Starting phenix.real_space_refine on Sat Apr 6 22:59:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op2_17038/04_2024/8op2_17038.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op2_17038/04_2024/8op2_17038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op2_17038/04_2024/8op2_17038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op2_17038/04_2024/8op2_17038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op2_17038/04_2024/8op2_17038.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op2_17038/04_2024/8op2_17038.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 140 5.49 5 S 320 5.16 5 C 37660 2.51 5 N 10420 2.21 5 O 11740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 56": "OD1" <-> "OD2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A ASP 221": "OD1" <-> "OD2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D ASP 221": "OD1" <-> "OD2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 108": "OE1" <-> "OE2" Residue "E PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E ASP 221": "OD1" <-> "OD2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "G PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 211": "OE1" <-> "OE2" Residue "G ASP 221": "OD1" <-> "OD2" Residue "H ASP 56": "OD1" <-> "OD2" Residue "H PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "H PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 211": "OE1" <-> "OE2" Residue "H ASP 221": "OD1" <-> "OD2" Residue "J ASP 56": "OD1" <-> "OD2" Residue "J PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 108": "OE1" <-> "OE2" Residue "J PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 211": "OE1" <-> "OE2" Residue "J ASP 221": "OD1" <-> "OD2" Residue "K ASP 56": "OD1" <-> "OD2" Residue "K PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "K PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 211": "OE1" <-> "OE2" Residue "K ASP 221": "OD1" <-> "OD2" Residue "M ASP 56": "OD1" <-> "OD2" Residue "M PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 108": "OE1" <-> "OE2" Residue "M PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 211": "OE1" <-> "OE2" Residue "M ASP 221": "OD1" <-> "OD2" Residue "N ASP 56": "OD1" <-> "OD2" Residue "N PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 108": "OE1" <-> "OE2" Residue "N PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 211": "OE1" <-> "OE2" Residue "N ASP 221": "OD1" <-> "OD2" Residue "P ASP 56": "OD1" <-> "OD2" Residue "P PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 108": "OE1" <-> "OE2" Residue "P PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 211": "OE1" <-> "OE2" Residue "P ASP 221": "OD1" <-> "OD2" Residue "Q ASP 56": "OD1" <-> "OD2" Residue "Q PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 108": "OE1" <-> "OE2" Residue "Q PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 211": "OE1" <-> "OE2" Residue "Q ASP 221": "OD1" <-> "OD2" Residue "S ASP 56": "OD1" <-> "OD2" Residue "S PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 108": "OE1" <-> "OE2" Residue "S PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 211": "OE1" <-> "OE2" Residue "S ASP 221": "OD1" <-> "OD2" Residue "T ASP 56": "OD1" <-> "OD2" Residue "T PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 108": "OE1" <-> "OE2" Residue "T PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 211": "OE1" <-> "OE2" Residue "T ASP 221": "OD1" <-> "OD2" Residue "c ASP 56": "OD1" <-> "OD2" Residue "c PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 108": "OE1" <-> "OE2" Residue "c PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 211": "OE1" <-> "OE2" Residue "c ASP 221": "OD1" <-> "OD2" Residue "d ASP 56": "OD1" <-> "OD2" Residue "d PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 108": "OE1" <-> "OE2" Residue "d PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 211": "OE1" <-> "OE2" Residue "d ASP 221": "OD1" <-> "OD2" Residue "g ASP 56": "OD1" <-> "OD2" Residue "g PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 108": "OE1" <-> "OE2" Residue "g PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 211": "OE1" <-> "OE2" Residue "g ASP 221": "OD1" <-> "OD2" Residue "h ASP 56": "OD1" <-> "OD2" Residue "h PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 108": "OE1" <-> "OE2" Residue "h PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 211": "OE1" <-> "OE2" Residue "h ASP 221": "OD1" <-> "OD2" Residue "k ASP 56": "OD1" <-> "OD2" Residue "k PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 108": "OE1" <-> "OE2" Residue "k PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 211": "OE1" <-> "OE2" Residue "k ASP 221": "OD1" <-> "OD2" Residue "l ASP 56": "OD1" <-> "OD2" Residue "l PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 108": "OE1" <-> "OE2" Residue "l PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 211": "OE1" <-> "OE2" Residue "l ASP 221": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 60280 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "U" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1400 Classifications: {'RNA': 70} Modifications used: {'rna2p_pyr': 10, 'rna3p_pyr': 60} Link IDs: {'rna2p': 10, 'rna3p': 59} Chain breaks: 4 Chain: "B" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "C" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1400 Classifications: {'RNA': 70} Modifications used: {'rna2p_pyr': 10, 'rna3p_pyr': 60} Link IDs: {'rna2p': 10, 'rna3p': 59} Chain breaks: 4 Chain: "D" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "E" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "G" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "H" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "J" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "K" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "M" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "N" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "P" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "Q" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "S" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "T" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "c" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "d" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "g" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "h" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "k" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Chain: "l" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2874 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 8, 'TRANS': 360} Time building chain proxies: 22.70, per 1000 atoms: 0.38 Number of scatterers: 60280 At special positions: 0 Unit cell: (184.345, 184.345, 162.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 320 16.00 P 140 15.00 O 11740 8.00 N 10420 7.00 C 37660 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: 17.16 Conformation dependent library (CDL) restraints added in 7.4 seconds 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13520 Finding SS restraints... Secondary structure from input PDB file: 420 helices and 60 sheets defined 70.2% alpha, 5.4% beta 0 base pairs and 100 stacking pairs defined. Time for finding SS restraints: 16.11 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 54 Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 143 removed outlier: 3.560A pdb=" N GLN A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 171 removed outlier: 3.550A pdb=" N ILE A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 216 through 232 removed outlier: 3.912A pdb=" N ILE A 220 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 249 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.917A pdb=" N ARG A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 274 through 295 removed outlier: 4.691A pdb=" N GLU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLN A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.619A pdb=" N PHE A 300 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 removed outlier: 3.809A pdb=" N SER A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 360 removed outlier: 4.051A pdb=" N LYS A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 54 Processing helix chain 'B' and resid 61 through 75 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 120 through 143 removed outlier: 3.560A pdb=" N GLN B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 171 removed outlier: 3.550A pdb=" N ILE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 216 through 232 removed outlier: 3.911A pdb=" N ILE B 220 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 221 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 249 Processing helix chain 'B' and resid 255 through 267 removed outlier: 3.916A pdb=" N ARG B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 274 through 295 removed outlier: 4.692A pdb=" N GLU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 removed outlier: 3.620A pdb=" N PHE B 300 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 removed outlier: 3.809A pdb=" N SER B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 360 removed outlier: 4.051A pdb=" N LYS B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 54 Processing helix chain 'D' and resid 61 through 75 Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 120 through 143 removed outlier: 3.559A pdb=" N GLN D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 171 removed outlier: 3.548A pdb=" N ILE D 160 " --> pdb=" O CYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 190 through 197 Processing helix chain 'D' and resid 201 through 216 Processing helix chain 'D' and resid 216 through 232 removed outlier: 3.914A pdb=" N ILE D 220 " --> pdb=" O HIS D 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D 221 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.916A pdb=" N ARG D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 274 through 295 removed outlier: 4.691A pdb=" N GLU D 282 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 301 removed outlier: 3.620A pdb=" N PHE D 300 " --> pdb=" O GLU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 313 removed outlier: 3.809A pdb=" N SER D 310 " --> pdb=" O PRO D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 331 Processing helix chain 'D' and resid 343 through 360 removed outlier: 4.051A pdb=" N LYS D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 54 Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 120 through 143 removed outlier: 3.560A pdb=" N GLN E 124 " --> pdb=" O THR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 171 removed outlier: 3.549A pdb=" N ILE E 160 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 178 through 189 Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 201 through 216 Processing helix chain 'E' and resid 216 through 232 removed outlier: 3.910A pdb=" N ILE E 220 " --> pdb=" O HIS E 216 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP E 221 " --> pdb=" O PRO E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 249 Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.917A pdb=" N ARG E 259 " --> pdb=" O GLN E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 274 through 295 removed outlier: 4.691A pdb=" N GLU E 282 " --> pdb=" O GLN E 278 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN E 283 " --> pdb=" O ALA E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 removed outlier: 3.620A pdb=" N PHE E 300 " --> pdb=" O GLU E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 313 removed outlier: 3.809A pdb=" N SER E 310 " --> pdb=" O PRO E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 331 Processing helix chain 'E' and resid 343 through 360 removed outlier: 4.051A pdb=" N LYS E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 9 through 20 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 40 through 54 Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 120 through 143 removed outlier: 3.560A pdb=" N GLN G 124 " --> pdb=" O THR G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 171 removed outlier: 3.549A pdb=" N ILE G 160 " --> pdb=" O CYS G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 178 through 189 Processing helix chain 'G' and resid 190 through 197 Processing helix chain 'G' and resid 201 through 216 Processing helix chain 'G' and resid 216 through 232 removed outlier: 3.913A pdb=" N ILE G 220 " --> pdb=" O HIS G 216 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 249 Processing helix chain 'G' and resid 255 through 267 removed outlier: 3.917A pdb=" N ARG G 259 " --> pdb=" O GLN G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'G' and resid 274 through 295 removed outlier: 4.691A pdb=" N GLU G 282 " --> pdb=" O GLN G 278 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN G 283 " --> pdb=" O ALA G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 301 removed outlier: 3.620A pdb=" N PHE G 300 " --> pdb=" O GLU G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 313 removed outlier: 3.810A pdb=" N SER G 310 " --> pdb=" O PRO G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 331 Processing helix chain 'G' and resid 343 through 360 removed outlier: 4.050A pdb=" N LYS G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU G 359 " --> pdb=" O GLU G 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 6 Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 40 through 54 Processing helix chain 'H' and resid 61 through 75 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 120 through 143 removed outlier: 3.561A pdb=" N GLN H 124 " --> pdb=" O THR H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 171 removed outlier: 3.549A pdb=" N ILE H 160 " --> pdb=" O CYS H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 178 through 189 Processing helix chain 'H' and resid 190 through 197 Processing helix chain 'H' and resid 201 through 216 Processing helix chain 'H' and resid 216 through 232 removed outlier: 3.911A pdb=" N ILE H 220 " --> pdb=" O HIS H 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP H 221 " --> pdb=" O PRO H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 249 Processing helix chain 'H' and resid 255 through 267 removed outlier: 3.916A pdb=" N ARG H 259 " --> pdb=" O GLN H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 273 Processing helix chain 'H' and resid 274 through 295 removed outlier: 4.692A pdb=" N GLU H 282 " --> pdb=" O GLN H 278 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN H 283 " --> pdb=" O ALA H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 301 removed outlier: 3.621A pdb=" N PHE H 300 " --> pdb=" O GLU H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 313 removed outlier: 3.809A pdb=" N SER H 310 " --> pdb=" O PRO H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 331 Processing helix chain 'H' and resid 343 through 360 removed outlier: 4.051A pdb=" N LYS H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU H 359 " --> pdb=" O GLU H 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 6 Processing helix chain 'J' and resid 9 through 20 Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 40 through 54 Processing helix chain 'J' and resid 61 through 75 Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 120 through 143 removed outlier: 3.559A pdb=" N GLN J 124 " --> pdb=" O THR J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 171 removed outlier: 3.549A pdb=" N ILE J 160 " --> pdb=" O CYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 178 through 189 Processing helix chain 'J' and resid 190 through 197 Processing helix chain 'J' and resid 201 through 216 Processing helix chain 'J' and resid 216 through 232 removed outlier: 3.912A pdb=" N ILE J 220 " --> pdb=" O HIS J 216 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP J 221 " --> pdb=" O PRO J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 249 Processing helix chain 'J' and resid 255 through 267 removed outlier: 3.916A pdb=" N ARG J 259 " --> pdb=" O GLN J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 273 Processing helix chain 'J' and resid 274 through 295 removed outlier: 4.691A pdb=" N GLU J 282 " --> pdb=" O GLN J 278 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN J 283 " --> pdb=" O ALA J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 301 removed outlier: 3.620A pdb=" N PHE J 300 " --> pdb=" O GLU J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 313 removed outlier: 3.810A pdb=" N SER J 310 " --> pdb=" O PRO J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 331 Processing helix chain 'J' and resid 343 through 360 removed outlier: 4.051A pdb=" N LYS J 358 " --> pdb=" O ALA J 354 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU J 359 " --> pdb=" O GLU J 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 6 Processing helix chain 'K' and resid 9 through 20 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 40 through 54 Processing helix chain 'K' and resid 61 through 75 Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'K' and resid 120 through 143 removed outlier: 3.559A pdb=" N GLN K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 171 removed outlier: 3.549A pdb=" N ILE K 160 " --> pdb=" O CYS K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 174 No H-bonds generated for 'chain 'K' and resid 172 through 174' Processing helix chain 'K' and resid 178 through 189 Processing helix chain 'K' and resid 190 through 197 Processing helix chain 'K' and resid 201 through 216 Processing helix chain 'K' and resid 216 through 232 removed outlier: 3.913A pdb=" N ILE K 220 " --> pdb=" O HIS K 216 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 249 Processing helix chain 'K' and resid 255 through 267 removed outlier: 3.917A pdb=" N ARG K 259 " --> pdb=" O GLN K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 273 Processing helix chain 'K' and resid 274 through 295 removed outlier: 4.691A pdb=" N GLU K 282 " --> pdb=" O GLN K 278 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN K 283 " --> pdb=" O ALA K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 301 removed outlier: 3.621A pdb=" N PHE K 300 " --> pdb=" O GLU K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 313 removed outlier: 3.809A pdb=" N SER K 310 " --> pdb=" O PRO K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 317 through 331 Processing helix chain 'K' and resid 343 through 360 removed outlier: 4.051A pdb=" N LYS K 358 " --> pdb=" O ALA K 354 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU K 359 " --> pdb=" O GLU K 355 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 6 Processing helix chain 'M' and resid 9 through 20 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 40 through 54 Processing helix chain 'M' and resid 61 through 75 Processing helix chain 'M' and resid 75 through 86 Processing helix chain 'M' and resid 120 through 143 removed outlier: 3.560A pdb=" N GLN M 124 " --> pdb=" O THR M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 171 removed outlier: 3.549A pdb=" N ILE M 160 " --> pdb=" O CYS M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 174 No H-bonds generated for 'chain 'M' and resid 172 through 174' Processing helix chain 'M' and resid 178 through 189 Processing helix chain 'M' and resid 190 through 197 Processing helix chain 'M' and resid 201 through 216 Processing helix chain 'M' and resid 216 through 232 removed outlier: 3.912A pdb=" N ILE M 220 " --> pdb=" O HIS M 216 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP M 221 " --> pdb=" O PRO M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 249 Processing helix chain 'M' and resid 255 through 267 removed outlier: 3.916A pdb=" N ARG M 259 " --> pdb=" O GLN M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 269 through 273 Processing helix chain 'M' and resid 274 through 295 removed outlier: 4.691A pdb=" N GLU M 282 " --> pdb=" O GLN M 278 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLN M 283 " --> pdb=" O ALA M 279 " (cutoff:3.500A) Processing helix chain 'M' and resid 296 through 301 removed outlier: 3.619A pdb=" N PHE M 300 " --> pdb=" O GLU M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 313 removed outlier: 3.810A pdb=" N SER M 310 " --> pdb=" O PRO M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 317 through 331 Processing helix chain 'M' and resid 343 through 360 removed outlier: 4.050A pdb=" N LYS M 358 " --> pdb=" O ALA M 354 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU M 359 " --> pdb=" O GLU M 355 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 6 Processing helix chain 'N' and resid 9 through 20 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 40 through 54 Processing helix chain 'N' and resid 61 through 75 Processing helix chain 'N' and resid 75 through 86 Processing helix chain 'N' and resid 120 through 143 removed outlier: 3.560A pdb=" N GLN N 124 " --> pdb=" O THR N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 171 removed outlier: 3.549A pdb=" N ILE N 160 " --> pdb=" O CYS N 156 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 174 No H-bonds generated for 'chain 'N' and resid 172 through 174' Processing helix chain 'N' and resid 178 through 189 Processing helix chain 'N' and resid 190 through 197 Processing helix chain 'N' and resid 201 through 216 Processing helix chain 'N' and resid 216 through 232 removed outlier: 3.912A pdb=" N ILE N 220 " --> pdb=" O HIS N 216 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP N 221 " --> pdb=" O PRO N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 249 Processing helix chain 'N' and resid 255 through 267 removed outlier: 3.916A pdb=" N ARG N 259 " --> pdb=" O GLN N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 269 through 273 Processing helix chain 'N' and resid 274 through 295 removed outlier: 4.691A pdb=" N GLU N 282 " --> pdb=" O GLN N 278 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN N 283 " --> pdb=" O ALA N 279 " (cutoff:3.500A) Processing helix chain 'N' and resid 296 through 301 removed outlier: 3.620A pdb=" N PHE N 300 " --> pdb=" O GLU N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 306 through 313 removed outlier: 3.809A pdb=" N SER N 310 " --> pdb=" O PRO N 307 " (cutoff:3.500A) Processing helix chain 'N' and resid 317 through 331 Processing helix chain 'N' and resid 343 through 360 removed outlier: 4.051A pdb=" N LYS N 358 " --> pdb=" O ALA N 354 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU N 359 " --> pdb=" O GLU N 355 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 6 Processing helix chain 'P' and resid 9 through 20 Processing helix chain 'P' and resid 37 through 39 No H-bonds generated for 'chain 'P' and resid 37 through 39' Processing helix chain 'P' and resid 40 through 54 Processing helix chain 'P' and resid 61 through 75 Processing helix chain 'P' and resid 75 through 86 Processing helix chain 'P' and resid 120 through 143 removed outlier: 3.560A pdb=" N GLN P 124 " --> pdb=" O THR P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 155 through 171 removed outlier: 3.550A pdb=" N ILE P 160 " --> pdb=" O CYS P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 174 No H-bonds generated for 'chain 'P' and resid 172 through 174' Processing helix chain 'P' and resid 178 through 189 Processing helix chain 'P' and resid 190 through 197 Processing helix chain 'P' and resid 201 through 216 Processing helix chain 'P' and resid 216 through 232 removed outlier: 3.912A pdb=" N ILE P 220 " --> pdb=" O HIS P 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP P 221 " --> pdb=" O PRO P 217 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 249 Processing helix chain 'P' and resid 255 through 267 removed outlier: 3.917A pdb=" N ARG P 259 " --> pdb=" O GLN P 255 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 273 Processing helix chain 'P' and resid 274 through 295 removed outlier: 4.691A pdb=" N GLU P 282 " --> pdb=" O GLN P 278 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN P 283 " --> pdb=" O ALA P 279 " (cutoff:3.500A) Processing helix chain 'P' and resid 296 through 301 removed outlier: 3.619A pdb=" N PHE P 300 " --> pdb=" O GLU P 297 " (cutoff:3.500A) Processing helix chain 'P' and resid 306 through 313 removed outlier: 3.809A pdb=" N SER P 310 " --> pdb=" O PRO P 307 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 331 Processing helix chain 'P' and resid 343 through 360 removed outlier: 4.051A pdb=" N LYS P 358 " --> pdb=" O ALA P 354 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU P 359 " --> pdb=" O GLU P 355 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 6 Processing helix chain 'Q' and resid 9 through 20 Processing helix chain 'Q' and resid 37 through 39 No H-bonds generated for 'chain 'Q' and resid 37 through 39' Processing helix chain 'Q' and resid 40 through 54 Processing helix chain 'Q' and resid 61 through 75 Processing helix chain 'Q' and resid 75 through 86 Processing helix chain 'Q' and resid 120 through 143 removed outlier: 3.559A pdb=" N GLN Q 124 " --> pdb=" O THR Q 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 155 through 171 removed outlier: 3.549A pdb=" N ILE Q 160 " --> pdb=" O CYS Q 156 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 174 No H-bonds generated for 'chain 'Q' and resid 172 through 174' Processing helix chain 'Q' and resid 178 through 189 Processing helix chain 'Q' and resid 190 through 197 Processing helix chain 'Q' and resid 201 through 216 Processing helix chain 'Q' and resid 216 through 232 removed outlier: 3.910A pdb=" N ILE Q 220 " --> pdb=" O HIS Q 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP Q 221 " --> pdb=" O PRO Q 217 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 249 Processing helix chain 'Q' and resid 255 through 267 removed outlier: 3.916A pdb=" N ARG Q 259 " --> pdb=" O GLN Q 255 " (cutoff:3.500A) Processing helix chain 'Q' and resid 269 through 273 Processing helix chain 'Q' and resid 274 through 295 removed outlier: 4.692A pdb=" N GLU Q 282 " --> pdb=" O GLN Q 278 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLN Q 283 " --> pdb=" O ALA Q 279 " (cutoff:3.500A) Processing helix chain 'Q' and resid 296 through 301 removed outlier: 3.619A pdb=" N PHE Q 300 " --> pdb=" O GLU Q 297 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 313 removed outlier: 3.809A pdb=" N SER Q 310 " --> pdb=" O PRO Q 307 " (cutoff:3.500A) Processing helix chain 'Q' and resid 317 through 331 Processing helix chain 'Q' and resid 343 through 360 removed outlier: 4.050A pdb=" N LYS Q 358 " --> pdb=" O ALA Q 354 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU Q 359 " --> pdb=" O GLU Q 355 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 6 Processing helix chain 'S' and resid 9 through 20 Processing helix chain 'S' and resid 37 through 39 No H-bonds generated for 'chain 'S' and resid 37 through 39' Processing helix chain 'S' and resid 40 through 54 Processing helix chain 'S' and resid 61 through 75 Processing helix chain 'S' and resid 75 through 86 Processing helix chain 'S' and resid 120 through 143 removed outlier: 3.558A pdb=" N GLN S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 155 through 171 removed outlier: 3.549A pdb=" N ILE S 160 " --> pdb=" O CYS S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 174 No H-bonds generated for 'chain 'S' and resid 172 through 174' Processing helix chain 'S' and resid 178 through 189 Processing helix chain 'S' and resid 190 through 197 Processing helix chain 'S' and resid 201 through 216 Processing helix chain 'S' and resid 216 through 232 removed outlier: 3.912A pdb=" N ILE S 220 " --> pdb=" O HIS S 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP S 221 " --> pdb=" O PRO S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 237 through 249 Processing helix chain 'S' and resid 255 through 267 removed outlier: 3.916A pdb=" N ARG S 259 " --> pdb=" O GLN S 255 " (cutoff:3.500A) Processing helix chain 'S' and resid 269 through 273 Processing helix chain 'S' and resid 274 through 295 removed outlier: 4.691A pdb=" N GLU S 282 " --> pdb=" O GLN S 278 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN S 283 " --> pdb=" O ALA S 279 " (cutoff:3.500A) Processing helix chain 'S' and resid 296 through 301 removed outlier: 3.620A pdb=" N PHE S 300 " --> pdb=" O GLU S 297 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 313 removed outlier: 3.809A pdb=" N SER S 310 " --> pdb=" O PRO S 307 " (cutoff:3.500A) Processing helix chain 'S' and resid 317 through 331 Processing helix chain 'S' and resid 343 through 360 removed outlier: 4.051A pdb=" N LYS S 358 " --> pdb=" O ALA S 354 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU S 359 " --> pdb=" O GLU S 355 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 6 Processing helix chain 'T' and resid 9 through 20 Processing helix chain 'T' and resid 37 through 39 No H-bonds generated for 'chain 'T' and resid 37 through 39' Processing helix chain 'T' and resid 40 through 54 Processing helix chain 'T' and resid 61 through 75 Processing helix chain 'T' and resid 75 through 86 Processing helix chain 'T' and resid 120 through 143 removed outlier: 3.558A pdb=" N GLN T 124 " --> pdb=" O THR T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 155 through 171 removed outlier: 3.549A pdb=" N ILE T 160 " --> pdb=" O CYS T 156 " (cutoff:3.500A) Processing helix chain 'T' and resid 172 through 174 No H-bonds generated for 'chain 'T' and resid 172 through 174' Processing helix chain 'T' and resid 178 through 189 Processing helix chain 'T' and resid 190 through 197 Processing helix chain 'T' and resid 201 through 216 Processing helix chain 'T' and resid 216 through 232 removed outlier: 3.911A pdb=" N ILE T 220 " --> pdb=" O HIS T 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP T 221 " --> pdb=" O PRO T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 237 through 249 Processing helix chain 'T' and resid 255 through 267 removed outlier: 3.917A pdb=" N ARG T 259 " --> pdb=" O GLN T 255 " (cutoff:3.500A) Processing helix chain 'T' and resid 269 through 273 Processing helix chain 'T' and resid 274 through 295 removed outlier: 4.691A pdb=" N GLU T 282 " --> pdb=" O GLN T 278 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLN T 283 " --> pdb=" O ALA T 279 " (cutoff:3.500A) Processing helix chain 'T' and resid 296 through 301 removed outlier: 3.620A pdb=" N PHE T 300 " --> pdb=" O GLU T 297 " (cutoff:3.500A) Processing helix chain 'T' and resid 306 through 313 removed outlier: 3.809A pdb=" N SER T 310 " --> pdb=" O PRO T 307 " (cutoff:3.500A) Processing helix chain 'T' and resid 317 through 331 Processing helix chain 'T' and resid 343 through 360 removed outlier: 4.052A pdb=" N LYS T 358 " --> pdb=" O ALA T 354 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU T 359 " --> pdb=" O GLU T 355 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 6 Processing helix chain 'c' and resid 9 through 20 Processing helix chain 'c' and resid 37 through 39 No H-bonds generated for 'chain 'c' and resid 37 through 39' Processing helix chain 'c' and resid 40 through 54 Processing helix chain 'c' and resid 61 through 75 Processing helix chain 'c' and resid 75 through 86 Processing helix chain 'c' and resid 120 through 143 removed outlier: 3.560A pdb=" N GLN c 124 " --> pdb=" O THR c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 155 through 171 removed outlier: 3.549A pdb=" N ILE c 160 " --> pdb=" O CYS c 156 " (cutoff:3.500A) Processing helix chain 'c' and resid 172 through 174 No H-bonds generated for 'chain 'c' and resid 172 through 174' Processing helix chain 'c' and resid 178 through 189 Processing helix chain 'c' and resid 190 through 197 Processing helix chain 'c' and resid 201 through 216 Processing helix chain 'c' and resid 216 through 232 removed outlier: 3.913A pdb=" N ILE c 220 " --> pdb=" O HIS c 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP c 221 " --> pdb=" O PRO c 217 " (cutoff:3.500A) Processing helix chain 'c' and resid 237 through 249 Processing helix chain 'c' and resid 255 through 267 removed outlier: 3.917A pdb=" N ARG c 259 " --> pdb=" O GLN c 255 " (cutoff:3.500A) Processing helix chain 'c' and resid 269 through 273 Processing helix chain 'c' and resid 274 through 295 removed outlier: 4.691A pdb=" N GLU c 282 " --> pdb=" O GLN c 278 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN c 283 " --> pdb=" O ALA c 279 " (cutoff:3.500A) Processing helix chain 'c' and resid 296 through 301 removed outlier: 3.620A pdb=" N PHE c 300 " --> pdb=" O GLU c 297 " (cutoff:3.500A) Processing helix chain 'c' and resid 306 through 313 removed outlier: 3.810A pdb=" N SER c 310 " --> pdb=" O PRO c 307 " (cutoff:3.500A) Processing helix chain 'c' and resid 317 through 331 Processing helix chain 'c' and resid 343 through 360 removed outlier: 4.051A pdb=" N LYS c 358 " --> pdb=" O ALA c 354 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU c 359 " --> pdb=" O GLU c 355 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 6 Processing helix chain 'd' and resid 9 through 20 Processing helix chain 'd' and resid 37 through 39 No H-bonds generated for 'chain 'd' and resid 37 through 39' Processing helix chain 'd' and resid 40 through 54 Processing helix chain 'd' and resid 61 through 75 Processing helix chain 'd' and resid 75 through 86 Processing helix chain 'd' and resid 120 through 143 removed outlier: 3.560A pdb=" N GLN d 124 " --> pdb=" O THR d 120 " (cutoff:3.500A) Processing helix chain 'd' and resid 155 through 171 removed outlier: 3.549A pdb=" N ILE d 160 " --> pdb=" O CYS d 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 172 through 174 No H-bonds generated for 'chain 'd' and resid 172 through 174' Processing helix chain 'd' and resid 178 through 189 Processing helix chain 'd' and resid 190 through 197 Processing helix chain 'd' and resid 201 through 216 Processing helix chain 'd' and resid 216 through 232 removed outlier: 3.911A pdb=" N ILE d 220 " --> pdb=" O HIS d 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP d 221 " --> pdb=" O PRO d 217 " (cutoff:3.500A) Processing helix chain 'd' and resid 237 through 249 Processing helix chain 'd' and resid 255 through 267 removed outlier: 3.917A pdb=" N ARG d 259 " --> pdb=" O GLN d 255 " (cutoff:3.500A) Processing helix chain 'd' and resid 269 through 273 Processing helix chain 'd' and resid 274 through 295 removed outlier: 4.693A pdb=" N GLU d 282 " --> pdb=" O GLN d 278 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN d 283 " --> pdb=" O ALA d 279 " (cutoff:3.500A) Processing helix chain 'd' and resid 296 through 301 removed outlier: 3.620A pdb=" N PHE d 300 " --> pdb=" O GLU d 297 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 313 removed outlier: 3.808A pdb=" N SER d 310 " --> pdb=" O PRO d 307 " (cutoff:3.500A) Processing helix chain 'd' and resid 317 through 331 Processing helix chain 'd' and resid 343 through 360 removed outlier: 4.050A pdb=" N LYS d 358 " --> pdb=" O ALA d 354 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU d 359 " --> pdb=" O GLU d 355 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 6 Processing helix chain 'g' and resid 9 through 20 Processing helix chain 'g' and resid 37 through 39 No H-bonds generated for 'chain 'g' and resid 37 through 39' Processing helix chain 'g' and resid 40 through 54 Processing helix chain 'g' and resid 61 through 75 Processing helix chain 'g' and resid 75 through 86 Processing helix chain 'g' and resid 120 through 143 removed outlier: 3.559A pdb=" N GLN g 124 " --> pdb=" O THR g 120 " (cutoff:3.500A) Processing helix chain 'g' and resid 155 through 171 removed outlier: 3.550A pdb=" N ILE g 160 " --> pdb=" O CYS g 156 " (cutoff:3.500A) Processing helix chain 'g' and resid 172 through 174 No H-bonds generated for 'chain 'g' and resid 172 through 174' Processing helix chain 'g' and resid 178 through 189 Processing helix chain 'g' and resid 190 through 197 Processing helix chain 'g' and resid 201 through 216 Processing helix chain 'g' and resid 216 through 232 removed outlier: 3.913A pdb=" N ILE g 220 " --> pdb=" O HIS g 216 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP g 221 " --> pdb=" O PRO g 217 " (cutoff:3.500A) Processing helix chain 'g' and resid 237 through 249 Processing helix chain 'g' and resid 255 through 267 removed outlier: 3.917A pdb=" N ARG g 259 " --> pdb=" O GLN g 255 " (cutoff:3.500A) Processing helix chain 'g' and resid 269 through 273 Processing helix chain 'g' and resid 274 through 295 removed outlier: 4.692A pdb=" N GLU g 282 " --> pdb=" O GLN g 278 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN g 283 " --> pdb=" O ALA g 279 " (cutoff:3.500A) Processing helix chain 'g' and resid 296 through 301 removed outlier: 3.619A pdb=" N PHE g 300 " --> pdb=" O GLU g 297 " (cutoff:3.500A) Processing helix chain 'g' and resid 306 through 313 removed outlier: 3.808A pdb=" N SER g 310 " --> pdb=" O PRO g 307 " (cutoff:3.500A) Processing helix chain 'g' and resid 317 through 331 Processing helix chain 'g' and resid 343 through 360 removed outlier: 4.051A pdb=" N LYS g 358 " --> pdb=" O ALA g 354 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU g 359 " --> pdb=" O GLU g 355 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 6 Processing helix chain 'h' and resid 9 through 20 Processing helix chain 'h' and resid 37 through 39 No H-bonds generated for 'chain 'h' and resid 37 through 39' Processing helix chain 'h' and resid 40 through 54 Processing helix chain 'h' and resid 61 through 75 Processing helix chain 'h' and resid 75 through 86 Processing helix chain 'h' and resid 120 through 143 removed outlier: 3.560A pdb=" N GLN h 124 " --> pdb=" O THR h 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 155 through 171 removed outlier: 3.549A pdb=" N ILE h 160 " --> pdb=" O CYS h 156 " (cutoff:3.500A) Processing helix chain 'h' and resid 172 through 174 No H-bonds generated for 'chain 'h' and resid 172 through 174' Processing helix chain 'h' and resid 178 through 189 Processing helix chain 'h' and resid 190 through 197 Processing helix chain 'h' and resid 201 through 216 Processing helix chain 'h' and resid 216 through 232 removed outlier: 3.912A pdb=" N ILE h 220 " --> pdb=" O HIS h 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP h 221 " --> pdb=" O PRO h 217 " (cutoff:3.500A) Processing helix chain 'h' and resid 237 through 249 Processing helix chain 'h' and resid 255 through 267 removed outlier: 3.916A pdb=" N ARG h 259 " --> pdb=" O GLN h 255 " (cutoff:3.500A) Processing helix chain 'h' and resid 269 through 273 Processing helix chain 'h' and resid 274 through 295 removed outlier: 4.691A pdb=" N GLU h 282 " --> pdb=" O GLN h 278 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN h 283 " --> pdb=" O ALA h 279 " (cutoff:3.500A) Processing helix chain 'h' and resid 296 through 301 removed outlier: 3.619A pdb=" N PHE h 300 " --> pdb=" O GLU h 297 " (cutoff:3.500A) Processing helix chain 'h' and resid 306 through 313 removed outlier: 3.809A pdb=" N SER h 310 " --> pdb=" O PRO h 307 " (cutoff:3.500A) Processing helix chain 'h' and resid 317 through 331 Processing helix chain 'h' and resid 343 through 360 removed outlier: 4.051A pdb=" N LYS h 358 " --> pdb=" O ALA h 354 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU h 359 " --> pdb=" O GLU h 355 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 6 Processing helix chain 'k' and resid 9 through 20 Processing helix chain 'k' and resid 37 through 39 No H-bonds generated for 'chain 'k' and resid 37 through 39' Processing helix chain 'k' and resid 40 through 54 Processing helix chain 'k' and resid 61 through 75 Processing helix chain 'k' and resid 75 through 86 Processing helix chain 'k' and resid 120 through 143 removed outlier: 3.560A pdb=" N GLN k 124 " --> pdb=" O THR k 120 " (cutoff:3.500A) Processing helix chain 'k' and resid 155 through 171 removed outlier: 3.549A pdb=" N ILE k 160 " --> pdb=" O CYS k 156 " (cutoff:3.500A) Processing helix chain 'k' and resid 172 through 174 No H-bonds generated for 'chain 'k' and resid 172 through 174' Processing helix chain 'k' and resid 178 through 189 Processing helix chain 'k' and resid 190 through 197 Processing helix chain 'k' and resid 201 through 216 Processing helix chain 'k' and resid 216 through 232 removed outlier: 3.912A pdb=" N ILE k 220 " --> pdb=" O HIS k 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP k 221 " --> pdb=" O PRO k 217 " (cutoff:3.500A) Processing helix chain 'k' and resid 237 through 249 Processing helix chain 'k' and resid 255 through 267 removed outlier: 3.916A pdb=" N ARG k 259 " --> pdb=" O GLN k 255 " (cutoff:3.500A) Processing helix chain 'k' and resid 269 through 273 Processing helix chain 'k' and resid 274 through 295 removed outlier: 4.691A pdb=" N GLU k 282 " --> pdb=" O GLN k 278 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN k 283 " --> pdb=" O ALA k 279 " (cutoff:3.500A) Processing helix chain 'k' and resid 296 through 301 removed outlier: 3.619A pdb=" N PHE k 300 " --> pdb=" O GLU k 297 " (cutoff:3.500A) Processing helix chain 'k' and resid 306 through 313 removed outlier: 3.810A pdb=" N SER k 310 " --> pdb=" O PRO k 307 " (cutoff:3.500A) Processing helix chain 'k' and resid 317 through 331 Processing helix chain 'k' and resid 343 through 360 removed outlier: 4.052A pdb=" N LYS k 358 " --> pdb=" O ALA k 354 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU k 359 " --> pdb=" O GLU k 355 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 6 Processing helix chain 'l' and resid 9 through 20 Processing helix chain 'l' and resid 37 through 39 No H-bonds generated for 'chain 'l' and resid 37 through 39' Processing helix chain 'l' and resid 40 through 54 Processing helix chain 'l' and resid 61 through 75 Processing helix chain 'l' and resid 75 through 86 Processing helix chain 'l' and resid 120 through 143 removed outlier: 3.560A pdb=" N GLN l 124 " --> pdb=" O THR l 120 " (cutoff:3.500A) Processing helix chain 'l' and resid 155 through 171 removed outlier: 3.549A pdb=" N ILE l 160 " --> pdb=" O CYS l 156 " (cutoff:3.500A) Processing helix chain 'l' and resid 172 through 174 No H-bonds generated for 'chain 'l' and resid 172 through 174' Processing helix chain 'l' and resid 178 through 189 Processing helix chain 'l' and resid 190 through 197 Processing helix chain 'l' and resid 201 through 216 Processing helix chain 'l' and resid 216 through 232 removed outlier: 3.912A pdb=" N ILE l 220 " --> pdb=" O HIS l 216 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP l 221 " --> pdb=" O PRO l 217 " (cutoff:3.500A) Processing helix chain 'l' and resid 237 through 249 Processing helix chain 'l' and resid 255 through 267 removed outlier: 3.916A pdb=" N ARG l 259 " --> pdb=" O GLN l 255 " (cutoff:3.500A) Processing helix chain 'l' and resid 269 through 273 Processing helix chain 'l' and resid 274 through 295 removed outlier: 4.691A pdb=" N GLU l 282 " --> pdb=" O GLN l 278 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN l 283 " --> pdb=" O ALA l 279 " (cutoff:3.500A) Processing helix chain 'l' and resid 296 through 301 removed outlier: 3.620A pdb=" N PHE l 300 " --> pdb=" O GLU l 297 " (cutoff:3.500A) Processing helix chain 'l' and resid 306 through 313 removed outlier: 3.809A pdb=" N SER l 310 " --> pdb=" O PRO l 307 " (cutoff:3.500A) Processing helix chain 'l' and resid 317 through 331 Processing helix chain 'l' and resid 343 through 360 removed outlier: 4.050A pdb=" N LYS l 358 " --> pdb=" O ALA l 354 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU l 359 " --> pdb=" O GLU l 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 6.794A pdb=" N ARG A 27 " --> pdb=" O HIS A 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 104 Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 28 removed outlier: 6.795A pdb=" N ARG B 27 " --> pdb=" O HIS B 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 104 Processing sheet with id=AA7, first strand: chain 'D' and resid 27 through 28 removed outlier: 6.794A pdb=" N ARG D 27 " --> pdb=" O HIS D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 33 through 35 Processing sheet with id=AA9, first strand: chain 'D' and resid 97 through 104 Processing sheet with id=AB1, first strand: chain 'E' and resid 27 through 28 removed outlier: 6.793A pdb=" N ARG E 27 " --> pdb=" O HIS E 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=AB3, first strand: chain 'E' and resid 97 through 104 Processing sheet with id=AB4, first strand: chain 'G' and resid 27 through 28 removed outlier: 6.794A pdb=" N ARG G 27 " --> pdb=" O HIS G 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 33 through 35 Processing sheet with id=AB6, first strand: chain 'G' and resid 97 through 104 Processing sheet with id=AB7, first strand: chain 'H' and resid 27 through 28 removed outlier: 6.795A pdb=" N ARG H 27 " --> pdb=" O HIS H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'H' and resid 33 through 35 Processing sheet with id=AB9, first strand: chain 'H' and resid 97 through 104 Processing sheet with id=AC1, first strand: chain 'J' and resid 27 through 28 removed outlier: 6.795A pdb=" N ARG J 27 " --> pdb=" O HIS J 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AC3, first strand: chain 'J' and resid 97 through 104 Processing sheet with id=AC4, first strand: chain 'K' and resid 27 through 28 removed outlier: 6.794A pdb=" N ARG K 27 " --> pdb=" O HIS K 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'K' and resid 33 through 35 Processing sheet with id=AC6, first strand: chain 'K' and resid 97 through 104 Processing sheet with id=AC7, first strand: chain 'M' and resid 27 through 28 removed outlier: 6.794A pdb=" N ARG M 27 " --> pdb=" O HIS M 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'M' and resid 33 through 35 Processing sheet with id=AC9, first strand: chain 'M' and resid 97 through 104 Processing sheet with id=AD1, first strand: chain 'N' and resid 27 through 28 removed outlier: 6.795A pdb=" N ARG N 27 " --> pdb=" O HIS N 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'N' and resid 33 through 35 Processing sheet with id=AD3, first strand: chain 'N' and resid 97 through 104 Processing sheet with id=AD4, first strand: chain 'P' and resid 27 through 28 removed outlier: 6.795A pdb=" N ARG P 27 " --> pdb=" O HIS P 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'P' and resid 33 through 35 Processing sheet with id=AD6, first strand: chain 'P' and resid 97 through 104 Processing sheet with id=AD7, first strand: chain 'Q' and resid 27 through 28 removed outlier: 6.794A pdb=" N ARG Q 27 " --> pdb=" O HIS Q 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'Q' and resid 33 through 35 Processing sheet with id=AD9, first strand: chain 'Q' and resid 97 through 104 Processing sheet with id=AE1, first strand: chain 'S' and resid 27 through 28 removed outlier: 6.795A pdb=" N ARG S 27 " --> pdb=" O HIS S 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'S' and resid 33 through 35 Processing sheet with id=AE3, first strand: chain 'S' and resid 97 through 104 Processing sheet with id=AE4, first strand: chain 'T' and resid 27 through 28 removed outlier: 6.795A pdb=" N ARG T 27 " --> pdb=" O HIS T 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'T' and resid 33 through 35 Processing sheet with id=AE6, first strand: chain 'T' and resid 97 through 104 Processing sheet with id=AE7, first strand: chain 'c' and resid 27 through 28 removed outlier: 6.795A pdb=" N ARG c 27 " --> pdb=" O HIS c 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'c' and resid 33 through 35 Processing sheet with id=AE9, first strand: chain 'c' and resid 97 through 104 Processing sheet with id=AF1, first strand: chain 'd' and resid 27 through 28 removed outlier: 6.793A pdb=" N ARG d 27 " --> pdb=" O HIS d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'd' and resid 33 through 35 Processing sheet with id=AF3, first strand: chain 'd' and resid 97 through 104 Processing sheet with id=AF4, first strand: chain 'g' and resid 27 through 28 removed outlier: 6.795A pdb=" N ARG g 27 " --> pdb=" O HIS g 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'g' and resid 33 through 35 Processing sheet with id=AF6, first strand: chain 'g' and resid 97 through 104 Processing sheet with id=AF7, first strand: chain 'h' and resid 27 through 28 removed outlier: 6.796A pdb=" N ARG h 27 " --> pdb=" O HIS h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'h' and resid 33 through 35 Processing sheet with id=AF9, first strand: chain 'h' and resid 97 through 104 Processing sheet with id=AG1, first strand: chain 'k' and resid 27 through 28 removed outlier: 6.794A pdb=" N ARG k 27 " --> pdb=" O HIS k 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'k' and resid 33 through 35 Processing sheet with id=AG3, first strand: chain 'k' and resid 97 through 104 Processing sheet with id=AG4, first strand: chain 'l' and resid 27 through 28 removed outlier: 6.794A pdb=" N ARG l 27 " --> pdb=" O HIS l 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'l' and resid 33 through 35 Processing sheet with id=AG6, first strand: chain 'l' and resid 97 through 104 3600 hydrogen bonds defined for protein. 10140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 100 stacking parallelities Total time for adding SS restraints: 26.24 Time building geometry restraints manager: 19.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 60620 1.57 - 1.91: 880 1.91 - 2.25: 0 2.25 - 2.59: 0 2.59 - 2.94: 10 Bond restraints: 61510 Sorted by residual: bond pdb=" O3' C C1028 " pdb=" P C C1029 " ideal model delta sigma weight residual 1.607 2.935 -1.328 1.50e-02 4.44e+03 7.84e+03 bond pdb=" O3' C C1049 " pdb=" P C C1050 " ideal model delta sigma weight residual 1.607 2.916 -1.309 1.50e-02 4.44e+03 7.61e+03 bond pdb=" O3' C C1042 " pdb=" P C C1043 " ideal model delta sigma weight residual 1.607 2.893 -1.286 1.50e-02 4.44e+03 7.35e+03 bond pdb=" O3' C U1063 " pdb=" P C U1064 " ideal model delta sigma weight residual 1.607 2.893 -1.286 1.50e-02 4.44e+03 7.35e+03 bond pdb=" O3' C U1007 " pdb=" P C U1008 " ideal model delta sigma weight residual 1.607 2.887 -1.280 1.50e-02 4.44e+03 7.28e+03 ... (remaining 61505 not shown) Histogram of bond angle deviations from ideal: 66.51 - 83.61: 11 83.61 - 100.71: 89 100.71 - 117.81: 46209 117.81 - 134.91: 37121 134.91 - 152.01: 10 Bond angle restraints: 83440 Sorted by residual: angle pdb=" O3' C U1063 " pdb=" P C U1064 " pdb=" O5' C U1064 " ideal model delta sigma weight residual 104.00 66.51 37.49 1.50e+00 4.44e-01 6.25e+02 angle pdb=" O3' C U1007 " pdb=" P C U1008 " pdb=" O5' C U1008 " ideal model delta sigma weight residual 104.00 71.37 32.63 1.50e+00 4.44e-01 4.73e+02 angle pdb=" O3' C C1028 " pdb=" P C C1029 " pdb=" O5' C C1029 " ideal model delta sigma weight residual 104.00 72.91 31.09 1.50e+00 4.44e-01 4.30e+02 angle pdb=" O3' C U1056 " pdb=" P C U1057 " pdb=" O5' C U1057 " ideal model delta sigma weight residual 104.00 73.96 30.04 1.50e+00 4.44e-01 4.01e+02 angle pdb=" O3' C C1042 " pdb=" P C C1043 " pdb=" O5' C C1043 " ideal model delta sigma weight residual 104.00 74.12 29.88 1.50e+00 4.44e-01 3.97e+02 ... (remaining 83435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 33192 17.63 - 35.26: 2918 35.26 - 52.88: 990 52.88 - 70.51: 210 70.51 - 88.14: 220 Dihedral angle restraints: 37530 sinusoidal: 16330 harmonic: 21200 Sorted by residual: dihedral pdb=" CG ARG k 101 " pdb=" CD ARG k 101 " pdb=" NE ARG k 101 " pdb=" CZ ARG k 101 " ideal model delta sinusoidal sigma weight residual 90.00 12.43 77.57 2 1.50e+01 4.44e-03 2.03e+01 dihedral pdb=" CG ARG E 101 " pdb=" CD ARG E 101 " pdb=" NE ARG E 101 " pdb=" CZ ARG E 101 " ideal model delta sinusoidal sigma weight residual 90.00 12.50 77.50 2 1.50e+01 4.44e-03 2.03e+01 dihedral pdb=" CG ARG g 101 " pdb=" CD ARG g 101 " pdb=" NE ARG g 101 " pdb=" CZ ARG g 101 " ideal model delta sinusoidal sigma weight residual 90.00 12.51 77.49 2 1.50e+01 4.44e-03 2.03e+01 ... (remaining 37527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 5051 0.031 - 0.062: 3042 0.062 - 0.093: 923 0.093 - 0.124: 471 0.124 - 0.155: 73 Chirality restraints: 9560 Sorted by residual: chirality pdb=" CA GLU B 55 " pdb=" N GLU B 55 " pdb=" C GLU B 55 " pdb=" CB GLU B 55 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA GLU g 55 " pdb=" N GLU g 55 " pdb=" C GLU g 55 " pdb=" CB GLU g 55 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA GLU d 55 " pdb=" N GLU d 55 " pdb=" C GLU d 55 " pdb=" CB GLU d 55 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 ... (remaining 9557 not shown) Planarity restraints: 10240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN P 192 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.36e+00 pdb=" CG ASN P 192 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN P 192 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN P 192 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN N 192 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" CG ASN N 192 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN N 192 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN N 192 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN k 192 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" CG ASN k 192 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN k 192 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN k 192 " 0.009 2.00e-02 2.50e+03 ... (remaining 10237 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 2410 2.71 - 3.26: 60561 3.26 - 3.81: 99696 3.81 - 4.35: 131497 4.35 - 4.90: 213390 Nonbonded interactions: 507554 Sorted by model distance: nonbonded pdb=" N GLU Q 77 " pdb=" OE1 GLU Q 77 " model vdw 2.165 2.520 nonbonded pdb=" N GLU K 77 " pdb=" OE1 GLU K 77 " model vdw 2.165 2.520 nonbonded pdb=" N GLU h 77 " pdb=" OE1 GLU h 77 " model vdw 2.165 2.520 nonbonded pdb=" N GLU N 77 " pdb=" OE1 GLU N 77 " model vdw 2.165 2.520 nonbonded pdb=" N GLU E 77 " pdb=" OE1 GLU E 77 " model vdw 2.165 2.520 ... (remaining 507549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'c' selection = chain 'd' selection = chain 'g' selection = chain 'h' selection = chain 'k' selection = chain 'l' } ncs_group { reference = chain 'C' selection = chain 'U' } 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: 2.360 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: 0.060 Extract box with map and model: 14.080 Check model and map are aligned: 0.640 Set scattering table: 0.410 Process input model: 134.630 Find NCS groups from input model: 3.280 Set up NCS constraints: 0.500 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: 0.030 Load rotamer database and sin/cos tables:15.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 0.017 1.328 61510 Z= 1.021 Angle : 1.062 44.007 83440 Z= 0.549 Chirality : 0.046 0.155 9560 Planarity : 0.003 0.029 10240 Dihedral : 16.529 88.140 24010 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.19 % Allowed : 4.20 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.10), residues: 7340 helix: 1.01 (0.08), residues: 4640 sheet: -0.12 (0.22), residues: 460 loop : -0.08 (0.14), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP l 260 HIS 0.007 0.001 HIS l 225 PHE 0.023 0.002 PHE N 111 TYR 0.012 0.002 TYR K 135 ARG 0.007 0.001 ARG g 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1473 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 1153 time to evaluate : 4.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.8002 (ttt180) cc_final: 0.7763 (ttm110) REVERT: A 221 ASP cc_start: 0.8401 (t70) cc_final: 0.8136 (t0) REVERT: A 338 ARG cc_start: 0.7672 (ttp-170) cc_final: 0.7402 (mtt180) REVERT: B 15 ASP cc_start: 0.8377 (t70) cc_final: 0.8129 (t70) REVERT: B 67 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8017 (tpp) REVERT: B 71 MET cc_start: 0.9012 (mtm) cc_final: 0.8749 (mtm) REVERT: B 191 LYS cc_start: 0.8204 (ptpt) cc_final: 0.7885 (ptpp) REVERT: B 198 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8173 (mmmm) REVERT: B 257 MET cc_start: 0.8831 (mmm) cc_final: 0.8332 (mmm) REVERT: D 24 THR cc_start: 0.8740 (p) cc_final: 0.8524 (p) REVERT: D 56 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: D 71 MET cc_start: 0.8955 (mtm) cc_final: 0.8650 (mtm) REVERT: D 248 MET cc_start: 0.8590 (mmm) cc_final: 0.8291 (tpt) REVERT: D 334 MET cc_start: 0.8635 (ttp) cc_final: 0.8314 (ttt) REVERT: E 67 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7651 (mmm) REVERT: E 198 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8101 (mmmm) REVERT: E 248 MET cc_start: 0.8554 (mmm) cc_final: 0.8333 (tpt) REVERT: G 56 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7349 (m-30) REVERT: G 67 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7998 (mmm) REVERT: G 338 ARG cc_start: 0.7707 (ttp-170) cc_final: 0.7426 (mtm180) REVERT: H 12 LEU cc_start: 0.8514 (tp) cc_final: 0.8304 (mt) REVERT: H 50 MET cc_start: 0.8216 (mtm) cc_final: 0.7956 (mtt) REVERT: H 67 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8040 (mmm) REVERT: H 71 MET cc_start: 0.9063 (mtm) cc_final: 0.8821 (mtm) REVERT: H 191 LYS cc_start: 0.8233 (ptpt) cc_final: 0.7905 (ptpp) REVERT: H 198 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8076 (mmmm) REVERT: H 334 MET cc_start: 0.8878 (ttp) cc_final: 0.8503 (ttt) REVERT: J 16 GLN cc_start: 0.8074 (tt0) cc_final: 0.7853 (tt0) REVERT: J 24 THR cc_start: 0.8682 (p) cc_final: 0.8475 (p) REVERT: J 56 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7205 (m-30) REVERT: J 76 ARG cc_start: 0.7942 (ttt180) cc_final: 0.7580 (ttp-110) REVERT: J 193 GLU cc_start: 0.7714 (mp0) cc_final: 0.7480 (mp0) REVERT: K 15 ASP cc_start: 0.8188 (t70) cc_final: 0.7966 (t0) REVERT: K 67 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7848 (mmm) REVERT: K 198 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8049 (mmmm) REVERT: K 257 MET cc_start: 0.8703 (mmm) cc_final: 0.8393 (mmm) REVERT: K 334 MET cc_start: 0.8842 (ttp) cc_final: 0.8453 (ttt) REVERT: M 76 ARG cc_start: 0.7981 (ttt180) cc_final: 0.7725 (ttp-110) REVERT: N 61 PHE cc_start: 0.8922 (m-80) cc_final: 0.8708 (m-80) REVERT: N 67 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8088 (mmm) REVERT: N 71 MET cc_start: 0.9040 (mtm) cc_final: 0.8621 (mtm) REVERT: N 191 LYS cc_start: 0.8315 (ptpt) cc_final: 0.7951 (ptpp) REVERT: N 198 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8126 (mmmm) REVERT: N 248 MET cc_start: 0.8606 (mmm) cc_final: 0.8392 (tpt) REVERT: P 24 THR cc_start: 0.8782 (p) cc_final: 0.8432 (t) REVERT: P 76 ARG cc_start: 0.7996 (ttt180) cc_final: 0.7756 (ttm110) REVERT: P 193 GLU cc_start: 0.7648 (mp0) cc_final: 0.7276 (mp0) REVERT: P 214 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7704 (mt-10) REVERT: P 221 ASP cc_start: 0.8407 (t70) cc_final: 0.8163 (t0) REVERT: P 338 ARG cc_start: 0.7695 (ttp-170) cc_final: 0.7442 (mtt180) REVERT: Q 15 ASP cc_start: 0.8340 (t70) cc_final: 0.8073 (t70) REVERT: Q 67 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7988 (tpp) REVERT: Q 71 MET cc_start: 0.9081 (mtm) cc_final: 0.8786 (mtm) REVERT: Q 191 LYS cc_start: 0.8161 (ptpt) cc_final: 0.7829 (ptpp) REVERT: Q 198 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8162 (mmmm) REVERT: Q 257 MET cc_start: 0.8837 (mmm) cc_final: 0.8347 (mmm) REVERT: S 24 THR cc_start: 0.8736 (p) cc_final: 0.8519 (p) REVERT: S 56 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7361 (m-30) REVERT: S 71 MET cc_start: 0.8952 (mtm) cc_final: 0.8655 (mtm) REVERT: S 203 LYS cc_start: 0.8651 (tttt) cc_final: 0.8360 (tttt) REVERT: S 248 MET cc_start: 0.8601 (mmm) cc_final: 0.8292 (tpt) REVERT: S 334 MET cc_start: 0.8628 (ttp) cc_final: 0.8293 (ttt) REVERT: T 67 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7879 (mmm) REVERT: T 198 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8085 (mmmm) REVERT: T 248 MET cc_start: 0.8585 (mmm) cc_final: 0.8359 (tpt) REVERT: c 56 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: c 67 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7989 (mmm) REVERT: c 338 ARG cc_start: 0.7708 (ttp-170) cc_final: 0.7432 (mtm180) REVERT: d 50 MET cc_start: 0.8267 (mtm) cc_final: 0.7994 (mtt) REVERT: d 67 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8161 (mmm) REVERT: d 191 LYS cc_start: 0.8278 (ptpt) cc_final: 0.7935 (ptpp) REVERT: d 198 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8071 (mmmm) REVERT: d 334 MET cc_start: 0.8854 (ttp) cc_final: 0.8479 (ttt) REVERT: g 16 GLN cc_start: 0.8066 (tt0) cc_final: 0.7854 (tt0) REVERT: g 24 THR cc_start: 0.8694 (p) cc_final: 0.8470 (p) REVERT: g 56 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7157 (m-30) REVERT: g 193 GLU cc_start: 0.7709 (mp0) cc_final: 0.7468 (mp0) REVERT: g 282 GLU cc_start: 0.6835 (mp0) cc_final: 0.6603 (mp0) REVERT: h 15 ASP cc_start: 0.8240 (t70) cc_final: 0.8030 (t0) REVERT: h 67 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7815 (mmm) REVERT: h 198 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8057 (mmmm) REVERT: h 257 MET cc_start: 0.8702 (mmm) cc_final: 0.8401 (mmm) REVERT: h 334 MET cc_start: 0.8835 (ttp) cc_final: 0.8461 (ttt) REVERT: k 76 ARG cc_start: 0.7982 (ttt180) cc_final: 0.7729 (ttp-110) REVERT: l 67 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8105 (mmm) REVERT: l 71 MET cc_start: 0.9035 (mtm) cc_final: 0.8623 (mtm) REVERT: l 191 LYS cc_start: 0.8329 (ptpt) cc_final: 0.7980 (ptpp) REVERT: l 198 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8141 (mmmm) REVERT: l 248 MET cc_start: 0.8594 (mmm) cc_final: 0.8378 (tpt) outliers start: 320 outliers final: 13 residues processed: 1307 average time/residue: 1.7109 time to fit residues: 2735.0383 Evaluate side-chains 773 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 732 time to evaluate : 4.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 MET Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 125 ILE Chi-restraints excluded: chain K residue 198 LYS Chi-restraints excluded: chain N residue 55 GLU Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 198 LYS Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 67 MET Chi-restraints excluded: chain Q residue 198 LYS Chi-restraints excluded: chain S residue 56 ASP Chi-restraints excluded: chain T residue 67 MET Chi-restraints excluded: chain T residue 198 LYS Chi-restraints excluded: chain c residue 56 ASP Chi-restraints excluded: chain c residue 67 MET Chi-restraints excluded: chain d residue 55 GLU Chi-restraints excluded: chain d residue 67 MET Chi-restraints excluded: chain d residue 198 LYS Chi-restraints excluded: chain g residue 56 ASP Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 67 MET Chi-restraints excluded: chain h residue 96 ASP Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain h residue 198 LYS Chi-restraints excluded: chain l residue 55 GLU Chi-restraints excluded: chain l residue 67 MET Chi-restraints excluded: chain l residue 198 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 619 optimal weight: 0.5980 chunk 556 optimal weight: 10.0000 chunk 308 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 375 optimal weight: 3.9990 chunk 297 optimal weight: 0.7980 chunk 575 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 349 optimal weight: 6.9990 chunk 428 optimal weight: 5.9990 chunk 666 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN B 26 GLN B 93 ASN B 356 GLN ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN E 292 GLN E 356 GLN ** E 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN G 192 ASN G 292 GLN H 26 GLN H 93 ASN H 356 GLN J 292 GLN K 26 GLN K 292 GLN K 360 ASN M 93 ASN M 102 GLN M 192 ASN M 292 GLN N 26 GLN N 292 GLN N 356 GLN N 360 ASN P 292 GLN Q 26 GLN Q 93 ASN Q 356 GLN S 192 ASN ** S 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 26 GLN T 292 GLN T 356 GLN ** T 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 26 GLN c 192 ASN c 292 GLN d 26 GLN d 93 ASN d 356 GLN g 292 GLN h 26 GLN h 292 GLN h 360 ASN k 93 ASN k 102 GLN k 192 ASN k 292 GLN l 26 GLN l 292 GLN l 356 GLN ** l 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 61510 Z= 0.286 Angle : 0.583 5.951 83440 Z= 0.313 Chirality : 0.044 0.187 9560 Planarity : 0.004 0.036 10240 Dihedral : 11.841 80.445 10332 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.70 % Allowed : 11.31 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.10), residues: 7340 helix: 1.12 (0.07), residues: 4760 sheet: 0.37 (0.20), residues: 500 loop : 0.29 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP c 260 HIS 0.009 0.001 HIS k 225 PHE 0.013 0.002 PHE J 226 TYR 0.016 0.002 TYR k 135 ARG 0.008 0.001 ARG l 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 875 time to evaluate : 5.023 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: A 110 LYS cc_start: 0.8056 (tmtt) cc_final: 0.7841 (tmtm) REVERT: A 193 GLU cc_start: 0.7896 (mp0) cc_final: 0.7581 (mp0) REVERT: A 195 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7761 (pttm) REVERT: A 198 LYS cc_start: 0.8062 (mmtm) cc_final: 0.7119 (mppt) REVERT: A 356 GLN cc_start: 0.6861 (OUTLIER) cc_final: 0.6468 (mt0) REVERT: B 15 ASP cc_start: 0.8374 (t70) cc_final: 0.8013 (t70) REVERT: B 71 MET cc_start: 0.9019 (mtm) cc_final: 0.8733 (mtp) REVERT: B 89 HIS cc_start: 0.6911 (t70) cc_final: 0.6610 (m-70) REVERT: B 93 ASN cc_start: 0.8123 (t0) cc_final: 0.7775 (t0) REVERT: B 191 LYS cc_start: 0.8172 (ptpt) cc_final: 0.7906 (ptpp) REVERT: B 257 MET cc_start: 0.8803 (mmm) cc_final: 0.8460 (mmm) REVERT: B 336 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7160 (tm-30) REVERT: D 71 MET cc_start: 0.9172 (mtm) cc_final: 0.8760 (mtm) REVERT: D 142 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6084 (tmm) REVERT: D 198 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7370 (mppt) REVERT: E 67 MET cc_start: 0.8367 (mmm) cc_final: 0.8135 (mmm) REVERT: E 359 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5093 (mp0) REVERT: G 12 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8249 (tp) REVERT: G 67 MET cc_start: 0.8807 (mmm) cc_final: 0.8398 (mmm) REVERT: G 93 ASN cc_start: 0.8216 (m-40) cc_final: 0.7677 (m-40) REVERT: G 130 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7603 (mp0) REVERT: G 198 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7869 (tppt) REVERT: G 201 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8045 (mt) REVERT: H 50 MET cc_start: 0.8168 (mtm) cc_final: 0.7857 (mtt) REVERT: H 93 ASN cc_start: 0.8227 (t0) cc_final: 0.7878 (t0) REVERT: H 96 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7911 (p0) REVERT: H 101 ARG cc_start: 0.8068 (ttm-80) cc_final: 0.7498 (tpp-160) REVERT: H 191 LYS cc_start: 0.8200 (ptpt) cc_final: 0.7980 (pttp) REVERT: H 334 MET cc_start: 0.8958 (ttp) cc_final: 0.8616 (ttt) REVERT: H 336 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: J 12 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8185 (tp) REVERT: J 16 GLN cc_start: 0.8149 (tt0) cc_final: 0.7857 (tt0) REVERT: J 24 THR cc_start: 0.8662 (p) cc_final: 0.8438 (p) REVERT: J 130 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: J 338 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.7207 (mtm110) REVERT: K 12 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8381 (tp) REVERT: K 15 ASP cc_start: 0.8311 (t70) cc_final: 0.8102 (t70) REVERT: K 191 LYS cc_start: 0.8421 (ptpt) cc_final: 0.8060 (pttp) REVERT: K 257 MET cc_start: 0.8682 (mmm) cc_final: 0.8432 (mmm) REVERT: K 334 MET cc_start: 0.8940 (ttp) cc_final: 0.8630 (ttt) REVERT: K 342 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7135 (ptp-170) REVERT: K 356 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6446 (mt0) REVERT: M 50 MET cc_start: 0.8685 (mtp) cc_final: 0.8453 (mtm) REVERT: M 122 GLU cc_start: 0.7365 (mp0) cc_final: 0.7079 (mp0) REVERT: M 123 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8124 (mp) REVERT: M 195 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7776 (ttpp) REVERT: N 71 MET cc_start: 0.9109 (mtm) cc_final: 0.8805 (mtp) REVERT: N 89 HIS cc_start: 0.6758 (t70) cc_final: 0.6537 (m-70) REVERT: N 191 LYS cc_start: 0.8252 (ptpt) cc_final: 0.7986 (pttp) REVERT: N 336 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7515 (pt0) REVERT: P 195 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7756 (pttm) REVERT: P 198 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7127 (mppt) REVERT: Q 15 ASP cc_start: 0.8376 (t70) cc_final: 0.8012 (t70) REVERT: Q 71 MET cc_start: 0.9018 (mtm) cc_final: 0.8780 (mtp) REVERT: Q 89 HIS cc_start: 0.6979 (t70) cc_final: 0.6687 (m-70) REVERT: Q 93 ASN cc_start: 0.8122 (t0) cc_final: 0.7757 (t0) REVERT: Q 191 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7907 (ptpp) REVERT: Q 257 MET cc_start: 0.8808 (mmm) cc_final: 0.8457 (mmm) REVERT: Q 336 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7175 (tm-30) REVERT: S 71 MET cc_start: 0.9167 (mtm) cc_final: 0.8764 (mtm) REVERT: S 123 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8498 (mt) REVERT: S 142 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6086 (tmm) REVERT: S 198 LYS cc_start: 0.8049 (mmtm) cc_final: 0.7358 (mppt) REVERT: T 67 MET cc_start: 0.8364 (mmm) cc_final: 0.8124 (mmm) REVERT: T 101 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.6590 (tpp-160) REVERT: T 359 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.5047 (mp0) REVERT: c 12 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8236 (tp) REVERT: c 67 MET cc_start: 0.8807 (mmm) cc_final: 0.8391 (mmm) REVERT: c 130 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7600 (mp0) REVERT: c 198 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7872 (tppt) REVERT: c 201 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8046 (mt) REVERT: d 50 MET cc_start: 0.8138 (mtm) cc_final: 0.7815 (mtt) REVERT: d 93 ASN cc_start: 0.8202 (t0) cc_final: 0.7859 (t0) REVERT: d 96 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7931 (p0) REVERT: d 191 LYS cc_start: 0.8199 (ptpt) cc_final: 0.7968 (pttp) REVERT: d 334 MET cc_start: 0.8957 (ttp) cc_final: 0.8624 (ttt) REVERT: d 336 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: g 12 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8149 (tp) REVERT: g 16 GLN cc_start: 0.8143 (tt0) cc_final: 0.7859 (tt0) REVERT: g 24 THR cc_start: 0.8658 (p) cc_final: 0.8432 (p) REVERT: g 195 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7826 (ttpp) REVERT: g 338 ARG cc_start: 0.7970 (mtm180) cc_final: 0.7765 (mtm-85) REVERT: h 12 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8371 (tp) REVERT: h 15 ASP cc_start: 0.8316 (t70) cc_final: 0.8100 (t70) REVERT: h 191 LYS cc_start: 0.8407 (ptpt) cc_final: 0.8068 (pttp) REVERT: h 257 MET cc_start: 0.8684 (mmm) cc_final: 0.8433 (mmm) REVERT: h 342 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.7139 (ptp-170) REVERT: h 356 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6465 (mt0) REVERT: k 50 MET cc_start: 0.8688 (mtp) cc_final: 0.8449 (mtm) REVERT: k 122 GLU cc_start: 0.7364 (mp0) cc_final: 0.7075 (mp0) REVERT: k 123 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8112 (mp) REVERT: k 194 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7719 (mtm) REVERT: k 195 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7778 (ttpp) REVERT: l 12 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8345 (mp) REVERT: l 71 MET cc_start: 0.9119 (mtm) cc_final: 0.8808 (mtp) REVERT: l 89 HIS cc_start: 0.6752 (t70) cc_final: 0.6534 (m-70) REVERT: l 191 LYS cc_start: 0.8268 (ptpt) cc_final: 0.8000 (pttp) REVERT: l 336 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7583 (pt0) outliers start: 228 outliers final: 53 residues processed: 990 average time/residue: 1.6706 time to fit residues: 2033.6813 Evaluate side-chains 834 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 745 time to evaluate : 4.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 336 GLU Chi-restraints excluded: chain H residue 359 GLU Chi-restraints excluded: chain H residue 362 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 356 GLN Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 195 LYS Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain N residue 359 GLU Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 195 LYS Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 110 LYS Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 123 ILE Chi-restraints excluded: chain S residue 142 MET Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 359 GLU Chi-restraints excluded: chain T residue 362 VAL Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 198 LYS Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 336 GLU Chi-restraints excluded: chain d residue 359 GLU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 195 LYS Chi-restraints excluded: chain g residue 336 GLU Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 39 ASP Chi-restraints excluded: chain h residue 96 ASP Chi-restraints excluded: chain h residue 342 ARG Chi-restraints excluded: chain h residue 356 GLN Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 123 ILE Chi-restraints excluded: chain k residue 194 MET Chi-restraints excluded: chain k residue 195 LYS Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 39 ASP Chi-restraints excluded: chain l residue 96 ASP Chi-restraints excluded: chain l residue 336 GLU Chi-restraints excluded: chain l residue 359 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 370 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 554 optimal weight: 1.9990 chunk 453 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 667 optimal weight: 0.5980 chunk 721 optimal weight: 2.9990 chunk 594 optimal weight: 4.9990 chunk 662 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 535 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 192 ASN B 356 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN D 102 GLN D 192 ASN D 292 GLN E 45 ASN E 93 ASN E 356 GLN ** E 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN H 45 ASN H 207 ASN H 356 GLN J 26 GLN J 93 ASN J 192 ASN K 45 ASN K 93 ASN M 26 GLN M 102 GLN M 192 ASN N 45 ASN N 192 ASN N 356 GLN P 26 GLN P 192 ASN Q 356 GLN ** Q 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 26 GLN S 102 GLN S 192 ASN S 292 GLN T 45 ASN T 93 ASN T 356 GLN ** T 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 93 ASN c 102 GLN d 45 ASN d 207 ASN d 356 GLN g 26 GLN g 93 ASN g 102 GLN g 192 ASN h 45 ASN h 93 ASN k 26 GLN k 102 GLN k 192 ASN l 356 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 61510 Z= 0.243 Angle : 0.530 6.235 83440 Z= 0.282 Chirality : 0.041 0.170 9560 Planarity : 0.003 0.036 10240 Dihedral : 11.179 73.932 10212 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.25 % Allowed : 13.78 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.10), residues: 7340 helix: 1.29 (0.07), residues: 4760 sheet: 0.48 (0.20), residues: 500 loop : 0.39 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 260 HIS 0.008 0.001 HIS k 225 PHE 0.013 0.002 PHE J 226 TYR 0.022 0.002 TYR g 135 ARG 0.009 0.000 ARG l 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 798 time to evaluate : 4.969 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: A 31 ASP cc_start: 0.6150 (OUTLIER) cc_final: 0.5619 (p0) REVERT: A 77 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: A 91 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7183 (tmtm) REVERT: A 195 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7818 (pttp) REVERT: A 198 LYS cc_start: 0.8254 (mmtm) cc_final: 0.7394 (mppt) REVERT: B 12 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8195 (tp) REVERT: B 15 ASP cc_start: 0.8464 (t70) cc_final: 0.8103 (t70) REVERT: B 71 MET cc_start: 0.9037 (mtm) cc_final: 0.8764 (mtp) REVERT: B 93 ASN cc_start: 0.8130 (t0) cc_final: 0.7803 (t0) REVERT: B 101 ARG cc_start: 0.8038 (ttm110) cc_final: 0.7616 (ttm110) REVERT: B 191 LYS cc_start: 0.8091 (ptpt) cc_final: 0.7812 (ptpp) REVERT: B 257 MET cc_start: 0.8790 (mmm) cc_final: 0.8317 (mmm) REVERT: D 71 MET cc_start: 0.9155 (mtm) cc_final: 0.8765 (mtm) REVERT: D 93 ASN cc_start: 0.8186 (m-40) cc_final: 0.7679 (m110) REVERT: D 142 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6158 (tmm) REVERT: D 195 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7858 (pttm) REVERT: D 198 LYS cc_start: 0.8301 (mmtm) cc_final: 0.7599 (mppt) REVERT: E 12 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7891 (mp) REVERT: E 93 ASN cc_start: 0.8073 (t0) cc_final: 0.7685 (t0) REVERT: E 101 ARG cc_start: 0.8241 (ttm110) cc_final: 0.7868 (ttm110) REVERT: G 12 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8280 (tp) REVERT: G 67 MET cc_start: 0.8792 (mmm) cc_final: 0.8471 (mmm) REVERT: G 93 ASN cc_start: 0.8199 (m-40) cc_final: 0.7686 (m-40) REVERT: G 101 ARG cc_start: 0.8007 (ttm110) cc_final: 0.7774 (ttm110) REVERT: G 198 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7895 (tppt) REVERT: G 201 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7940 (mt) REVERT: G 356 GLN cc_start: 0.6666 (OUTLIER) cc_final: 0.6174 (mt0) REVERT: H 12 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8224 (tp) REVERT: H 50 MET cc_start: 0.8149 (mtm) cc_final: 0.7829 (mtt) REVERT: H 93 ASN cc_start: 0.8163 (t0) cc_final: 0.7614 (t0) REVERT: H 96 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7948 (p0) REVERT: H 334 MET cc_start: 0.8929 (ttp) cc_final: 0.8607 (ttt) REVERT: J 12 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8164 (tp) REVERT: J 16 GLN cc_start: 0.8181 (tt0) cc_final: 0.7906 (tt0) REVERT: J 24 THR cc_start: 0.8755 (p) cc_final: 0.8550 (p) REVERT: J 67 MET cc_start: 0.8793 (mmm) cc_final: 0.8493 (mmm) REVERT: J 93 ASN cc_start: 0.8213 (m-40) cc_final: 0.7680 (m110) REVERT: J 130 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: J 195 LYS cc_start: 0.8380 (mtmm) cc_final: 0.8124 (ttpp) REVERT: J 297 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7438 (pm20) REVERT: J 334 MET cc_start: 0.8827 (ttp) cc_final: 0.8203 (ttt) REVERT: J 338 ARG cc_start: 0.7471 (mtm-85) cc_final: 0.7241 (mpp-170) REVERT: J 356 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6599 (mt0) REVERT: K 12 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8366 (tp) REVERT: K 15 ASP cc_start: 0.8206 (t70) cc_final: 0.7965 (t70) REVERT: K 93 ASN cc_start: 0.8231 (t0) cc_final: 0.7626 (t0) REVERT: K 191 LYS cc_start: 0.8401 (ptpt) cc_final: 0.8059 (pttp) REVERT: K 198 LYS cc_start: 0.8704 (mmpt) cc_final: 0.8488 (mmtm) REVERT: K 201 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8201 (mt) REVERT: K 342 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7288 (ptp-170) REVERT: K 356 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6579 (mt0) REVERT: M 50 MET cc_start: 0.8758 (mtp) cc_final: 0.8517 (mtm) REVERT: M 98 THR cc_start: 0.8608 (p) cc_final: 0.8051 (t) REVERT: M 122 GLU cc_start: 0.7410 (mp0) cc_final: 0.7129 (mp0) REVERT: M 356 GLN cc_start: 0.6678 (OUTLIER) cc_final: 0.6167 (mt0) REVERT: N 71 MET cc_start: 0.9059 (mtm) cc_final: 0.8766 (mtp) REVERT: N 356 GLN cc_start: 0.6451 (mt0) cc_final: 0.6185 (mt0) REVERT: P 77 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: P 91 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7201 (tmtm) REVERT: P 195 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7811 (pttp) REVERT: P 198 LYS cc_start: 0.8256 (mmtm) cc_final: 0.7400 (mppt) REVERT: P 356 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.6292 (mt0) REVERT: Q 12 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8198 (tp) REVERT: Q 15 ASP cc_start: 0.8467 (t70) cc_final: 0.8100 (t70) REVERT: Q 71 MET cc_start: 0.9031 (mtm) cc_final: 0.8781 (mtp) REVERT: Q 93 ASN cc_start: 0.8128 (t0) cc_final: 0.7779 (t0) REVERT: Q 101 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7725 (ttm110) REVERT: Q 191 LYS cc_start: 0.8108 (ptpt) cc_final: 0.7814 (ptpp) REVERT: Q 257 MET cc_start: 0.8793 (mmm) cc_final: 0.8322 (mmm) REVERT: Q 336 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7174 (tm-30) REVERT: S 71 MET cc_start: 0.9149 (mtm) cc_final: 0.8741 (mtm) REVERT: S 123 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8511 (mt) REVERT: S 142 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6167 (tmm) REVERT: S 195 LYS cc_start: 0.8279 (mtmm) cc_final: 0.7854 (pttm) REVERT: S 198 LYS cc_start: 0.8293 (mmtm) cc_final: 0.7603 (mppt) REVERT: T 12 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7894 (mp) REVERT: T 93 ASN cc_start: 0.8063 (t0) cc_final: 0.7678 (t0) REVERT: T 138 MET cc_start: 0.7970 (tmm) cc_final: 0.7764 (ppp) REVERT: c 12 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8274 (tp) REVERT: c 67 MET cc_start: 0.8788 (mmm) cc_final: 0.8462 (mmm) REVERT: c 101 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7681 (ttm110) REVERT: c 198 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7893 (tppt) REVERT: c 201 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7941 (mt) REVERT: c 356 GLN cc_start: 0.6711 (OUTLIER) cc_final: 0.6150 (mt0) REVERT: d 50 MET cc_start: 0.8184 (mtm) cc_final: 0.7851 (mtt) REVERT: d 93 ASN cc_start: 0.8219 (t0) cc_final: 0.7863 (t0) REVERT: d 96 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8007 (p0) REVERT: d 334 MET cc_start: 0.8931 (ttp) cc_final: 0.8609 (ttt) REVERT: g 12 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8158 (tp) REVERT: g 16 GLN cc_start: 0.8178 (tt0) cc_final: 0.7910 (tt0) REVERT: g 24 THR cc_start: 0.8754 (p) cc_final: 0.8547 (p) REVERT: g 67 MET cc_start: 0.8797 (mmm) cc_final: 0.8504 (mmm) REVERT: g 130 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: g 195 LYS cc_start: 0.8163 (mtpm) cc_final: 0.7881 (ttpp) REVERT: g 297 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: g 334 MET cc_start: 0.8855 (ttp) cc_final: 0.8262 (ttp) REVERT: h 12 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8355 (tp) REVERT: h 15 ASP cc_start: 0.8206 (t70) cc_final: 0.7971 (t70) REVERT: h 93 ASN cc_start: 0.8216 (t0) cc_final: 0.7624 (t0) REVERT: h 191 LYS cc_start: 0.8395 (ptpt) cc_final: 0.8055 (pttp) REVERT: h 198 LYS cc_start: 0.8690 (mmpt) cc_final: 0.8481 (mmtm) REVERT: h 201 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8252 (mt) REVERT: h 342 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7309 (ptp-170) REVERT: h 356 GLN cc_start: 0.6860 (OUTLIER) cc_final: 0.6636 (mt0) REVERT: k 50 MET cc_start: 0.8754 (mtp) cc_final: 0.8517 (mtm) REVERT: k 98 THR cc_start: 0.8618 (p) cc_final: 0.8042 (t) REVERT: k 122 GLU cc_start: 0.7410 (mp0) cc_final: 0.7126 (mp0) REVERT: k 356 GLN cc_start: 0.6673 (OUTLIER) cc_final: 0.6164 (mt0) REVERT: l 12 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8338 (mp) REVERT: l 67 MET cc_start: 0.8382 (mmp) cc_final: 0.8172 (mmm) REVERT: l 71 MET cc_start: 0.9073 (mtm) cc_final: 0.8779 (mtp) REVERT: l 356 GLN cc_start: 0.6496 (mt0) cc_final: 0.6253 (mt0) outliers start: 200 outliers final: 70 residues processed: 930 average time/residue: 1.6354 time to fit residues: 1882.6354 Evaluate side-chains 845 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 731 time to evaluate : 4.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 356 GLN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 359 GLU Chi-restraints excluded: chain H residue 362 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain J residue 356 GLN Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 356 GLN Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 356 GLN Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 359 GLU Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 195 LYS Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 356 GLN Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 363 ILE Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 338 ARG Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 123 ILE Chi-restraints excluded: chain S residue 142 MET Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 362 VAL Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 198 LYS Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 356 GLN Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 359 GLU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 22 LYS Chi-restraints excluded: chain g residue 32 SER Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 297 GLU Chi-restraints excluded: chain g residue 336 GLU Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 39 ASP Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain h residue 201 LEU Chi-restraints excluded: chain h residue 342 ARG Chi-restraints excluded: chain h residue 356 GLN Chi-restraints excluded: chain k residue 31 ASP Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 356 GLN Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 39 ASP Chi-restraints excluded: chain l residue 96 ASP Chi-restraints excluded: chain l residue 120 THR Chi-restraints excluded: chain l residue 359 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 659 optimal weight: 1.9990 chunk 502 optimal weight: 6.9990 chunk 346 optimal weight: 0.0670 chunk 73 optimal weight: 0.8980 chunk 318 optimal weight: 1.9990 chunk 448 optimal weight: 2.9990 chunk 670 optimal weight: 3.9990 chunk 709 optimal weight: 10.0000 chunk 350 optimal weight: 2.9990 chunk 635 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 192 ASN B 45 ASN D 102 GLN D 192 ASN ** E 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN M 192 ASN P 102 GLN P 192 ASN Q 45 ASN S 93 ASN S 102 GLN S 192 ASN ** T 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 GLN k 192 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 61510 Z= 0.209 Angle : 0.511 12.673 83440 Z= 0.269 Chirality : 0.040 0.169 9560 Planarity : 0.003 0.048 10240 Dihedral : 11.074 73.884 10210 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.25 % Allowed : 15.31 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.10), residues: 7340 helix: 1.47 (0.08), residues: 4760 sheet: 0.28 (0.20), residues: 460 loop : 0.50 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP c 260 HIS 0.007 0.001 HIS M 225 PHE 0.012 0.002 PHE J 226 TYR 0.014 0.001 TYR M 135 ARG 0.007 0.000 ARG g 338 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 757 time to evaluate : 4.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: A 101 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7940 (ttm110) REVERT: A 130 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7760 (mm-30) REVERT: A 193 GLU cc_start: 0.7728 (mp0) cc_final: 0.7468 (mp0) REVERT: A 195 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7839 (pttp) REVERT: A 198 LYS cc_start: 0.8270 (mmtm) cc_final: 0.7564 (mppt) REVERT: A 356 GLN cc_start: 0.6848 (OUTLIER) cc_final: 0.6430 (mt0) REVERT: B 15 ASP cc_start: 0.8397 (t70) cc_final: 0.8147 (t70) REVERT: B 71 MET cc_start: 0.9021 (mtm) cc_final: 0.8748 (mtp) REVERT: B 93 ASN cc_start: 0.8124 (t0) cc_final: 0.7809 (t0) REVERT: B 191 LYS cc_start: 0.8093 (ptpt) cc_final: 0.7793 (ptpp) REVERT: B 248 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8354 (mmm) REVERT: B 257 MET cc_start: 0.8774 (mmm) cc_final: 0.8361 (mmm) REVERT: D 71 MET cc_start: 0.9158 (mtm) cc_final: 0.8734 (mtm) REVERT: D 101 ARG cc_start: 0.8145 (ttm110) cc_final: 0.7788 (ttm110) REVERT: D 142 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6079 (pp-130) REVERT: D 195 LYS cc_start: 0.8249 (mtmm) cc_final: 0.7843 (pttm) REVERT: D 198 LYS cc_start: 0.8326 (mmtm) cc_final: 0.7753 (mppt) REVERT: D 334 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8209 (ttp) REVERT: D 356 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6357 (mt0) REVERT: E 12 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8103 (mp) REVERT: E 67 MET cc_start: 0.8541 (mmp) cc_final: 0.8228 (mmm) REVERT: E 93 ASN cc_start: 0.7916 (t0) cc_final: 0.7490 (t0) REVERT: E 359 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5135 (mp0) REVERT: G 12 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8317 (tp) REVERT: G 46 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7796 (mtpt) REVERT: G 67 MET cc_start: 0.8787 (mmm) cc_final: 0.8379 (mmm) REVERT: G 93 ASN cc_start: 0.8200 (m-40) cc_final: 0.7713 (m-40) REVERT: G 130 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: G 142 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6661 (tmm) REVERT: G 198 LYS cc_start: 0.8243 (tppp) cc_final: 0.7892 (tppt) REVERT: G 201 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7883 (mt) REVERT: G 356 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6398 (mt0) REVERT: H 12 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8225 (tp) REVERT: H 50 MET cc_start: 0.8154 (mtm) cc_final: 0.7856 (mtt) REVERT: H 93 ASN cc_start: 0.8157 (t0) cc_final: 0.7627 (t0) REVERT: H 96 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7936 (p0) REVERT: H 101 ARG cc_start: 0.8299 (tpp-160) cc_final: 0.7952 (tpp-160) REVERT: H 126 ASN cc_start: 0.8698 (m-40) cc_final: 0.8484 (m-40) REVERT: H 334 MET cc_start: 0.8934 (ttp) cc_final: 0.8655 (ttp) REVERT: J 16 GLN cc_start: 0.8171 (tt0) cc_final: 0.7897 (tt0) REVERT: J 24 THR cc_start: 0.8720 (p) cc_final: 0.8477 (p) REVERT: J 67 MET cc_start: 0.8797 (mmm) cc_final: 0.8419 (mmm) REVERT: J 130 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: J 195 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7990 (ttpp) REVERT: J 198 LYS cc_start: 0.8688 (tppp) cc_final: 0.8252 (mmpt) REVERT: J 334 MET cc_start: 0.8817 (ttp) cc_final: 0.8266 (ttp) REVERT: J 356 GLN cc_start: 0.6901 (OUTLIER) cc_final: 0.6572 (mt0) REVERT: K 12 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8423 (tp) REVERT: K 93 ASN cc_start: 0.8103 (t0) cc_final: 0.7722 (t0) REVERT: K 191 LYS cc_start: 0.8316 (ptpt) cc_final: 0.7961 (pttp) REVERT: K 342 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7283 (ptp-170) REVERT: K 356 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6548 (mt0) REVERT: M 50 MET cc_start: 0.8737 (mtp) cc_final: 0.8505 (mtm) REVERT: M 122 GLU cc_start: 0.7349 (mp0) cc_final: 0.7100 (mp0) REVERT: M 356 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.6349 (mt0) REVERT: N 71 MET cc_start: 0.9085 (mtm) cc_final: 0.8792 (mtp) REVERT: N 93 ASN cc_start: 0.8051 (t0) cc_final: 0.7702 (t0) REVERT: N 282 GLU cc_start: 0.6490 (pm20) cc_final: 0.6276 (pm20) REVERT: N 356 GLN cc_start: 0.6467 (mt0) cc_final: 0.6239 (mt0) REVERT: P 77 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: P 101 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7934 (ttm110) REVERT: P 193 GLU cc_start: 0.7694 (mp0) cc_final: 0.7443 (mp0) REVERT: P 198 LYS cc_start: 0.8291 (mmtm) cc_final: 0.7586 (mppt) REVERT: P 356 GLN cc_start: 0.6276 (OUTLIER) cc_final: 0.5996 (mt0) REVERT: Q 15 ASP cc_start: 0.8405 (t70) cc_final: 0.8157 (t70) REVERT: Q 71 MET cc_start: 0.8998 (mtm) cc_final: 0.8772 (mtp) REVERT: Q 93 ASN cc_start: 0.8121 (t0) cc_final: 0.7803 (t0) REVERT: Q 191 LYS cc_start: 0.8098 (ptpt) cc_final: 0.7785 (ptpp) REVERT: Q 248 MET cc_start: 0.8397 (mmm) cc_final: 0.8071 (mmp) REVERT: Q 257 MET cc_start: 0.8781 (mmm) cc_final: 0.8369 (mmm) REVERT: S 71 MET cc_start: 0.9149 (mtm) cc_final: 0.8738 (mtm) REVERT: S 110 LYS cc_start: 0.8176 (tttm) cc_final: 0.7829 (ttpt) REVERT: S 142 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.6063 (pp-130) REVERT: S 195 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7831 (pttm) REVERT: S 198 LYS cc_start: 0.8318 (mmtm) cc_final: 0.7751 (mppt) REVERT: S 334 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8203 (ttp) REVERT: S 356 GLN cc_start: 0.6732 (OUTLIER) cc_final: 0.6361 (mt0) REVERT: T 12 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8115 (mp) REVERT: T 67 MET cc_start: 0.8547 (mmp) cc_final: 0.8230 (mmm) REVERT: T 93 ASN cc_start: 0.7931 (t0) cc_final: 0.7505 (t0) REVERT: T 110 LYS cc_start: 0.8296 (tptm) cc_final: 0.7922 (tptt) REVERT: T 359 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.5127 (mp0) REVERT: c 12 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8301 (tp) REVERT: c 46 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7798 (mtpt) REVERT: c 67 MET cc_start: 0.8787 (mmm) cc_final: 0.8369 (mmm) REVERT: c 130 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: c 142 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6676 (tmm) REVERT: c 198 LYS cc_start: 0.8246 (tppp) cc_final: 0.7890 (tppt) REVERT: c 201 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7887 (mt) REVERT: c 356 GLN cc_start: 0.6725 (OUTLIER) cc_final: 0.6392 (mt0) REVERT: d 50 MET cc_start: 0.8159 (mtm) cc_final: 0.7860 (mtt) REVERT: d 93 ASN cc_start: 0.8194 (t0) cc_final: 0.7876 (t0) REVERT: d 96 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7990 (p0) REVERT: d 126 ASN cc_start: 0.8686 (m-40) cc_final: 0.8476 (m-40) REVERT: d 334 MET cc_start: 0.8921 (ttp) cc_final: 0.8629 (ttp) REVERT: g 16 GLN cc_start: 0.8186 (tt0) cc_final: 0.7917 (tt0) REVERT: g 24 THR cc_start: 0.8749 (p) cc_final: 0.8510 (p) REVERT: g 67 MET cc_start: 0.8801 (mmm) cc_final: 0.8429 (mmm) REVERT: g 130 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: g 195 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7842 (ttpp) REVERT: g 198 LYS cc_start: 0.8705 (tppp) cc_final: 0.8180 (mmpt) REVERT: g 334 MET cc_start: 0.8870 (ttp) cc_final: 0.8259 (ttt) REVERT: g 338 ARG cc_start: 0.7470 (mtm-85) cc_final: 0.7206 (mpp-170) REVERT: h 12 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8414 (tp) REVERT: h 93 ASN cc_start: 0.8077 (t0) cc_final: 0.7696 (t0) REVERT: h 191 LYS cc_start: 0.8297 (ptpt) cc_final: 0.7940 (pttp) REVERT: h 282 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.6154 (tt0) REVERT: h 342 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7291 (ptp-170) REVERT: k 50 MET cc_start: 0.8737 (mtp) cc_final: 0.8509 (mtm) REVERT: k 122 GLU cc_start: 0.7348 (mp0) cc_final: 0.7096 (mp0) REVERT: k 356 GLN cc_start: 0.6646 (OUTLIER) cc_final: 0.6355 (mt0) REVERT: l 12 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8332 (mp) REVERT: l 67 MET cc_start: 0.8517 (mmp) cc_final: 0.8288 (mmm) REVERT: l 71 MET cc_start: 0.9093 (mtm) cc_final: 0.8804 (mtp) REVERT: l 93 ASN cc_start: 0.7955 (t0) cc_final: 0.7632 (t0) REVERT: l 281 MET cc_start: 0.8420 (mmm) cc_final: 0.8063 (tpp) REVERT: l 282 GLU cc_start: 0.6498 (pm20) cc_final: 0.6281 (pm20) REVERT: l 356 GLN cc_start: 0.6483 (mt0) cc_final: 0.6252 (mt0) outliers start: 200 outliers final: 70 residues processed: 899 average time/residue: 1.6757 time to fit residues: 1858.0236 Evaluate side-chains 833 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 717 time to evaluate : 5.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 356 GLN Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 356 GLN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 362 VAL Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 356 GLN Chi-restraints excluded: chain J residue 363 ILE Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 356 GLN Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 356 GLN Chi-restraints excluded: chain M residue 363 ILE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 316 GLN Chi-restraints excluded: chain N residue 359 GLU Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 356 GLN Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 363 ILE Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 142 MET Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 334 MET Chi-restraints excluded: chain S residue 356 GLN Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 359 GLU Chi-restraints excluded: chain T residue 362 VAL Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 130 GLU Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 316 GLN Chi-restraints excluded: chain c residue 356 GLN Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 191 LYS Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 195 LYS Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 34 ASP Chi-restraints excluded: chain h residue 39 ASP Chi-restraints excluded: chain h residue 96 ASP Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain h residue 282 GLU Chi-restraints excluded: chain h residue 342 ARG Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 356 GLN Chi-restraints excluded: chain k residue 363 ILE Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 39 ASP Chi-restraints excluded: chain l residue 96 ASP Chi-restraints excluded: chain l residue 120 THR Chi-restraints excluded: chain l residue 316 GLN Chi-restraints excluded: chain l residue 359 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 590 optimal weight: 7.9990 chunk 402 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 528 optimal weight: 2.9990 chunk 292 optimal weight: 0.5980 chunk 605 optimal weight: 5.9990 chunk 490 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 362 optimal weight: 0.9990 chunk 636 optimal weight: 6.9990 chunk 179 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 102 GLN A 151 HIS A 192 ASN D 93 ASN D 102 GLN D 192 ASN M 102 GLN M 192 ASN P 93 ASN P 102 GLN P 151 HIS P 192 ASN S 102 GLN S 192 ASN ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 GLN l 45 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 61510 Z= 0.176 Angle : 0.497 12.115 83440 Z= 0.261 Chirality : 0.039 0.168 9560 Planarity : 0.003 0.052 10240 Dihedral : 11.000 73.802 10210 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.26 % Allowed : 15.75 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.10), residues: 7340 helix: 1.62 (0.08), residues: 4760 sheet: 0.27 (0.21), residues: 440 loop : 0.67 (0.14), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 260 HIS 0.006 0.001 HIS M 225 PHE 0.012 0.001 PHE J 111 TYR 0.018 0.001 TYR J 135 ARG 0.011 0.000 ARG c 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 762 time to evaluate : 5.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: A 98 THR cc_start: 0.8605 (p) cc_final: 0.8121 (t) REVERT: A 132 ARG cc_start: 0.7600 (mtm-85) cc_final: 0.7372 (mtt90) REVERT: A 198 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7579 (mppt) REVERT: A 356 GLN cc_start: 0.6520 (OUTLIER) cc_final: 0.6319 (mt0) REVERT: B 15 ASP cc_start: 0.8320 (t70) cc_final: 0.8077 (t70) REVERT: B 71 MET cc_start: 0.9008 (mtm) cc_final: 0.8771 (mtp) REVERT: B 93 ASN cc_start: 0.8099 (t0) cc_final: 0.7807 (t0) REVERT: B 248 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8309 (mmm) REVERT: B 257 MET cc_start: 0.8807 (mmm) cc_final: 0.8341 (mmm) REVERT: D 71 MET cc_start: 0.9156 (mtm) cc_final: 0.8736 (mtm) REVERT: D 93 ASN cc_start: 0.8404 (m-40) cc_final: 0.7860 (m-40) REVERT: D 101 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7819 (ttm110) REVERT: D 142 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6228 (pp-130) REVERT: D 195 LYS cc_start: 0.8180 (mtmm) cc_final: 0.7890 (pttm) REVERT: D 198 LYS cc_start: 0.8276 (mmtm) cc_final: 0.7761 (mppt) REVERT: D 334 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8262 (ttp) REVERT: D 356 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6453 (mt0) REVERT: E 12 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7877 (mp) REVERT: E 67 MET cc_start: 0.8609 (mmp) cc_final: 0.8226 (mmm) REVERT: E 93 ASN cc_start: 0.7930 (t0) cc_final: 0.7480 (t0) REVERT: E 359 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.5357 (mp0) REVERT: G 12 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8305 (tp) REVERT: G 46 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7997 (mtmm) REVERT: G 67 MET cc_start: 0.8775 (mmm) cc_final: 0.8364 (mmm) REVERT: G 91 LYS cc_start: 0.7061 (tptp) cc_final: 0.6815 (tmtm) REVERT: G 93 ASN cc_start: 0.8200 (m-40) cc_final: 0.7688 (m-40) REVERT: G 130 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: G 142 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6724 (tmm) REVERT: G 201 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7845 (mt) REVERT: H 12 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8233 (tp) REVERT: H 50 MET cc_start: 0.8136 (mtm) cc_final: 0.7833 (mtt) REVERT: H 93 ASN cc_start: 0.8139 (t0) cc_final: 0.7684 (t0) REVERT: H 101 ARG cc_start: 0.8190 (tpp-160) cc_final: 0.7626 (ttm-80) REVERT: H 126 ASN cc_start: 0.8694 (m-40) cc_final: 0.8473 (m-40) REVERT: H 334 MET cc_start: 0.8945 (ttp) cc_final: 0.8697 (ttp) REVERT: H 359 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.5064 (mp0) REVERT: J 12 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8159 (tp) REVERT: J 16 GLN cc_start: 0.8166 (tt0) cc_final: 0.7888 (tt0) REVERT: J 24 THR cc_start: 0.8756 (p) cc_final: 0.8521 (p) REVERT: J 67 MET cc_start: 0.8791 (mmm) cc_final: 0.8461 (mmm) REVERT: J 130 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: J 198 LYS cc_start: 0.8655 (tppp) cc_final: 0.8171 (mmpt) REVERT: J 248 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8708 (mmm) REVERT: J 334 MET cc_start: 0.8844 (ttp) cc_final: 0.8268 (ttt) REVERT: J 338 ARG cc_start: 0.7604 (mpp-170) cc_final: 0.7398 (mtm110) REVERT: J 356 GLN cc_start: 0.6914 (OUTLIER) cc_final: 0.6618 (mt0) REVERT: K 93 ASN cc_start: 0.8055 (t0) cc_final: 0.7615 (t0) REVERT: K 191 LYS cc_start: 0.8291 (ptpt) cc_final: 0.7931 (pttp) REVERT: K 198 LYS cc_start: 0.8613 (mmpt) cc_final: 0.8273 (mmpt) REVERT: K 201 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8142 (mt) REVERT: K 257 MET cc_start: 0.8659 (mmt) cc_final: 0.8232 (mmm) REVERT: K 282 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.6107 (tt0) REVERT: K 356 GLN cc_start: 0.6848 (OUTLIER) cc_final: 0.6537 (mt0) REVERT: M 50 MET cc_start: 0.8719 (mtp) cc_final: 0.8488 (mtm) REVERT: M 109 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7042 (mtp) REVERT: M 122 GLU cc_start: 0.7292 (mp0) cc_final: 0.7013 (mp0) REVERT: N 71 MET cc_start: 0.9042 (mtm) cc_final: 0.8765 (mtp) REVERT: N 93 ASN cc_start: 0.7987 (t0) cc_final: 0.7654 (t0) REVERT: N 356 GLN cc_start: 0.6519 (mt0) cc_final: 0.6300 (mt0) REVERT: P 77 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: P 195 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7797 (pttp) REVERT: P 198 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7650 (mppt) REVERT: P 356 GLN cc_start: 0.6276 (OUTLIER) cc_final: 0.6045 (mt0) REVERT: Q 15 ASP cc_start: 0.8327 (t70) cc_final: 0.8087 (t70) REVERT: Q 71 MET cc_start: 0.8999 (mtm) cc_final: 0.8772 (mtp) REVERT: Q 93 ASN cc_start: 0.8110 (t0) cc_final: 0.7816 (t0) REVERT: Q 257 MET cc_start: 0.8812 (mmm) cc_final: 0.8347 (mmm) REVERT: Q 336 GLU cc_start: 0.7325 (tm-30) cc_final: 0.7109 (tm-30) REVERT: S 71 MET cc_start: 0.9152 (mtm) cc_final: 0.8741 (mtm) REVERT: S 93 ASN cc_start: 0.8355 (m-40) cc_final: 0.7807 (m110) REVERT: S 101 ARG cc_start: 0.8174 (ttm110) cc_final: 0.7819 (ttm110) REVERT: S 142 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6209 (pp-130) REVERT: S 195 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7847 (pttm) REVERT: S 198 LYS cc_start: 0.8272 (mmtm) cc_final: 0.7763 (mppt) REVERT: S 334 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8251 (ttp) REVERT: S 356 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.6459 (mt0) REVERT: T 12 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8095 (mp) REVERT: T 67 MET cc_start: 0.8557 (mmp) cc_final: 0.8225 (mmm) REVERT: T 93 ASN cc_start: 0.7966 (t0) cc_final: 0.7516 (t0) REVERT: T 138 MET cc_start: 0.7971 (tmm) cc_final: 0.7710 (ppp) REVERT: T 359 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.5203 (mp0) REVERT: c 12 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8303 (tp) REVERT: c 46 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7997 (mtmm) REVERT: c 67 MET cc_start: 0.8774 (mmm) cc_final: 0.8355 (mmm) REVERT: c 130 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: c 142 MET cc_start: 0.6871 (OUTLIER) cc_final: 0.6545 (tmm) REVERT: c 201 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7846 (mt) REVERT: d 50 MET cc_start: 0.8139 (mtm) cc_final: 0.7835 (mtt) REVERT: d 93 ASN cc_start: 0.8190 (t0) cc_final: 0.7881 (t0) REVERT: d 96 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8033 (p0) REVERT: d 126 ASN cc_start: 0.8677 (m-40) cc_final: 0.8460 (m-40) REVERT: d 334 MET cc_start: 0.8945 (ttp) cc_final: 0.8686 (ttp) REVERT: d 359 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.5077 (mp0) REVERT: g 12 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8118 (tp) REVERT: g 16 GLN cc_start: 0.8174 (tt0) cc_final: 0.7895 (tt0) REVERT: g 24 THR cc_start: 0.8746 (p) cc_final: 0.8504 (p) REVERT: g 67 MET cc_start: 0.8791 (mmm) cc_final: 0.8467 (mmm) REVERT: g 130 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: g 195 LYS cc_start: 0.8198 (mtpm) cc_final: 0.7966 (ttpp) REVERT: g 198 LYS cc_start: 0.8664 (tppp) cc_final: 0.8216 (mmpt) REVERT: g 334 MET cc_start: 0.8874 (ttp) cc_final: 0.8318 (ttt) REVERT: h 93 ASN cc_start: 0.8126 (t0) cc_final: 0.7604 (t0) REVERT: h 191 LYS cc_start: 0.8285 (ptpt) cc_final: 0.7928 (pttp) REVERT: h 201 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8143 (mt) REVERT: h 257 MET cc_start: 0.8665 (mmt) cc_final: 0.8233 (mmm) REVERT: h 342 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7294 (ptp-170) REVERT: k 50 MET cc_start: 0.8719 (mtp) cc_final: 0.8485 (mtm) REVERT: k 109 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7063 (mtp) REVERT: k 122 GLU cc_start: 0.7292 (mp0) cc_final: 0.7000 (mp0) REVERT: l 12 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8329 (mp) REVERT: l 67 MET cc_start: 0.8465 (mmp) cc_final: 0.8251 (mmm) REVERT: l 71 MET cc_start: 0.9087 (mtm) cc_final: 0.8819 (mtp) REVERT: l 93 ASN cc_start: 0.7967 (t0) cc_final: 0.7648 (t0) REVERT: l 142 MET cc_start: 0.5296 (pp-130) cc_final: 0.5029 (tmm) REVERT: l 281 MET cc_start: 0.8362 (mmm) cc_final: 0.8088 (tpp) REVERT: l 356 GLN cc_start: 0.6535 (mt0) cc_final: 0.6279 (mt0) outliers start: 201 outliers final: 75 residues processed: 901 average time/residue: 1.6429 time to fit residues: 1830.8077 Evaluate side-chains 844 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 725 time to evaluate : 4.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 356 GLN Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 363 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 359 GLU Chi-restraints excluded: chain H residue 362 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 356 GLN Chi-restraints excluded: chain J residue 363 ILE Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 282 GLU Chi-restraints excluded: chain K residue 356 GLN Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain M residue 363 ILE Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 359 GLU Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 195 LYS Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 356 GLN Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 363 ILE Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 316 GLN Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 142 MET Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain S residue 334 MET Chi-restraints excluded: chain S residue 356 GLN Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 110 LYS Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 359 GLU Chi-restraints excluded: chain T residue 362 VAL Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 130 GLU Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 316 GLN Chi-restraints excluded: chain c residue 363 ILE Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 359 GLU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 22 LYS Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 96 ASP Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain h residue 201 LEU Chi-restraints excluded: chain h residue 342 ARG Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 109 MET Chi-restraints excluded: chain k residue 363 ILE Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 39 ASP Chi-restraints excluded: chain l residue 96 ASP Chi-restraints excluded: chain l residue 120 THR Chi-restraints excluded: chain l residue 201 LEU Chi-restraints excluded: chain l residue 359 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 238 optimal weight: 0.5980 chunk 638 optimal weight: 10.0000 chunk 140 optimal weight: 0.5980 chunk 416 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 710 optimal weight: 8.9990 chunk 589 optimal weight: 6.9990 chunk 328 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 234 optimal weight: 5.9990 chunk 372 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 102 GLN A 151 HIS A 192 ASN D 102 GLN D 192 ASN G 356 GLN M 102 GLN M 356 GLN P 93 ASN P 102 GLN P 151 HIS P 192 ASN S 102 GLN S 192 ASN c 356 GLN ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 GLN k 356 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 61510 Z= 0.167 Angle : 0.493 11.790 83440 Z= 0.257 Chirality : 0.039 0.166 9560 Planarity : 0.003 0.046 10240 Dihedral : 10.958 73.780 10210 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.10 % Allowed : 16.59 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.10), residues: 7340 helix: 1.73 (0.08), residues: 4740 sheet: 0.32 (0.21), residues: 440 loop : 0.72 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 260 HIS 0.006 0.001 HIS k 225 PHE 0.013 0.001 PHE J 111 TYR 0.015 0.001 TYR A 135 ARG 0.011 0.000 ARG c 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 737 time to evaluate : 4.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: A 101 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7918 (ttm110) REVERT: A 198 LYS cc_start: 0.8228 (mmtm) cc_final: 0.7623 (mppt) REVERT: B 12 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8173 (tp) REVERT: B 15 ASP cc_start: 0.8271 (t70) cc_final: 0.8033 (t70) REVERT: B 71 MET cc_start: 0.9006 (mtm) cc_final: 0.8772 (mtp) REVERT: B 93 ASN cc_start: 0.8084 (t0) cc_final: 0.7788 (t0) REVERT: B 248 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8349 (mmm) REVERT: B 257 MET cc_start: 0.8805 (mmm) cc_final: 0.8400 (mmm) REVERT: D 71 MET cc_start: 0.9154 (mtm) cc_final: 0.8739 (mtm) REVERT: D 77 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: D 125 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8454 (mt) REVERT: D 142 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6257 (pp-130) REVERT: D 195 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7886 (pttp) REVERT: D 198 LYS cc_start: 0.8209 (mmtm) cc_final: 0.7836 (mppt) REVERT: D 334 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8264 (ttp) REVERT: E 12 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8076 (mp) REVERT: E 67 MET cc_start: 0.8607 (mmp) cc_final: 0.8183 (mmm) REVERT: E 93 ASN cc_start: 0.7919 (t0) cc_final: 0.7438 (t0) REVERT: E 359 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5420 (mp0) REVERT: G 46 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8023 (mtmm) REVERT: G 67 MET cc_start: 0.8766 (mmm) cc_final: 0.8350 (mmm) REVERT: G 93 ASN cc_start: 0.8198 (m-40) cc_final: 0.7713 (m-40) REVERT: G 142 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6521 (tmm) REVERT: G 201 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7826 (mt) REVERT: H 12 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8259 (tp) REVERT: H 50 MET cc_start: 0.8101 (mtm) cc_final: 0.7808 (mtt) REVERT: H 93 ASN cc_start: 0.8128 (t0) cc_final: 0.7682 (t0) REVERT: H 96 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7967 (p0) REVERT: H 126 ASN cc_start: 0.8680 (m-40) cc_final: 0.8463 (m-40) REVERT: H 334 MET cc_start: 0.8943 (ttp) cc_final: 0.8609 (ttp) REVERT: J 12 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8158 (tp) REVERT: J 16 GLN cc_start: 0.8164 (tt0) cc_final: 0.7882 (tt0) REVERT: J 24 THR cc_start: 0.8757 (p) cc_final: 0.8520 (p) REVERT: J 67 MET cc_start: 0.8755 (mmm) cc_final: 0.8434 (mmm) REVERT: J 130 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: J 198 LYS cc_start: 0.8613 (tppp) cc_final: 0.8141 (mmpt) REVERT: J 248 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8707 (mmm) REVERT: J 334 MET cc_start: 0.8852 (ttp) cc_final: 0.8176 (ttt) REVERT: J 338 ARG cc_start: 0.7552 (mpp-170) cc_final: 0.7333 (mtm110) REVERT: J 356 GLN cc_start: 0.6881 (OUTLIER) cc_final: 0.6581 (mt0) REVERT: K 93 ASN cc_start: 0.7963 (t0) cc_final: 0.7569 (t0) REVERT: K 142 MET cc_start: 0.5315 (pp-130) cc_final: 0.4936 (tmm) REVERT: K 191 LYS cc_start: 0.8280 (ptpt) cc_final: 0.7946 (pttp) REVERT: K 201 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8128 (mt) REVERT: K 257 MET cc_start: 0.8642 (mmt) cc_final: 0.8275 (mmm) REVERT: K 282 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6122 (tt0) REVERT: M 50 MET cc_start: 0.8716 (mtp) cc_final: 0.8478 (mtm) REVERT: M 122 GLU cc_start: 0.7242 (mp0) cc_final: 0.6998 (mp0) REVERT: N 71 MET cc_start: 0.9076 (mtm) cc_final: 0.8822 (mtp) REVERT: N 93 ASN cc_start: 0.7969 (t0) cc_final: 0.7702 (t0) REVERT: P 77 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6755 (mp0) REVERT: P 101 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7922 (ttm110) REVERT: P 198 LYS cc_start: 0.8254 (mmtm) cc_final: 0.7685 (mppt) REVERT: P 356 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.6111 (mt0) REVERT: Q 12 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8179 (tp) REVERT: Q 15 ASP cc_start: 0.8281 (t70) cc_final: 0.8046 (t70) REVERT: Q 71 MET cc_start: 0.8997 (mtm) cc_final: 0.8766 (mtp) REVERT: Q 93 ASN cc_start: 0.8091 (t0) cc_final: 0.7796 (t0) REVERT: Q 257 MET cc_start: 0.8809 (mmm) cc_final: 0.8406 (mmm) REVERT: S 71 MET cc_start: 0.9152 (mtm) cc_final: 0.8743 (mtm) REVERT: S 77 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: S 93 ASN cc_start: 0.8406 (m-40) cc_final: 0.7867 (m110) REVERT: S 125 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8459 (mt) REVERT: S 142 MET cc_start: 0.6837 (OUTLIER) cc_final: 0.6230 (tmm) REVERT: S 195 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7897 (pttp) REVERT: S 198 LYS cc_start: 0.8204 (mmtm) cc_final: 0.7841 (mppt) REVERT: S 334 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8253 (ttp) REVERT: T 12 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8086 (mp) REVERT: T 67 MET cc_start: 0.8612 (mmp) cc_final: 0.8186 (mmm) REVERT: T 93 ASN cc_start: 0.7946 (t0) cc_final: 0.7466 (t0) REVERT: T 359 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.5424 (mp0) REVERT: c 46 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8022 (mtmm) REVERT: c 67 MET cc_start: 0.8763 (mmm) cc_final: 0.8341 (mmm) REVERT: c 142 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6547 (tmm) REVERT: c 201 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7827 (mt) REVERT: d 50 MET cc_start: 0.8104 (mtm) cc_final: 0.7806 (mtt) REVERT: d 93 ASN cc_start: 0.8196 (t0) cc_final: 0.7900 (t0) REVERT: d 96 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8012 (p0) REVERT: d 126 ASN cc_start: 0.8643 (m-40) cc_final: 0.8419 (m-40) REVERT: d 334 MET cc_start: 0.8944 (ttp) cc_final: 0.8616 (ttp) REVERT: g 16 GLN cc_start: 0.8166 (tt0) cc_final: 0.7882 (tt0) REVERT: g 24 THR cc_start: 0.8742 (p) cc_final: 0.8508 (p) REVERT: g 67 MET cc_start: 0.8758 (mmm) cc_final: 0.8443 (mmm) REVERT: g 130 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: g 195 LYS cc_start: 0.8193 (mtpm) cc_final: 0.7977 (ttpp) REVERT: g 198 LYS cc_start: 0.8627 (tppp) cc_final: 0.8214 (mmpt) REVERT: g 334 MET cc_start: 0.8879 (ttp) cc_final: 0.8222 (ttt) REVERT: h 93 ASN cc_start: 0.7921 (t0) cc_final: 0.7540 (t0) REVERT: h 142 MET cc_start: 0.5281 (pp-130) cc_final: 0.4903 (tmm) REVERT: h 191 LYS cc_start: 0.8273 (ptpt) cc_final: 0.7934 (pttp) REVERT: h 201 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8116 (mt) REVERT: h 257 MET cc_start: 0.8656 (mmt) cc_final: 0.8281 (mmm) REVERT: k 50 MET cc_start: 0.8714 (mtp) cc_final: 0.8484 (mtm) REVERT: l 67 MET cc_start: 0.8456 (mmp) cc_final: 0.8226 (mmm) REVERT: l 71 MET cc_start: 0.9092 (mtm) cc_final: 0.8834 (mtp) REVERT: l 93 ASN cc_start: 0.7948 (t0) cc_final: 0.7705 (t0) REVERT: l 119 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8010 (mt) REVERT: l 281 MET cc_start: 0.8405 (mmm) cc_final: 0.8129 (tpp) outliers start: 191 outliers final: 79 residues processed: 867 average time/residue: 1.6535 time to fit residues: 1772.5075 Evaluate side-chains 829 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 712 time to evaluate : 5.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 363 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 362 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 356 GLN Chi-restraints excluded: chain J residue 363 ILE Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 282 GLU Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain M residue 363 ILE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 359 GLU Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 356 GLN Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 363 ILE Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 142 MET Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain S residue 334 MET Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 359 GLU Chi-restraints excluded: chain T residue 362 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 316 GLN Chi-restraints excluded: chain c residue 363 ILE Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain g residue 22 LYS Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 39 ASP Chi-restraints excluded: chain h residue 96 ASP Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain h residue 201 LEU Chi-restraints excluded: chain h residue 338 ARG Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 109 MET Chi-restraints excluded: chain k residue 363 ILE Chi-restraints excluded: chain l residue 39 ASP Chi-restraints excluded: chain l residue 96 ASP Chi-restraints excluded: chain l residue 119 LEU Chi-restraints excluded: chain l residue 120 THR Chi-restraints excluded: chain l residue 201 LEU Chi-restraints excluded: chain l residue 359 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 684 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 404 optimal weight: 2.9990 chunk 518 optimal weight: 7.9990 chunk 401 optimal weight: 7.9990 chunk 597 optimal weight: 3.9990 chunk 396 optimal weight: 1.9990 chunk 707 optimal weight: 20.0000 chunk 442 optimal weight: 1.9990 chunk 431 optimal weight: 5.9990 chunk 326 optimal weight: 1.9990 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 102 GLN A 192 ASN D 93 ASN D 102 GLN D 192 ASN D 356 GLN G 102 GLN G 192 ASN J 102 GLN M 102 GLN P 102 GLN P 192 ASN S 102 GLN S 192 ASN S 356 GLN c 102 GLN c 192 ASN ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 16 GLN k 102 GLN l 45 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 61510 Z= 0.313 Angle : 0.579 12.310 83440 Z= 0.300 Chirality : 0.043 0.179 9560 Planarity : 0.004 0.049 10240 Dihedral : 11.119 74.074 10210 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.36 % Allowed : 16.66 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.10), residues: 7340 helix: 1.33 (0.07), residues: 4740 sheet: 0.30 (0.21), residues: 440 loop : 0.61 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP P 260 HIS 0.011 0.001 HIS M 225 PHE 0.018 0.002 PHE J 111 TYR 0.021 0.002 TYR T 365 ARG 0.013 0.001 ARG G 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 708 time to evaluate : 4.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: A 98 THR cc_start: 0.8580 (p) cc_final: 0.8083 (t) REVERT: A 101 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.8019 (ttm110) REVERT: A 129 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7944 (mp) REVERT: A 198 LYS cc_start: 0.8355 (mmtm) cc_final: 0.7814 (mppt) REVERT: B 12 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8160 (tp) REVERT: B 71 MET cc_start: 0.9003 (mtm) cc_final: 0.8782 (mtp) REVERT: B 93 ASN cc_start: 0.8119 (t0) cc_final: 0.7791 (t0) REVERT: B 248 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8287 (mmm) REVERT: B 257 MET cc_start: 0.8718 (mmm) cc_final: 0.8465 (mmm) REVERT: D 71 MET cc_start: 0.9167 (mtm) cc_final: 0.8761 (mtm) REVERT: D 77 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: D 110 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7785 (ttpm) REVERT: D 125 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8636 (mt) REVERT: D 142 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.6314 (pp-130) REVERT: D 195 LYS cc_start: 0.8083 (mtmm) cc_final: 0.7867 (pttp) REVERT: D 198 LYS cc_start: 0.8222 (mmtm) cc_final: 0.7774 (mppt) REVERT: D 334 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8182 (ttp) REVERT: E 12 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8130 (mp) REVERT: E 67 MET cc_start: 0.8545 (mmp) cc_final: 0.8198 (mmm) REVERT: E 93 ASN cc_start: 0.8101 (t0) cc_final: 0.7607 (t0) REVERT: E 359 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.5429 (mp0) REVERT: G 12 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8273 (tp) REVERT: G 67 MET cc_start: 0.8820 (mmm) cc_final: 0.8418 (mmm) REVERT: G 201 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8046 (mt) REVERT: H 12 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8176 (tp) REVERT: H 50 MET cc_start: 0.8165 (mtm) cc_final: 0.7871 (mtt) REVERT: H 93 ASN cc_start: 0.8165 (t0) cc_final: 0.7619 (t0) REVERT: H 96 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8033 (p0) REVERT: H 126 ASN cc_start: 0.8673 (m-40) cc_final: 0.8447 (m-40) REVERT: H 359 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.5528 (mp0) REVERT: J 12 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8174 (tp) REVERT: J 16 GLN cc_start: 0.8273 (tt0) cc_final: 0.7987 (tt0) REVERT: J 67 MET cc_start: 0.8837 (mmm) cc_final: 0.8428 (mmm) REVERT: J 198 LYS cc_start: 0.8665 (tppp) cc_final: 0.8171 (mmpt) REVERT: J 334 MET cc_start: 0.8839 (ttp) cc_final: 0.8219 (ttt) REVERT: J 356 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6607 (mt0) REVERT: K 12 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8376 (tp) REVERT: K 93 ASN cc_start: 0.7971 (t0) cc_final: 0.7594 (t0) REVERT: K 142 MET cc_start: 0.5356 (pp-130) cc_final: 0.5008 (tmm) REVERT: K 191 LYS cc_start: 0.8328 (ptpt) cc_final: 0.7942 (pttp) REVERT: K 198 LYS cc_start: 0.8688 (mmpt) cc_final: 0.8470 (mmtm) REVERT: K 201 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8211 (mt) REVERT: K 257 MET cc_start: 0.8691 (mmt) cc_final: 0.8206 (mmm) REVERT: K 282 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.6226 (tt0) REVERT: M 50 MET cc_start: 0.8835 (mtp) cc_final: 0.8611 (mtm) REVERT: M 195 LYS cc_start: 0.8137 (ttpp) cc_final: 0.7819 (mtpm) REVERT: N 71 MET cc_start: 0.9032 (mtm) cc_final: 0.8749 (mtp) REVERT: N 93 ASN cc_start: 0.7984 (t0) cc_final: 0.7708 (t0) REVERT: N 137 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8280 (ttpp) REVERT: P 77 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: P 101 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7988 (ttm110) REVERT: P 129 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8046 (mp) REVERT: P 195 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7863 (pttp) REVERT: P 198 LYS cc_start: 0.8272 (mmtm) cc_final: 0.7710 (mppt) REVERT: P 356 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.6042 (mt0) REVERT: Q 12 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8159 (tp) REVERT: Q 71 MET cc_start: 0.8947 (mtm) cc_final: 0.8708 (mtp) REVERT: Q 93 ASN cc_start: 0.8101 (t0) cc_final: 0.7767 (t0) REVERT: Q 138 MET cc_start: 0.7943 (tmm) cc_final: 0.7698 (ppp) REVERT: Q 257 MET cc_start: 0.8709 (mmm) cc_final: 0.8377 (mmm) REVERT: S 71 MET cc_start: 0.9165 (mtm) cc_final: 0.8769 (mtm) REVERT: S 77 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: S 110 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7677 (ttpm) REVERT: S 125 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8633 (mt) REVERT: S 142 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6357 (pp-130) REVERT: S 195 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7861 (pttp) REVERT: S 198 LYS cc_start: 0.8217 (mmtm) cc_final: 0.7781 (mppt) REVERT: S 334 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8267 (ttp) REVERT: T 12 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8138 (mp) REVERT: T 67 MET cc_start: 0.8549 (mmp) cc_final: 0.8195 (mmm) REVERT: T 93 ASN cc_start: 0.8086 (t0) cc_final: 0.7590 (t0) REVERT: T 359 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.5435 (mp0) REVERT: c 67 MET cc_start: 0.8820 (mmm) cc_final: 0.8413 (mmm) REVERT: c 201 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8046 (mt) REVERT: d 50 MET cc_start: 0.8167 (mtm) cc_final: 0.7875 (mtt) REVERT: d 93 ASN cc_start: 0.8210 (t0) cc_final: 0.7841 (t0) REVERT: d 96 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8063 (p0) REVERT: d 126 ASN cc_start: 0.8662 (m-40) cc_final: 0.8443 (m-40) REVERT: d 359 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.5538 (mp0) REVERT: g 12 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8135 (tp) REVERT: g 16 GLN cc_start: 0.8264 (tt0) cc_final: 0.7986 (tt0) REVERT: g 24 THR cc_start: 0.8816 (p) cc_final: 0.8612 (p) REVERT: g 67 MET cc_start: 0.8860 (mmm) cc_final: 0.8561 (mmm) REVERT: g 130 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: g 195 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7996 (ttpp) REVERT: g 198 LYS cc_start: 0.8683 (tppp) cc_final: 0.8262 (mmpt) REVERT: g 334 MET cc_start: 0.8846 (ttp) cc_final: 0.8218 (ttp) REVERT: h 12 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8365 (tp) REVERT: h 93 ASN cc_start: 0.7960 (t0) cc_final: 0.7578 (t0) REVERT: h 142 MET cc_start: 0.5302 (pp-130) cc_final: 0.4951 (tmm) REVERT: h 191 LYS cc_start: 0.8303 (ptpt) cc_final: 0.7919 (pttp) REVERT: h 198 LYS cc_start: 0.8711 (mmpt) cc_final: 0.8450 (mmtm) REVERT: h 201 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8218 (mt) REVERT: k 50 MET cc_start: 0.8834 (mtp) cc_final: 0.8610 (mtm) REVERT: k 195 LYS cc_start: 0.8152 (ttpp) cc_final: 0.7828 (mtpm) REVERT: l 12 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8338 (mp) REVERT: l 67 MET cc_start: 0.8619 (mmp) cc_final: 0.8314 (mmm) REVERT: l 71 MET cc_start: 0.9046 (mtm) cc_final: 0.8753 (mtp) REVERT: l 93 ASN cc_start: 0.7968 (t0) cc_final: 0.7707 (t0) REVERT: l 119 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8077 (mt) REVERT: l 137 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8248 (ttpp) outliers start: 207 outliers final: 99 residues processed: 849 average time/residue: 1.6449 time to fit residues: 1727.2383 Evaluate side-chains 828 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 682 time to evaluate : 4.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 363 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 359 GLU Chi-restraints excluded: chain H residue 362 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain J residue 356 GLN Chi-restraints excluded: chain J residue 363 ILE Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 282 GLU Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain M residue 363 ILE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 137 LYS Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 359 GLU Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain P residue 195 LYS Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 310 SER Chi-restraints excluded: chain P residue 356 GLN Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 363 ILE Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain S residue 110 LYS Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 129 ILE Chi-restraints excluded: chain S residue 142 MET Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain S residue 334 MET Chi-restraints excluded: chain S residue 363 ILE Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 96 ASP Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 359 GLU Chi-restraints excluded: chain T residue 362 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 129 ILE Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 316 GLN Chi-restraints excluded: chain c residue 363 ILE Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 359 GLU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 22 LYS Chi-restraints excluded: chain g residue 32 SER Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 195 LYS Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 34 ASP Chi-restraints excluded: chain h residue 39 ASP Chi-restraints excluded: chain h residue 96 ASP Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain h residue 201 LEU Chi-restraints excluded: chain h residue 338 ARG Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 109 MET Chi-restraints excluded: chain k residue 363 ILE Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 39 ASP Chi-restraints excluded: chain l residue 96 ASP Chi-restraints excluded: chain l residue 119 LEU Chi-restraints excluded: chain l residue 120 THR Chi-restraints excluded: chain l residue 137 LYS Chi-restraints excluded: chain l residue 201 LEU Chi-restraints excluded: chain l residue 359 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 437 optimal weight: 0.6980 chunk 282 optimal weight: 3.9990 chunk 422 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 137 optimal weight: 3.9990 chunk 449 optimal weight: 3.9990 chunk 481 optimal weight: 6.9990 chunk 349 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 556 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 192 ASN B 45 ASN D 102 GLN D 192 ASN G 192 ASN H 45 ASN M 102 GLN N 45 ASN N 360 ASN P 102 GLN P 192 ASN Q 45 ASN S 102 GLN S 192 ASN T 43 HIS c 102 GLN c 192 ASN d 45 ASN ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 61510 Z= 0.411 Angle : 0.640 12.597 83440 Z= 0.331 Chirality : 0.046 0.190 9560 Planarity : 0.004 0.047 10240 Dihedral : 11.232 74.228 10210 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.43 % Allowed : 17.08 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.10), residues: 7340 helix: 0.94 (0.07), residues: 4760 sheet: 0.28 (0.20), residues: 460 loop : 0.50 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP G 260 HIS 0.012 0.001 HIS M 225 PHE 0.016 0.003 PHE J 111 TYR 0.021 0.002 TYR E 365 ARG 0.014 0.001 ARG c 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 690 time to evaluate : 5.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: A 129 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7971 (mp) REVERT: A 195 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7899 (pttp) REVERT: A 198 LYS cc_start: 0.8347 (mmtm) cc_final: 0.7814 (mppt) REVERT: B 12 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8199 (tp) REVERT: B 71 MET cc_start: 0.8944 (mtm) cc_final: 0.8710 (mtp) REVERT: B 93 ASN cc_start: 0.8092 (t0) cc_final: 0.7657 (t0) REVERT: B 248 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8282 (mmm) REVERT: B 257 MET cc_start: 0.8679 (mmm) cc_final: 0.8378 (mmm) REVERT: D 71 MET cc_start: 0.9168 (mtm) cc_final: 0.8877 (mtm) REVERT: D 77 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: D 110 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7713 (ttpm) REVERT: D 125 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8683 (mt) REVERT: D 142 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6299 (pp-130) REVERT: D 195 LYS cc_start: 0.8124 (mtmm) cc_final: 0.7867 (pttp) REVERT: D 198 LYS cc_start: 0.8296 (mmtm) cc_final: 0.7775 (mppt) REVERT: D 334 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8354 (ttp) REVERT: E 12 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.7926 (mp) REVERT: E 67 MET cc_start: 0.8540 (mmp) cc_final: 0.8281 (mmm) REVERT: E 93 ASN cc_start: 0.8160 (t0) cc_final: 0.7689 (t0) REVERT: E 359 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.5297 (mp0) REVERT: G 12 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8301 (tp) REVERT: G 67 MET cc_start: 0.8840 (mmm) cc_final: 0.8441 (mmm) REVERT: H 12 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8220 (tp) REVERT: H 50 MET cc_start: 0.8192 (mtm) cc_final: 0.7898 (mtt) REVERT: H 93 ASN cc_start: 0.8178 (t0) cc_final: 0.7610 (t0) REVERT: H 96 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8125 (p0) REVERT: H 158 MET cc_start: 0.8723 (mmm) cc_final: 0.8495 (mmm) REVERT: H 359 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5541 (mp0) REVERT: J 12 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8134 (tp) REVERT: J 16 GLN cc_start: 0.8275 (tt0) cc_final: 0.7980 (tt0) REVERT: J 67 MET cc_start: 0.8842 (mmm) cc_final: 0.8434 (mmm) REVERT: J 130 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: J 198 LYS cc_start: 0.8745 (tppp) cc_final: 0.8259 (mmpt) REVERT: J 334 MET cc_start: 0.8827 (ttp) cc_final: 0.8304 (ttp) REVERT: J 356 GLN cc_start: 0.7043 (OUTLIER) cc_final: 0.6578 (mt0) REVERT: K 12 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8393 (tp) REVERT: K 93 ASN cc_start: 0.8032 (t0) cc_final: 0.7647 (t0) REVERT: K 142 MET cc_start: 0.5357 (pp-130) cc_final: 0.5017 (tmm) REVERT: K 191 LYS cc_start: 0.8325 (ptpt) cc_final: 0.7848 (pttp) REVERT: K 198 LYS cc_start: 0.8752 (mmpt) cc_final: 0.8465 (mmtm) REVERT: K 201 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8287 (mt) REVERT: M 50 MET cc_start: 0.8876 (mtp) cc_final: 0.8628 (mtm) REVERT: M 195 LYS cc_start: 0.8165 (ttpp) cc_final: 0.7838 (mtpm) REVERT: N 71 MET cc_start: 0.9035 (mtm) cc_final: 0.8742 (mtp) REVERT: N 93 ASN cc_start: 0.8031 (t0) cc_final: 0.7733 (t0) REVERT: N 142 MET cc_start: 0.5221 (pp-130) cc_final: 0.4956 (tmm) REVERT: P 77 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: P 98 THR cc_start: 0.8589 (p) cc_final: 0.8113 (t) REVERT: P 101 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.8021 (ttm110) REVERT: P 129 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8011 (mp) REVERT: P 195 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7877 (pttp) REVERT: P 198 LYS cc_start: 0.8270 (mmtm) cc_final: 0.7701 (mppt) REVERT: P 356 GLN cc_start: 0.6364 (OUTLIER) cc_final: 0.6065 (mt0) REVERT: Q 12 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8200 (tp) REVERT: Q 71 MET cc_start: 0.8941 (mtm) cc_final: 0.8706 (mtp) REVERT: Q 93 ASN cc_start: 0.8123 (t0) cc_final: 0.7749 (t0) REVERT: Q 257 MET cc_start: 0.8683 (mmm) cc_final: 0.8380 (mmm) REVERT: S 71 MET cc_start: 0.9164 (mtm) cc_final: 0.8878 (mtm) REVERT: S 77 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: S 110 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7827 (ttpt) REVERT: S 125 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8686 (mt) REVERT: S 142 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6322 (pp-130) REVERT: S 195 LYS cc_start: 0.8128 (mtmm) cc_final: 0.7862 (pttp) REVERT: S 198 LYS cc_start: 0.8291 (mmtm) cc_final: 0.7787 (mppt) REVERT: S 334 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8338 (ttp) REVERT: T 12 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.7938 (mp) REVERT: T 93 ASN cc_start: 0.8142 (t0) cc_final: 0.7667 (t0) REVERT: T 359 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.5344 (mp0) REVERT: c 67 MET cc_start: 0.8837 (mmm) cc_final: 0.8431 (mmm) REVERT: d 50 MET cc_start: 0.8193 (mtm) cc_final: 0.7921 (mtt) REVERT: d 93 ASN cc_start: 0.8203 (t0) cc_final: 0.7757 (t0) REVERT: d 96 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8084 (p0) REVERT: d 158 MET cc_start: 0.8723 (mmm) cc_final: 0.8495 (mmm) REVERT: d 359 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.5547 (mp0) REVERT: g 12 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8143 (tp) REVERT: g 16 GLN cc_start: 0.8281 (tt0) cc_final: 0.7994 (tt0) REVERT: g 24 THR cc_start: 0.8798 (p) cc_final: 0.8593 (p) REVERT: g 67 MET cc_start: 0.8845 (mmm) cc_final: 0.8442 (mmm) REVERT: g 130 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: g 138 MET cc_start: 0.7270 (tmm) cc_final: 0.7023 (tmt) REVERT: g 195 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7863 (pttp) REVERT: g 334 MET cc_start: 0.8830 (ttp) cc_final: 0.8249 (ttp) REVERT: h 12 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8377 (tp) REVERT: h 93 ASN cc_start: 0.8013 (t0) cc_final: 0.7656 (t0) REVERT: h 191 LYS cc_start: 0.8314 (ptpt) cc_final: 0.7905 (pttp) REVERT: h 198 LYS cc_start: 0.8748 (mmpt) cc_final: 0.8443 (mmtm) REVERT: h 201 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8331 (mt) REVERT: k 50 MET cc_start: 0.8878 (mtp) cc_final: 0.8627 (mtm) REVERT: k 195 LYS cc_start: 0.8170 (ttpp) cc_final: 0.7843 (mtpm) REVERT: l 12 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8335 (mp) REVERT: l 71 MET cc_start: 0.9036 (mtm) cc_final: 0.8752 (mtp) REVERT: l 93 ASN cc_start: 0.7939 (t0) cc_final: 0.7628 (t0) REVERT: l 119 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8042 (mt) outliers start: 211 outliers final: 107 residues processed: 840 average time/residue: 1.6427 time to fit residues: 1713.4982 Evaluate side-chains 824 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 674 time to evaluate : 4.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 363 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 359 GLU Chi-restraints excluded: chain H residue 362 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 195 LYS Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 336 GLU Chi-restraints excluded: chain J residue 356 GLN Chi-restraints excluded: chain J residue 363 ILE Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain M residue 363 ILE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 359 GLU Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain P residue 195 LYS Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 233 THR Chi-restraints excluded: chain P residue 310 SER Chi-restraints excluded: chain P residue 356 GLN Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 363 ILE Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 142 MET Chi-restraints excluded: chain Q residue 338 ARG Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain S residue 110 LYS Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 129 ILE Chi-restraints excluded: chain S residue 142 MET Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain S residue 334 MET Chi-restraints excluded: chain S residue 363 ILE Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 359 GLU Chi-restraints excluded: chain T residue 362 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 125 ILE Chi-restraints excluded: chain c residue 129 ILE Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 191 LYS Chi-restraints excluded: chain c residue 316 GLN Chi-restraints excluded: chain c residue 363 ILE Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 359 GLU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 32 SER Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 195 LYS Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 34 ASP Chi-restraints excluded: chain h residue 39 ASP Chi-restraints excluded: chain h residue 96 ASP Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain h residue 201 LEU Chi-restraints excluded: chain h residue 338 ARG Chi-restraints excluded: chain k residue 31 ASP Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 109 MET Chi-restraints excluded: chain k residue 363 ILE Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 39 ASP Chi-restraints excluded: chain l residue 96 ASP Chi-restraints excluded: chain l residue 119 LEU Chi-restraints excluded: chain l residue 120 THR Chi-restraints excluded: chain l residue 201 LEU Chi-restraints excluded: chain l residue 359 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 643 optimal weight: 4.9990 chunk 677 optimal weight: 0.0070 chunk 618 optimal weight: 0.8980 chunk 659 optimal weight: 1.9990 chunk 396 optimal weight: 0.7980 chunk 287 optimal weight: 4.9990 chunk 517 optimal weight: 6.9990 chunk 202 optimal weight: 0.7980 chunk 595 optimal weight: 0.6980 chunk 623 optimal weight: 0.7980 chunk 656 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 151 HIS A 192 ASN B 45 ASN D 102 GLN D 151 HIS D 192 ASN E 43 HIS G 192 ASN H 45 ASN ** J 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN N 45 ASN P 102 GLN P 151 HIS P 192 ASN Q 45 ASN S 102 GLN S 151 HIS S 192 ASN T 43 HIS T 100 HIS c 102 GLN c 192 ASN ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 GLN l 45 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 61510 Z= 0.140 Angle : 0.504 11.455 83440 Z= 0.261 Chirality : 0.038 0.170 9560 Planarity : 0.003 0.059 10240 Dihedral : 11.027 73.609 10210 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.31 % Allowed : 18.56 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.10), residues: 7340 helix: 1.61 (0.08), residues: 4740 sheet: 0.33 (0.21), residues: 440 loop : 0.69 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 260 HIS 0.004 0.001 HIS D 151 PHE 0.012 0.001 PHE J 111 TYR 0.014 0.001 TYR D 135 ARG 0.014 0.000 ARG G 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 725 time to evaluate : 5.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: A 198 LYS cc_start: 0.8158 (mmtm) cc_final: 0.7652 (mppt) REVERT: A 338 ARG cc_start: 0.7585 (mtm180) cc_final: 0.7376 (mtm110) REVERT: B 15 ASP cc_start: 0.8210 (t70) cc_final: 0.7957 (t70) REVERT: B 71 MET cc_start: 0.9008 (mtm) cc_final: 0.8781 (mtp) REVERT: B 93 ASN cc_start: 0.8093 (t0) cc_final: 0.7788 (t0) REVERT: B 248 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8363 (mmm) REVERT: B 257 MET cc_start: 0.8792 (mmm) cc_final: 0.8322 (mmm) REVERT: D 71 MET cc_start: 0.9107 (mtm) cc_final: 0.8719 (mtm) REVERT: D 77 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: D 93 ASN cc_start: 0.8272 (m-40) cc_final: 0.7869 (m-40) REVERT: D 110 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7602 (ttpm) REVERT: D 125 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8412 (mt) REVERT: D 138 MET cc_start: 0.7485 (tmm) cc_final: 0.7240 (tmt) REVERT: D 142 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6586 (pp-130) REVERT: D 195 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7860 (pttp) REVERT: D 198 LYS cc_start: 0.8114 (mmtm) cc_final: 0.7871 (mppt) REVERT: D 334 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8253 (ttt) REVERT: E 12 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8042 (mp) REVERT: E 67 MET cc_start: 0.8593 (mmp) cc_final: 0.8264 (mmm) REVERT: E 93 ASN cc_start: 0.8007 (t0) cc_final: 0.7503 (t0) REVERT: E 359 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5553 (mp0) REVERT: G 46 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8006 (mtmm) REVERT: G 67 MET cc_start: 0.8745 (mmm) cc_final: 0.8325 (mmm) REVERT: G 130 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: H 50 MET cc_start: 0.8162 (mtm) cc_final: 0.7856 (mtt) REVERT: H 93 ASN cc_start: 0.8126 (t0) cc_final: 0.7658 (t0) REVERT: H 96 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8056 (p0) REVERT: J 16 GLN cc_start: 0.8142 (tt0) cc_final: 0.7871 (tt0) REVERT: J 67 MET cc_start: 0.8792 (mmm) cc_final: 0.8374 (mmm) REVERT: J 198 LYS cc_start: 0.8612 (tppp) cc_final: 0.8202 (mmpt) REVERT: J 201 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7674 (mt) REVERT: J 271 MET cc_start: 0.7005 (mmm) cc_final: 0.6721 (mmp) REVERT: J 334 MET cc_start: 0.8839 (ttp) cc_final: 0.8290 (ttt) REVERT: J 356 GLN cc_start: 0.6891 (OUTLIER) cc_final: 0.6581 (mt0) REVERT: K 93 ASN cc_start: 0.7875 (t0) cc_final: 0.7525 (t0) REVERT: K 142 MET cc_start: 0.5312 (pp-130) cc_final: 0.5035 (tmm) REVERT: K 191 LYS cc_start: 0.8270 (ptpt) cc_final: 0.7947 (pttp) REVERT: K 198 LYS cc_start: 0.8710 (mmpt) cc_final: 0.8450 (mmtm) REVERT: K 201 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8106 (mt) REVERT: M 50 MET cc_start: 0.8727 (mtp) cc_final: 0.8492 (mtm) REVERT: M 195 LYS cc_start: 0.8150 (ttpp) cc_final: 0.7876 (mtpm) REVERT: N 67 MET cc_start: 0.8584 (mmp) cc_final: 0.8301 (mmm) REVERT: N 71 MET cc_start: 0.9085 (mtm) cc_final: 0.8826 (mtp) REVERT: N 93 ASN cc_start: 0.7878 (t0) cc_final: 0.7645 (t0) REVERT: P 77 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: P 98 THR cc_start: 0.8505 (p) cc_final: 0.8189 (t) REVERT: P 101 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7921 (ttm110) REVERT: P 198 LYS cc_start: 0.8203 (mmtm) cc_final: 0.7673 (mppt) REVERT: P 338 ARG cc_start: 0.7585 (mtm180) cc_final: 0.7373 (mtm110) REVERT: Q 15 ASP cc_start: 0.8213 (t70) cc_final: 0.7962 (t70) REVERT: Q 71 MET cc_start: 0.9007 (mtm) cc_final: 0.8781 (mtp) REVERT: Q 93 ASN cc_start: 0.8062 (t0) cc_final: 0.7747 (t0) REVERT: Q 257 MET cc_start: 0.8791 (mmm) cc_final: 0.8329 (mmm) REVERT: S 71 MET cc_start: 0.9103 (mtm) cc_final: 0.8725 (mtm) REVERT: S 93 ASN cc_start: 0.8402 (m-40) cc_final: 0.7891 (m110) REVERT: S 110 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7634 (ttpm) REVERT: S 125 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8434 (mt) REVERT: S 138 MET cc_start: 0.7473 (tmm) cc_final: 0.7228 (tmt) REVERT: S 142 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6588 (pp-130) REVERT: S 198 LYS cc_start: 0.8115 (mmtm) cc_final: 0.7878 (mppt) REVERT: S 334 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8242 (ttt) REVERT: T 93 ASN cc_start: 0.7998 (t0) cc_final: 0.7497 (t0) REVERT: T 359 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.5576 (mp0) REVERT: c 46 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.8009 (mtmm) REVERT: c 67 MET cc_start: 0.8741 (mmm) cc_final: 0.8318 (mmm) REVERT: d 50 MET cc_start: 0.8164 (mtm) cc_final: 0.7859 (mtt) REVERT: d 93 ASN cc_start: 0.8179 (t0) cc_final: 0.7859 (t0) REVERT: d 96 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8100 (p0) REVERT: g 16 GLN cc_start: 0.8151 (tt0) cc_final: 0.7882 (tt0) REVERT: g 24 THR cc_start: 0.8741 (p) cc_final: 0.8505 (p) REVERT: g 67 MET cc_start: 0.8792 (mmm) cc_final: 0.8380 (mmm) REVERT: g 198 LYS cc_start: 0.8629 (tppp) cc_final: 0.8210 (mmpt) REVERT: g 201 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7668 (mt) REVERT: g 334 MET cc_start: 0.8857 (ttp) cc_final: 0.8278 (ttt) REVERT: g 338 ARG cc_start: 0.7465 (mtm180) cc_final: 0.7202 (mpp-170) REVERT: h 93 ASN cc_start: 0.7886 (t0) cc_final: 0.7547 (t0) REVERT: h 142 MET cc_start: 0.5038 (pp-130) cc_final: 0.4737 (tmm) REVERT: h 191 LYS cc_start: 0.8256 (ptpt) cc_final: 0.7929 (pttp) REVERT: h 198 LYS cc_start: 0.8713 (mmpt) cc_final: 0.8449 (mmtm) REVERT: h 201 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8128 (mt) REVERT: k 50 MET cc_start: 0.8728 (mtp) cc_final: 0.8497 (mtm) REVERT: k 195 LYS cc_start: 0.8148 (ttpp) cc_final: 0.7875 (mtpm) REVERT: l 71 MET cc_start: 0.9087 (mtm) cc_final: 0.8838 (mtp) REVERT: l 93 ASN cc_start: 0.7826 (t0) cc_final: 0.7602 (t0) REVERT: l 119 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8018 (mt) outliers start: 142 outliers final: 62 residues processed: 823 average time/residue: 1.6121 time to fit residues: 1648.2920 Evaluate side-chains 777 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 688 time to evaluate : 4.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 362 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 356 GLN Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 359 GLU Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 338 ARG Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain S residue 110 LYS Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 142 MET Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain S residue 334 MET Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 359 GLU Chi-restraints excluded: chain T residue 362 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain h residue 34 ASP Chi-restraints excluded: chain h residue 39 ASP Chi-restraints excluded: chain h residue 96 ASP Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain h residue 201 LEU Chi-restraints excluded: chain h residue 338 ARG Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 109 MET Chi-restraints excluded: chain l residue 96 ASP Chi-restraints excluded: chain l residue 119 LEU Chi-restraints excluded: chain l residue 120 THR Chi-restraints excluded: chain l residue 201 LEU Chi-restraints excluded: chain l residue 359 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 432 optimal weight: 0.9980 chunk 697 optimal weight: 4.9990 chunk 425 optimal weight: 3.9990 chunk 330 optimal weight: 3.9990 chunk 484 optimal weight: 0.7980 chunk 731 optimal weight: 0.0030 chunk 673 optimal weight: 3.9990 chunk 582 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 449 optimal weight: 3.9990 chunk 357 optimal weight: 3.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 192 ASN D 102 GLN D 192 ASN G 102 GLN J 360 ASN M 16 GLN M 102 GLN P 102 GLN P 151 HIS P 192 ASN S 102 GLN S 192 ASN T 43 HIS c 102 GLN d 45 ASN ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 61510 Z= 0.231 Angle : 0.552 11.845 83440 Z= 0.285 Chirality : 0.041 0.171 9560 Planarity : 0.003 0.049 10240 Dihedral : 11.000 73.966 10210 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.06 % Allowed : 19.01 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.10), residues: 7340 helix: 1.49 (0.07), residues: 4760 sheet: 0.35 (0.20), residues: 460 loop : 0.71 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 260 HIS 0.008 0.001 HIS M 225 PHE 0.018 0.002 PHE J 111 TYR 0.016 0.001 TYR T 365 ARG 0.010 0.000 ARG T 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 689 time to evaluate : 5.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: A 98 THR cc_start: 0.8594 (p) cc_final: 0.8100 (t) REVERT: A 110 LYS cc_start: 0.8088 (ttpp) cc_final: 0.7861 (tttm) REVERT: A 138 MET cc_start: 0.7553 (tmm) cc_final: 0.7230 (tmt) REVERT: A 195 LYS cc_start: 0.8253 (mtpm) cc_final: 0.7880 (pttp) REVERT: A 198 LYS cc_start: 0.8194 (mmtm) cc_final: 0.7691 (mppt) REVERT: B 15 ASP cc_start: 0.8380 (t70) cc_final: 0.8125 (t70) REVERT: B 71 MET cc_start: 0.9005 (mtm) cc_final: 0.8766 (mtp) REVERT: B 93 ASN cc_start: 0.8093 (t0) cc_final: 0.7789 (t0) REVERT: B 248 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8363 (mmm) REVERT: B 257 MET cc_start: 0.8784 (mmm) cc_final: 0.8303 (mmm) REVERT: D 71 MET cc_start: 0.9159 (mtm) cc_final: 0.8750 (mtm) REVERT: D 77 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: D 110 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7714 (ttpm) REVERT: D 125 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8548 (mt) REVERT: D 142 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6383 (pp-130) REVERT: D 195 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7913 (pttp) REVERT: D 198 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7889 (mppt) REVERT: D 334 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8215 (ttp) REVERT: E 12 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8104 (mp) REVERT: E 67 MET cc_start: 0.8531 (mmp) cc_final: 0.8176 (mmm) REVERT: E 93 ASN cc_start: 0.7950 (t0) cc_final: 0.7489 (t0) REVERT: E 359 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.5463 (mp0) REVERT: G 67 MET cc_start: 0.8757 (mmm) cc_final: 0.8382 (mmm) REVERT: G 130 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: G 138 MET cc_start: 0.7501 (tmm) cc_final: 0.7113 (tmt) REVERT: G 271 MET cc_start: 0.7065 (mmp) cc_final: 0.6549 (mmp) REVERT: H 12 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8211 (tp) REVERT: H 50 MET cc_start: 0.8149 (mtm) cc_final: 0.7862 (mtt) REVERT: H 93 ASN cc_start: 0.8129 (t0) cc_final: 0.7654 (t0) REVERT: H 96 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8096 (p0) REVERT: H 359 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.5498 (mp0) REVERT: J 16 GLN cc_start: 0.8186 (tt0) cc_final: 0.7904 (tt0) REVERT: J 67 MET cc_start: 0.8806 (mmm) cc_final: 0.8476 (mmm) REVERT: J 198 LYS cc_start: 0.8656 (tppp) cc_final: 0.8212 (mmpt) REVERT: J 334 MET cc_start: 0.8858 (ttp) cc_final: 0.8307 (ttt) REVERT: J 356 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6572 (mt0) REVERT: K 93 ASN cc_start: 0.7893 (t0) cc_final: 0.7537 (t0) REVERT: K 142 MET cc_start: 0.5301 (pp-130) cc_final: 0.4941 (tmm) REVERT: K 191 LYS cc_start: 0.8318 (ptpt) cc_final: 0.7961 (pttp) REVERT: K 198 LYS cc_start: 0.8703 (mmpt) cc_final: 0.8450 (mmtm) REVERT: K 201 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8139 (mt) REVERT: M 50 MET cc_start: 0.8785 (mtp) cc_final: 0.8554 (mtm) REVERT: M 195 LYS cc_start: 0.8096 (ttpp) cc_final: 0.7742 (mtpm) REVERT: N 71 MET cc_start: 0.9062 (mtm) cc_final: 0.8769 (mtp) REVERT: N 93 ASN cc_start: 0.7856 (t0) cc_final: 0.7537 (t0) REVERT: P 77 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: P 98 THR cc_start: 0.8544 (p) cc_final: 0.8202 (t) REVERT: P 101 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7953 (ttm110) REVERT: P 195 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7833 (pttp) REVERT: P 198 LYS cc_start: 0.8182 (mmtm) cc_final: 0.7696 (mppt) REVERT: Q 15 ASP cc_start: 0.8387 (t70) cc_final: 0.8129 (t70) REVERT: Q 71 MET cc_start: 0.8971 (mtm) cc_final: 0.8728 (mtp) REVERT: Q 93 ASN cc_start: 0.8071 (t0) cc_final: 0.7760 (t0) REVERT: Q 257 MET cc_start: 0.8790 (mmm) cc_final: 0.8315 (mmm) REVERT: S 71 MET cc_start: 0.9151 (mtm) cc_final: 0.8753 (mtm) REVERT: S 77 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: S 110 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7827 (ttpt) REVERT: S 125 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8550 (mt) REVERT: S 142 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6449 (pp-130) REVERT: S 198 LYS cc_start: 0.8162 (mmtm) cc_final: 0.7900 (mppt) REVERT: S 334 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8203 (ttp) REVERT: T 12 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8104 (mp) REVERT: T 93 ASN cc_start: 0.7926 (t0) cc_final: 0.7471 (t0) REVERT: T 359 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.5455 (mp0) REVERT: c 67 MET cc_start: 0.8757 (mmm) cc_final: 0.8374 (mmm) REVERT: c 130 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: c 138 MET cc_start: 0.7466 (tmm) cc_final: 0.7076 (tmt) REVERT: d 50 MET cc_start: 0.8157 (mtm) cc_final: 0.7871 (mtt) REVERT: d 93 ASN cc_start: 0.8179 (t0) cc_final: 0.7841 (t0) REVERT: d 96 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8110 (p0) REVERT: d 359 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5506 (mp0) REVERT: g 12 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8165 (tp) REVERT: g 16 GLN cc_start: 0.8185 (tt0) cc_final: 0.7908 (tt0) REVERT: g 24 THR cc_start: 0.8785 (p) cc_final: 0.8540 (p) REVERT: g 67 MET cc_start: 0.8810 (mmm) cc_final: 0.8488 (mmm) REVERT: g 138 MET cc_start: 0.7294 (tmm) cc_final: 0.6913 (tmt) REVERT: g 198 LYS cc_start: 0.8653 (tppp) cc_final: 0.8196 (mmpt) REVERT: g 201 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7919 (mt) REVERT: g 334 MET cc_start: 0.8857 (ttp) cc_final: 0.8283 (ttp) REVERT: h 142 MET cc_start: 0.5008 (pp-130) cc_final: 0.4715 (tmm) REVERT: h 191 LYS cc_start: 0.8297 (ptpt) cc_final: 0.7933 (pttp) REVERT: h 198 LYS cc_start: 0.8718 (mmpt) cc_final: 0.8446 (mmtm) REVERT: h 201 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8205 (mt) REVERT: k 50 MET cc_start: 0.8784 (mtp) cc_final: 0.8552 (mtm) REVERT: k 195 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7798 (mtpm) REVERT: l 71 MET cc_start: 0.9071 (mtm) cc_final: 0.8791 (mtp) REVERT: l 93 ASN cc_start: 0.7838 (t0) cc_final: 0.7508 (t0) REVERT: l 119 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8045 (mt) outliers start: 127 outliers final: 70 residues processed: 780 average time/residue: 1.6521 time to fit residues: 1600.0981 Evaluate side-chains 782 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 680 time to evaluate : 4.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 359 GLU Chi-restraints excluded: chain H residue 362 VAL Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 356 GLN Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 359 GLU Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 195 LYS Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 338 ARG Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain S residue 110 LYS Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 142 MET Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain S residue 334 MET Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 359 GLU Chi-restraints excluded: chain T residue 362 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 109 MET Chi-restraints excluded: chain c residue 125 ILE Chi-restraints excluded: chain c residue 130 GLU Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 359 GLU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain h residue 34 ASP Chi-restraints excluded: chain h residue 39 ASP Chi-restraints excluded: chain h residue 96 ASP Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain h residue 201 LEU Chi-restraints excluded: chain h residue 338 ARG Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 109 MET Chi-restraints excluded: chain l residue 96 ASP Chi-restraints excluded: chain l residue 119 LEU Chi-restraints excluded: chain l residue 120 THR Chi-restraints excluded: chain l residue 201 LEU Chi-restraints excluded: chain l residue 359 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 462 optimal weight: 2.9990 chunk 620 optimal weight: 0.5980 chunk 178 optimal weight: 4.9990 chunk 536 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 583 optimal weight: 0.7980 chunk 244 optimal weight: 7.9990 chunk 598 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 151 HIS A 192 ASN D 102 GLN D 192 ASN G 102 GLN M 16 GLN M 102 GLN P 102 GLN P 151 HIS P 192 ASN S 102 GLN S 192 ASN T 43 HIS c 102 GLN ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 93 ASN k 102 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.157750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119630 restraints weight = 67345.654| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.72 r_work: 0.3214 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 61510 Z= 0.155 Angle : 0.511 11.251 83440 Z= 0.264 Chirality : 0.039 0.168 9560 Planarity : 0.003 0.068 10240 Dihedral : 10.925 73.693 10210 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.95 % Allowed : 19.32 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.10), residues: 7340 helix: 1.72 (0.08), residues: 4740 sheet: 0.35 (0.21), residues: 440 loop : 0.74 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 260 HIS 0.005 0.001 HIS c 225 PHE 0.014 0.001 PHE J 111 TYR 0.015 0.001 TYR J 135 ARG 0.015 0.000 ARG c 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24586.13 seconds wall clock time: 424 minutes 20.43 seconds (25460.43 seconds total)