (mm-30) REVERT: K 293 ASN cc_start: 0.7032 (m-40) cc_final: 0.6725 (m-40) outliers start: 149 outliers final: 125 residues processed: 983 average time/residue: 0.5110 time to fit residues: 824.1206 Evaluate side-chains 987 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 859 time to evaluate : 5.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 278 ARG Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 413 MET Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 192 HIS Chi-restraints excluded: chain K residue 255 PHE Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 342 GLN Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 302 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain P residue 307 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 452 optimal weight: 0.9980 chunk 476 optimal weight: 0.7980 chunk 434 optimal weight: 1.9990 chunk 463 optimal weight: 0.0870 chunk 278 optimal weight: 0.8980 chunk 201 optimal weight: 0.9990 chunk 363 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 418 optimal weight: 3.9990 chunk 438 optimal weight: 0.0050 chunk 461 optimal weight: 5.9990 overall best weight: 0.5372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 300 ASN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN D 350 ASN T 311 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 ASN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 GLN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 HIS ** H 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 176 GLN L 192 HIS ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN K 192 HIS K 342 GLN ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 42070 Z= 0.169 Angle : 0.566 9.755 57162 Z= 0.287 Chirality : 0.041 0.209 6252 Planarity : 0.004 0.048 7436 Dihedral : 10.480 156.029 5928 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.88 % Allowed : 21.90 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.00 (0.12), residues: 5160 helix: 1.54 (0.11), residues: 2362 sheet: 1.61 (0.20), residues: 714 loop : -0.69 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 346 HIS 0.011 0.001 HIS K 192 PHE 0.025 0.001 PHE J 255 TYR 0.024 0.001 TYR L 24 ARG 0.011 0.000 ARG D 400 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 923 time to evaluate : 5.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 GLU cc_start: 0.7194 (pt0) cc_final: 0.6882 (pt0) REVERT: D 127 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7315 (mp0) REVERT: E 47 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: F 205 ASP cc_start: 0.6693 (t70) cc_final: 0.6383 (t70) REVERT: J 254 GLU cc_start: 0.4575 (mm-30) cc_final: 0.3912 (mm-30) REVERT: J 432 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.7821 (t80) REVERT: H 205 ASP cc_start: 0.6593 (t0) cc_final: 0.6172 (t0) REVERT: L 47 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8205 (m-30) REVERT: L 425 MET cc_start: 0.8131 (tpp) cc_final: 0.7903 (tpt) REVERT: G 205 ASP cc_start: 0.7117 (t0) cc_final: 0.6871 (t0) REVERT: K 112 LYS cc_start: 0.7904 (mtmm) cc_final: 0.7614 (pttm) REVERT: K 151 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.7887 (t) REVERT: K 254 GLU cc_start: 0.4643 (mm-30) cc_final: 0.4098 (mm-30) REVERT: K 293 ASN cc_start: 0.6828 (m-40) cc_final: 0.6581 (m-40) outliers start: 127 outliers final: 99 residues processed: 992 average time/residue: 0.5064 time to fit residues: 826.1536 Evaluate side-chains 974 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 871 time to evaluate : 4.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 293 GLN Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 379 SER Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 413 MET Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 342 GLN Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 302 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain P residue 307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 304 optimal weight: 1.9990 chunk 490 optimal weight: 4.9990 chunk 299 optimal weight: 5.9990 chunk 232 optimal weight: 0.9980 chunk 340 optimal weight: 0.0670 chunk 514 optimal weight: 0.0870 chunk 473 optimal weight: 0.0470 chunk 409 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 316 optimal weight: 0.9980 chunk 251 optimal weight: 3.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 300 ASN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN D 309 HIS T 311 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS G 167 ASN ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 42070 Z= 0.167 Angle : 0.571 9.158 57162 Z= 0.289 Chirality : 0.041 0.199 6252 Planarity : 0.004 0.048 7436 Dihedral : 10.271 151.677 5927 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.38 % Allowed : 22.74 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.00 (0.12), residues: 5160 helix: 1.52 (0.11), residues: 2362 sheet: 1.56 (0.19), residues: 750 loop : -0.70 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 346 HIS 0.008 0.001 HIS A 88 PHE 0.027 0.001 PHE K 343 TYR 0.024 0.001 TYR L 24 ARG 0.011 0.000 ARG D 400 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 927 time to evaluate : 4.683 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: B 259 MET cc_start: 0.6912 (mmm) cc_final: 0.6303 (mmt) REVERT: C 71 GLU cc_start: 0.7204 (pt0) cc_final: 0.6859 (pt0) REVERT: D 127 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7306 (mp0) REVERT: F 205 ASP cc_start: 0.6698 (t70) cc_final: 0.6416 (t70) REVERT: F 290 GLU cc_start: 0.5413 (tt0) cc_final: 0.5212 (tt0) REVERT: J 254 GLU cc_start: 0.4544 (mm-30) cc_final: 0.3907 (mm-30) REVERT: J 432 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.7975 (t80) REVERT: H 205 ASP cc_start: 0.6561 (t0) cc_final: 0.6132 (t0) REVERT: L 47 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8198 (m-30) REVERT: L 425 MET cc_start: 0.8129 (tpp) cc_final: 0.7878 (tpt) REVERT: L 432 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7470 (t80) REVERT: G 205 ASP cc_start: 0.7074 (t0) cc_final: 0.6816 (t0) REVERT: K 112 LYS cc_start: 0.7805 (mtmm) cc_final: 0.7542 (pttm) REVERT: K 151 SER cc_start: 0.8216 (OUTLIER) cc_final: 0.7965 (t) REVERT: K 254 GLU cc_start: 0.4608 (mm-30) cc_final: 0.3878 (mm-30) outliers start: 105 outliers final: 87 residues processed: 983 average time/residue: 0.5266 time to fit residues: 850.5490 Evaluate side-chains 980 residues out of total 4450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 889 time to evaluate : 4.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 413 MET Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain P residue 307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 325 optimal weight: 3.9990 chunk 436 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 377 optimal weight: 4.9990 chunk 60 optimal weight: 0.0000 chunk 113 optimal weight: 0.8980 chunk 410 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 421 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 300 ASN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 311 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 HIS ** H 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN K 256 GLN K 342 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 ASN ** I 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.092361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.076711 restraints weight = 71978.598| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.17 r_work: 0.2978 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 42070 Z= 0.213 Angle : 0.586 12.177 57162 Z= 0.296 Chirality : 0.042 0.165 6252 Planarity : 0.004 0.050 7436 Dihedral : 10.158 147.397 5925 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.45 % Allowed : 23.04 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.00 (0.12), residues: 5160 helix: 1.57 (0.11), residues: 2356 sheet: 1.59 (0.20), residues: 714 loop : -0.72 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP H 346 HIS 0.006 0.001 HIS C 88 PHE 0.021 0.001 PHE K 255 TYR 0.021 0.001 TYR L 24 ARG 0.011 0.000 ARG B 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14110.63 seconds wall clock time: 251 minutes 53.98 seconds (15113.98 seconds total)