Starting phenix.real_space_refine on Thu Sep 26 07:35:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op2_17038/09_2024/8op2_17038.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op2_17038/09_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_17038/09_2024/8op2_17038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op2_17038/09_2024/8op2_17038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op2_17038/09_2024/8op2_17038.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op2_17038/09_2024/8op2_17038.cif" } 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. Time to flip 120 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 26.74, per 1000 atoms: 0.44 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.63 Conformation dependent library (CDL) restraints added in 6.2 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: 16.36 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: 25.54 Time building geometry restraints manager: 14.00 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: 0.00 - 8.80: 83330 8.80 - 17.60: 82 17.60 - 26.40: 9 26.40 - 35.21: 10 35.21 - 44.01: 9 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 3.120 nonbonded pdb=" N GLU K 77 " pdb=" OE1 GLU K 77 " model vdw 2.165 3.120 nonbonded pdb=" N GLU h 77 " pdb=" OE1 GLU h 77 " model vdw 2.165 3.120 nonbonded pdb=" N GLU N 77 " pdb=" OE1 GLU N 77 " model vdw 2.165 3.120 nonbonded pdb=" N GLU E 77 " pdb=" OE1 GLU E 77 " model vdw 2.165 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 5.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 1.810 Check model and map are aligned: 0.350 Set scattering table: 0.430 Process input model: 121.270 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.420 ------------------------------------------------------------------------------- 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 : 5.024 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: 1.7536 time to fit residues: 2799.4018 Evaluate side-chains 773 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 732 time to evaluate : 5.060 ------------------------------------------------------------------------------- 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: 0.9990 chunk 556 optimal weight: 8.9990 chunk 308 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 375 optimal weight: 3.9990 chunk 297 optimal weight: 0.7980 chunk 575 optimal weight: 0.9990 chunk 222 optimal weight: 5.9990 chunk 349 optimal weight: 6.9990 chunk 428 optimal weight: 5.9990 chunk 666 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN E 45 ASN 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 ** H 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 GLN K 26 GLN K 292 GLN ** K 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 ASN M 102 GLN M 192 ASN M 292 GLN N 26 GLN N 356 GLN ** N 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 292 GLN ** P 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 26 GLN Q 93 ASN Q 356 GLN ** Q 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 192 ASN T 26 GLN T 45 ASN 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 ** d 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 292 GLN h 26 GLN h 45 ASN h 292 GLN ** h 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 ASN k 102 GLN k 192 ASN k 292 GLN l 26 GLN l 356 GLN ** l 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 61510 Z= 0.221 Angle : 0.554 5.662 83440 Z= 0.300 Chirality : 0.042 0.185 9560 Planarity : 0.003 0.032 10240 Dihedral : 11.766 73.880 10332 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.25 % Allowed : 11.07 % Favored : 85.68 % 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: 1.30 (0.10), residues: 7340 helix: 1.25 (0.08), residues: 4780 sheet: 0.45 (0.20), residues: 500 loop : 0.29 (0.15), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 260 HIS 0.007 0.001 HIS M 225 PHE 0.013 0.002 PHE g 226 TYR 0.016 0.002 TYR k 135 ARG 0.007 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 1090 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 890 time to evaluate : 5.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7789 (pttm) REVERT: A 198 LYS cc_start: 0.8168 (mmtm) cc_final: 0.7291 (mppt) REVERT: A 356 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.6390 (mt0) REVERT: B 15 ASP cc_start: 0.8453 (t70) cc_final: 0.8074 (t70) REVERT: B 71 MET cc_start: 0.9031 (mtm) cc_final: 0.8783 (mtp) REVERT: B 93 ASN cc_start: 0.8108 (t0) cc_final: 0.7746 (t0) REVERT: B 101 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.7849 (ttm110) REVERT: B 191 LYS cc_start: 0.8164 (ptpt) cc_final: 0.7864 (ptpp) REVERT: B 257 MET cc_start: 0.8817 (mmm) cc_final: 0.8354 (mmm) REVERT: B 336 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7137 (tm-30) REVERT: D 24 THR cc_start: 0.8622 (p) cc_final: 0.8409 (p) REVERT: D 56 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: D 71 MET cc_start: 0.9177 (mtm) cc_final: 0.8761 (mtm) REVERT: D 112 GLU cc_start: 0.7232 (tt0) cc_final: 0.6985 (mt-10) REVERT: D 142 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6094 (tmm) REVERT: D 198 LYS cc_start: 0.7948 (mmtm) cc_final: 0.7243 (mppt) REVERT: D 365 TYR cc_start: 0.6430 (m-80) cc_final: 0.6228 (m-80) REVERT: E 67 MET cc_start: 0.8318 (mmm) cc_final: 0.8076 (mmm) REVERT: G 12 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8170 (tp) REVERT: G 67 MET cc_start: 0.8785 (mmm) cc_final: 0.8386 (mmm) REVERT: G 130 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7569 (mp0) REVERT: G 198 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7913 (tppt) REVERT: G 201 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8016 (mt) REVERT: H 50 MET cc_start: 0.8139 (mtm) cc_final: 0.7818 (mtt) REVERT: H 89 HIS cc_start: 0.7225 (t70) cc_final: 0.6875 (m-70) REVERT: H 93 ASN cc_start: 0.8204 (t0) cc_final: 0.7723 (t0) REVERT: H 101 ARG cc_start: 0.8068 (ttm-80) cc_final: 0.7549 (tpp-160) REVERT: H 334 MET cc_start: 0.8889 (ttp) cc_final: 0.8545 (ttt) REVERT: H 336 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: J 16 GLN cc_start: 0.8259 (tt0) cc_final: 0.8001 (tt0) REVERT: J 24 THR cc_start: 0.8690 (p) cc_final: 0.8451 (p) REVERT: J 67 MET cc_start: 0.8906 (mmm) cc_final: 0.8430 (mmm) REVERT: J 130 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: J 198 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8038 (tppt) REVERT: J 334 MET cc_start: 0.8678 (ttp) cc_final: 0.8158 (ttt) REVERT: J 338 ARG cc_start: 0.7397 (mtm-85) cc_final: 0.7175 (mtm110) REVERT: K 12 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8355 (tp) REVERT: K 67 MET cc_start: 0.8442 (mmm) cc_final: 0.8238 (mmp) REVERT: K 191 LYS cc_start: 0.8443 (ptpt) cc_final: 0.8088 (pttp) REVERT: K 257 MET cc_start: 0.8673 (mmm) cc_final: 0.8414 (mmm) REVERT: K 342 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7136 (ptp-170) REVERT: K 356 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6430 (mt0) REVERT: M 50 MET cc_start: 0.8683 (mtp) cc_final: 0.8475 (mtm) REVERT: M 76 ARG cc_start: 0.8091 (ttt180) cc_final: 0.7768 (ttp-110) REVERT: M 122 GLU cc_start: 0.7158 (mp0) cc_final: 0.6937 (mp0) REVERT: M 195 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7760 (ttpp) REVERT: N 67 MET cc_start: 0.8454 (mmm) cc_final: 0.8089 (mmp) REVERT: N 71 MET cc_start: 0.9090 (mtm) cc_final: 0.8734 (mtp) REVERT: N 101 ARG cc_start: 0.8159 (mpt90) cc_final: 0.7146 (ttm-80) REVERT: N 191 LYS cc_start: 0.8210 (ptpt) cc_final: 0.7934 (pttp) REVERT: N 336 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7551 (pt0) REVERT: P 195 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7787 (pttm) REVERT: P 198 LYS cc_start: 0.8175 (mmtm) cc_final: 0.7292 (mppt) REVERT: P 356 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6394 (mt0) REVERT: Q 15 ASP cc_start: 0.8458 (t70) cc_final: 0.8096 (t70) REVERT: Q 71 MET cc_start: 0.9028 (mtm) cc_final: 0.8788 (mtp) REVERT: Q 93 ASN cc_start: 0.8107 (t0) cc_final: 0.7757 (t0) REVERT: Q 191 LYS cc_start: 0.8190 (ptpt) cc_final: 0.7886 (ptpp) REVERT: Q 257 MET cc_start: 0.8811 (mmm) cc_final: 0.8354 (mmm) REVERT: Q 336 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7158 (tm-30) REVERT: S 24 THR cc_start: 0.8616 (p) cc_final: 0.8400 (p) REVERT: S 56 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: S 71 MET cc_start: 0.9173 (mtm) cc_final: 0.8767 (mtm) REVERT: S 112 GLU cc_start: 0.7191 (tt0) cc_final: 0.6952 (mt-10) REVERT: S 123 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8449 (mt) REVERT: S 142 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6092 (tmm) REVERT: S 198 LYS cc_start: 0.7958 (mmtm) cc_final: 0.7237 (mppt) REVERT: T 67 MET cc_start: 0.8313 (mmm) cc_final: 0.8058 (mmm) REVERT: c 12 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8169 (tp) REVERT: c 67 MET cc_start: 0.8785 (mmm) cc_final: 0.8378 (mmm) REVERT: c 130 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7560 (mp0) REVERT: c 198 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7910 (tppt) REVERT: c 201 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8013 (mt) REVERT: d 50 MET cc_start: 0.8115 (mtm) cc_final: 0.7789 (mtt) REVERT: d 93 ASN cc_start: 0.8176 (t0) cc_final: 0.7744 (t0) REVERT: d 101 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7519 (tpp-160) REVERT: d 334 MET cc_start: 0.8900 (ttp) cc_final: 0.8544 (ttt) REVERT: d 336 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: g 12 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8140 (tp) REVERT: g 16 GLN cc_start: 0.8259 (tt0) cc_final: 0.8006 (tt0) REVERT: g 24 THR cc_start: 0.8689 (p) cc_final: 0.8446 (p) REVERT: g 67 MET cc_start: 0.8921 (mmm) cc_final: 0.8459 (mmm) REVERT: g 130 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: g 195 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7862 (ttpp) REVERT: g 198 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8000 (tppt) REVERT: h 12 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8346 (tp) REVERT: h 89 HIS cc_start: 0.7076 (t70) cc_final: 0.6838 (m-70) REVERT: h 191 LYS cc_start: 0.8435 (ptpt) cc_final: 0.8097 (pttp) REVERT: h 257 MET cc_start: 0.8675 (mmm) cc_final: 0.8410 (mmm) REVERT: h 342 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7142 (ptp-170) REVERT: h 356 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6482 (mt0) REVERT: k 50 MET cc_start: 0.8688 (mtp) cc_final: 0.8480 (mtm) REVERT: k 76 ARG cc_start: 0.8097 (ttt180) cc_final: 0.7776 (ttp-110) REVERT: k 122 GLU cc_start: 0.7162 (mp0) cc_final: 0.6940 (mp0) REVERT: k 195 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7766 (ttpp) REVERT: k 338 ARG cc_start: 0.7474 (mtt180) cc_final: 0.7262 (mpp-170) REVERT: l 12 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8354 (mp) REVERT: l 71 MET cc_start: 0.9102 (mtm) cc_final: 0.8756 (mtp) REVERT: l 101 ARG cc_start: 0.8142 (mpt90) cc_final: 0.7112 (ttm-80) REVERT: l 191 LYS cc_start: 0.8227 (ptpt) cc_final: 0.7955 (pttp) REVERT: l 281 MET cc_start: 0.8453 (mmm) cc_final: 0.8198 (tpp) REVERT: l 336 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7563 (tm-30) outliers start: 200 outliers final: 36 residues processed: 982 average time/residue: 1.7264 time to fit residues: 2084.1697 Evaluate side-chains 816 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 746 time to evaluate : 5.035 ------------------------------------------------------------------------------- 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 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 56 ASP Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 201 LEU 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 125 ILE 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 39 ASP Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 198 LYS Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 356 GLN Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 195 LYS Chi-restraints excluded: chain N residue 12 LEU 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 356 GLN 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 56 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 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 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 130 GLU Chi-restraints excluded: chain g residue 195 LYS Chi-restraints excluded: chain g residue 198 LYS Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 342 ARG Chi-restraints excluded: chain h residue 356 GLN Chi-restraints excluded: chain h residue 362 VAL Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 195 LYS Chi-restraints excluded: chain l residue 12 LEU 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: 6.9990 chunk 206 optimal weight: 5.9990 chunk 554 optimal weight: 2.9990 chunk 453 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 667 optimal weight: 0.0770 chunk 721 optimal weight: 10.0000 chunk 594 optimal weight: 4.9990 chunk 662 optimal weight: 0.9990 chunk 227 optimal weight: 6.9990 chunk 535 optimal weight: 7.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 93 ASN A 102 GLN A 151 HIS A 192 ASN B 45 ASN B 356 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN D 93 ASN D 102 GLN D 192 ASN D 292 GLN E 93 ASN E 356 GLN ** E 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN G 102 GLN G 192 ASN H 45 ASN H 207 ASN H 356 GLN J 26 GLN J 93 ASN J 192 ASN K 45 ASN K 192 ASN ** K 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 GLN M 102 GLN N 26 GLN N 45 ASN N 89 HIS N 192 ASN N 356 GLN ** N 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 ASN P 102 GLN P 151 HIS P 192 ASN Q 45 ASN Q 356 GLN ** Q 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 26 GLN S 93 ASN S 102 GLN S 192 ASN S 292 GLN T 356 GLN ** T 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 102 GLN c 192 ASN d 45 ASN d 207 ASN d 356 GLN g 26 GLN g 93 ASN g 102 GLN g 192 ASN h 93 ASN h 192 ASN ** h 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 26 GLN k 102 GLN l 26 GLN l 45 ASN l 89 HIS l 192 ASN l 356 GLN ** l 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2326 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= 0.260 Angle : 0.553 5.823 83440 Z= 0.296 Chirality : 0.042 0.180 9560 Planarity : 0.003 0.036 10240 Dihedral : 11.211 73.967 10214 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.12 % Allowed : 12.69 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.10), residues: 7340 helix: 1.30 (0.08), residues: 4760 sheet: 0.66 (0.20), residues: 500 loop : 0.35 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP k 260 HIS 0.009 0.001 HIS M 225 PHE 0.013 0.002 PHE g 226 TYR 0.018 0.002 TYR J 135 ARG 0.010 0.001 ARG N 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 994 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 802 time to evaluate : 5.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: A 195 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7819 (pttp) REVERT: A 198 LYS cc_start: 0.8227 (mmtm) cc_final: 0.7376 (mppt) REVERT: A 338 ARG cc_start: 0.7732 (mtm180) cc_final: 0.7531 (mtp180) REVERT: A 356 GLN cc_start: 0.6358 (OUTLIER) cc_final: 0.6011 (mt0) REVERT: B 12 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8174 (tp) REVERT: B 71 MET cc_start: 0.9027 (mtm) cc_final: 0.8785 (mtp) REVERT: B 93 ASN cc_start: 0.8073 (t0) cc_final: 0.7809 (t0) REVERT: B 110 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8326 (mtpp) REVERT: B 191 LYS cc_start: 0.8116 (ptpt) cc_final: 0.7853 (ptpp) REVERT: B 248 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8273 (mmm) REVERT: B 257 MET cc_start: 0.8777 (mmm) cc_final: 0.8305 (mmm) REVERT: D 71 MET cc_start: 0.9158 (mtm) cc_final: 0.8792 (mtm) REVERT: D 93 ASN cc_start: 0.8407 (m-40) cc_final: 0.7812 (m110) REVERT: D 142 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6168 (tmm) REVERT: D 195 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7846 (pttm) REVERT: D 198 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7602 (mppt) REVERT: D 356 GLN cc_start: 0.6661 (mp10) cc_final: 0.6336 (mt0) REVERT: D 365 TYR cc_start: 0.6436 (m-80) cc_final: 0.6228 (m-80) REVERT: E 12 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7903 (mp) REVERT: E 93 ASN cc_start: 0.8046 (t0) cc_final: 0.7654 (t0) REVERT: E 138 MET cc_start: 0.7909 (tmm) cc_final: 0.7691 (ppp) REVERT: E 359 GLU cc_start: 0.6419 (OUTLIER) cc_final: 0.4990 (mp0) REVERT: G 12 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8262 (tp) REVERT: G 67 MET cc_start: 0.8792 (mmm) cc_final: 0.8462 (mmm) REVERT: G 130 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7646 (mp0) REVERT: G 198 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7839 (tppt) REVERT: G 201 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7997 (mt) REVERT: G 356 GLN cc_start: 0.6669 (OUTLIER) cc_final: 0.6206 (mt0) REVERT: H 12 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8220 (tp) REVERT: H 50 MET cc_start: 0.8204 (mtm) cc_final: 0.7895 (mtt) REVERT: H 93 ASN cc_start: 0.8164 (t0) cc_final: 0.7624 (t0) REVERT: H 334 MET cc_start: 0.8930 (ttp) cc_final: 0.8641 (ttt) REVERT: H 336 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7329 (tm-30) REVERT: J 12 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8123 (tp) REVERT: J 16 GLN cc_start: 0.8304 (tt0) cc_final: 0.8015 (tt0) REVERT: J 93 ASN cc_start: 0.8226 (m-40) cc_final: 0.7648 (m-40) REVERT: J 123 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8174 (mp) REVERT: J 130 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: J 334 MET cc_start: 0.8826 (ttp) cc_final: 0.8294 (ttt) REVERT: J 338 ARG cc_start: 0.7527 (mtm-85) cc_final: 0.7296 (mpp-170) REVERT: J 356 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6559 (mt0) REVERT: K 12 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8366 (tp) REVERT: K 93 ASN cc_start: 0.8133 (t0) cc_final: 0.7641 (t0) REVERT: K 191 LYS cc_start: 0.8420 (ptpt) cc_final: 0.8063 (pttp) REVERT: K 201 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8238 (mt) REVERT: K 336 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: K 342 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7292 (ptp-170) REVERT: K 356 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6549 (mt0) REVERT: M 50 MET cc_start: 0.8786 (mtp) cc_final: 0.8529 (mtm) REVERT: M 98 THR cc_start: 0.8588 (p) cc_final: 0.8059 (t) REVERT: M 122 GLU cc_start: 0.7480 (mp0) cc_final: 0.7117 (mp0) REVERT: M 338 ARG cc_start: 0.7726 (mtm180) cc_final: 0.7423 (mpp-170) REVERT: M 356 GLN cc_start: 0.6656 (OUTLIER) cc_final: 0.6308 (mt0) REVERT: N 71 MET cc_start: 0.9098 (mtm) cc_final: 0.8810 (mtp) REVERT: P 77 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: P 195 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7809 (pttp) REVERT: P 198 LYS cc_start: 0.8232 (mmtm) cc_final: 0.7381 (mppt) REVERT: P 356 GLN cc_start: 0.6656 (OUTLIER) cc_final: 0.6308 (mt0) REVERT: Q 12 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8177 (tp) REVERT: Q 71 MET cc_start: 0.9029 (mtm) cc_final: 0.8783 (mtp) REVERT: Q 93 ASN cc_start: 0.8077 (t0) cc_final: 0.7807 (t0) REVERT: Q 191 LYS cc_start: 0.8156 (ptpt) cc_final: 0.7883 (ptpp) REVERT: Q 248 MET cc_start: 0.8416 (mmm) cc_final: 0.8153 (mmp) REVERT: Q 257 MET cc_start: 0.8780 (mmm) cc_final: 0.8308 (mmm) REVERT: S 24 THR cc_start: 0.8646 (p) cc_final: 0.8446 (p) REVERT: S 71 MET cc_start: 0.9151 (mtm) cc_final: 0.8793 (mtm) REVERT: S 93 ASN cc_start: 0.8411 (m-40) cc_final: 0.7815 (m110) REVERT: S 122 GLU cc_start: 0.7561 (mp0) cc_final: 0.7328 (mp0) REVERT: S 123 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8528 (mt) REVERT: S 142 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.6173 (tmm) REVERT: S 195 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7844 (pttm) REVERT: S 198 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7591 (mppt) REVERT: S 356 GLN cc_start: 0.6678 (mp10) cc_final: 0.6347 (mt0) REVERT: T 12 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7918 (mp) REVERT: T 138 MET cc_start: 0.7941 (tmm) cc_final: 0.7713 (ppp) REVERT: T 359 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.4993 (mp0) REVERT: c 12 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8263 (tp) REVERT: c 67 MET cc_start: 0.8787 (mmm) cc_final: 0.8454 (mmm) REVERT: c 130 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7608 (mp0) REVERT: c 198 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7835 (tppt) REVERT: c 201 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7997 (mt) REVERT: c 356 GLN cc_start: 0.6713 (OUTLIER) cc_final: 0.6167 (mt0) REVERT: d 50 MET cc_start: 0.8201 (mtm) cc_final: 0.7893 (mtt) REVERT: d 93 ASN cc_start: 0.8192 (t0) cc_final: 0.7849 (t0) REVERT: d 334 MET cc_start: 0.8925 (ttp) cc_final: 0.8627 (ttt) REVERT: d 336 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: g 12 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8138 (tp) REVERT: g 16 GLN cc_start: 0.8302 (tt0) cc_final: 0.8024 (tt0) REVERT: g 195 LYS cc_start: 0.8180 (mtpm) cc_final: 0.7870 (ttpp) REVERT: g 338 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.7277 (mtm180) REVERT: h 12 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8346 (tp) REVERT: h 93 ASN cc_start: 0.8231 (t0) cc_final: 0.7589 (t0) REVERT: h 191 LYS cc_start: 0.8411 (ptpt) cc_final: 0.8058 (pttp) REVERT: h 201 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8263 (mt) REVERT: h 342 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7308 (ptp-170) REVERT: h 356 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6543 (mt0) REVERT: k 50 MET cc_start: 0.8789 (mtp) cc_final: 0.8534 (mtm) REVERT: k 98 THR cc_start: 0.8595 (p) cc_final: 0.8055 (t) REVERT: k 122 GLU cc_start: 0.7481 (mp0) cc_final: 0.7117 (mp0) REVERT: k 356 GLN cc_start: 0.6692 (OUTLIER) cc_final: 0.6349 (mt0) REVERT: l 12 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8330 (mp) REVERT: l 71 MET cc_start: 0.9153 (mtm) cc_final: 0.8866 (mtp) outliers start: 192 outliers final: 61 residues processed: 923 average time/residue: 1.7157 time to fit residues: 1959.2476 Evaluate side-chains 835 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 730 time to evaluate : 5.041 ------------------------------------------------------------------------------- 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 363 ILE Chi-restraints excluded: chain B residue 12 LEU 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 39 ASP Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 310 SER 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 12 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain G residue 356 GLN Chi-restraints excluded: chain H residue 12 LEU 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 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 22 LYS Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 123 ILE 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 201 LEU Chi-restraints excluded: chain K residue 336 GLU 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 89 HIS 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 363 ILE Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 110 LYS 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 123 ILE Chi-restraints excluded: chain S residue 142 MET Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 310 SER Chi-restraints excluded: chain T residue 12 LEU 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 198 LYS Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 310 SER Chi-restraints excluded: chain c residue 356 GLN Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 125 ILE 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 22 LYS Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 248 MET Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 133 LYS 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 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 89 HIS 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: 0.5980 chunk 502 optimal weight: 9.9990 chunk 346 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 318 optimal weight: 2.9990 chunk 448 optimal weight: 0.9990 chunk 670 optimal weight: 4.9990 chunk 709 optimal weight: 5.9990 chunk 350 optimal weight: 0.9980 chunk 635 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN B 192 ASN D 102 GLN D 192 ASN ** E 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 192 ASN ** K 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN N 26 GLN N 356 GLN ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 192 ASN Q 192 ASN S 102 GLN S 192 ASN ** T 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 102 GLN c 192 ASN ** h 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 GLN l 26 GLN l 45 ASN l 356 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 61510 Z= 0.266 Angle : 0.551 12.890 83440 Z= 0.293 Chirality : 0.042 0.177 9560 Planarity : 0.004 0.053 10240 Dihedral : 11.155 73.982 10210 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.95 % Allowed : 14.42 % Favored : 82.63 % 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: 1.37 (0.10), residues: 7340 helix: 1.27 (0.07), residues: 4760 sheet: 0.50 (0.19), residues: 500 loop : 0.40 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP k 260 HIS 0.014 0.001 HIS N 89 PHE 0.013 0.002 PHE J 226 TYR 0.016 0.002 TYR H 365 ARG 0.010 0.001 ARG c 101 *********************** 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 931 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 749 time to evaluate : 5.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: A 195 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7863 (pttp) REVERT: A 198 LYS cc_start: 0.8233 (mmtm) cc_final: 0.7675 (mppt) REVERT: A 356 GLN cc_start: 0.6385 (OUTLIER) cc_final: 0.6126 (mt0) REVERT: B 12 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8198 (tp) REVERT: B 71 MET cc_start: 0.8999 (mtm) cc_final: 0.8764 (mtp) REVERT: B 93 ASN cc_start: 0.8083 (t0) cc_final: 0.7804 (t0) REVERT: B 191 LYS cc_start: 0.8117 (ptpt) cc_final: 0.7793 (ptpp) REVERT: B 248 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8268 (mmm) REVERT: B 257 MET cc_start: 0.8789 (mmm) cc_final: 0.8445 (mmm) REVERT: D 71 MET cc_start: 0.9151 (mtm) cc_final: 0.8770 (mtm) REVERT: D 77 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: D 101 ARG cc_start: 0.8180 (ttm110) cc_final: 0.7817 (ttm110) REVERT: D 142 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6059 (pp-130) REVERT: D 195 LYS cc_start: 0.8264 (mtmm) cc_final: 0.7850 (pttm) REVERT: D 198 LYS cc_start: 0.8244 (mmtm) cc_final: 0.7778 (mppt) REVERT: D 356 GLN cc_start: 0.6833 (OUTLIER) cc_final: 0.6344 (mt0) REVERT: D 365 TYR cc_start: 0.6405 (m-80) cc_final: 0.6187 (m-80) REVERT: E 12 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8113 (mp) REVERT: E 15 ASP cc_start: 0.8532 (t70) cc_final: 0.8318 (t0) REVERT: E 67 MET cc_start: 0.8540 (mmt) cc_final: 0.8246 (mmm) REVERT: E 89 HIS cc_start: 0.7219 (t70) cc_final: 0.6838 (m-70) REVERT: E 93 ASN cc_start: 0.7988 (t0) cc_final: 0.7520 (t0) REVERT: E 359 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.5052 (mp0) REVERT: G 12 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8262 (tp) REVERT: G 67 MET cc_start: 0.8816 (mmm) cc_final: 0.8396 (mmm) REVERT: G 198 LYS cc_start: 0.8188 (tppp) cc_final: 0.7886 (tppt) REVERT: G 201 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7986 (mt) REVERT: G 356 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.6414 (mt0) REVERT: H 12 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8207 (tp) REVERT: H 50 MET cc_start: 0.8184 (mtm) cc_final: 0.7884 (mtt) REVERT: H 93 ASN cc_start: 0.8159 (t0) cc_final: 0.7593 (t0) REVERT: H 101 ARG cc_start: 0.8278 (tpp-160) cc_final: 0.7872 (tpp-160) REVERT: J 12 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8128 (tp) REVERT: J 16 GLN cc_start: 0.8314 (tt0) cc_final: 0.8023 (tt0) REVERT: J 67 MET cc_start: 0.8767 (mmm) cc_final: 0.8475 (mmm) REVERT: J 123 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8219 (mp) REVERT: J 130 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: J 195 LYS cc_start: 0.8330 (mtmm) cc_final: 0.8044 (ttpp) REVERT: J 198 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8188 (mmpt) REVERT: J 334 MET cc_start: 0.8821 (ttp) cc_final: 0.8272 (ttp) REVERT: J 338 ARG cc_start: 0.7565 (mtm-85) cc_final: 0.7346 (mpp-170) REVERT: J 356 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6525 (mt0) REVERT: K 93 ASN cc_start: 0.8115 (t0) cc_final: 0.7639 (t0) REVERT: K 191 LYS cc_start: 0.8426 (ptpt) cc_final: 0.7948 (pttp) REVERT: K 198 LYS cc_start: 0.8612 (mmtm) cc_final: 0.8304 (mmpt) REVERT: K 257 MET cc_start: 0.8698 (mmt) cc_final: 0.8302 (mmm) REVERT: K 336 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7440 (pt0) REVERT: K 342 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7311 (ptp-170) REVERT: K 356 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6573 (mt0) REVERT: M 50 MET cc_start: 0.8802 (mtp) cc_final: 0.8574 (mtm) REVERT: M 122 GLU cc_start: 0.7388 (mp0) cc_final: 0.7114 (mp0) REVERT: M 338 ARG cc_start: 0.7599 (mtm180) cc_final: 0.7349 (mpp-170) REVERT: M 356 GLN cc_start: 0.6668 (OUTLIER) cc_final: 0.6412 (mt0) REVERT: N 67 MET cc_start: 0.8527 (mmp) cc_final: 0.8286 (mmm) REVERT: N 71 MET cc_start: 0.9030 (mtm) cc_final: 0.8748 (mtp) REVERT: N 93 ASN cc_start: 0.8037 (t0) cc_final: 0.7679 (t0) REVERT: P 77 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: P 110 LYS cc_start: 0.8180 (tmtm) cc_final: 0.7907 (tmtm) REVERT: P 195 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7871 (pttp) REVERT: P 198 LYS cc_start: 0.8251 (mmtm) cc_final: 0.7681 (mppt) REVERT: P 356 GLN cc_start: 0.6437 (OUTLIER) cc_final: 0.6226 (mt0) REVERT: Q 12 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8201 (tp) REVERT: Q 71 MET cc_start: 0.8996 (mtm) cc_final: 0.8761 (mtp) REVERT: Q 93 ASN cc_start: 0.8082 (t0) cc_final: 0.7796 (t0) REVERT: Q 101 ARG cc_start: 0.8023 (ttm110) cc_final: 0.7669 (ttm110) REVERT: Q 191 LYS cc_start: 0.8130 (ptpt) cc_final: 0.7815 (ptpp) REVERT: Q 257 MET cc_start: 0.8793 (mmm) cc_final: 0.8447 (mmm) REVERT: S 71 MET cc_start: 0.9145 (mtm) cc_final: 0.8773 (mtm) REVERT: S 77 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: S 101 ARG cc_start: 0.8178 (ttm110) cc_final: 0.7830 (ttm110) REVERT: S 142 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6058 (pp-130) REVERT: S 195 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7847 (pttm) REVERT: S 198 LYS cc_start: 0.8226 (mmtm) cc_final: 0.7779 (mppt) REVERT: S 356 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6348 (mt0) REVERT: T 12 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8123 (mp) REVERT: T 15 ASP cc_start: 0.8539 (t70) cc_final: 0.8322 (t0) REVERT: T 67 MET cc_start: 0.8546 (mmt) cc_final: 0.8251 (mmm) REVERT: T 89 HIS cc_start: 0.7215 (t70) cc_final: 0.6846 (m-70) REVERT: T 359 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.5153 (mp0) REVERT: c 12 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8242 (tp) REVERT: c 67 MET cc_start: 0.8811 (mmm) cc_final: 0.8386 (mmm) REVERT: c 198 LYS cc_start: 0.8196 (tppp) cc_final: 0.7885 (tppt) REVERT: c 201 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7984 (mt) REVERT: c 356 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.6390 (mt0) REVERT: d 50 MET cc_start: 0.8187 (mtm) cc_final: 0.7884 (mtt) REVERT: d 93 ASN cc_start: 0.8188 (t0) cc_final: 0.7852 (t0) REVERT: d 101 ARG cc_start: 0.8271 (tpp-160) cc_final: 0.7867 (tpp-160) REVERT: g 12 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8152 (tp) REVERT: g 16 GLN cc_start: 0.8315 (tt0) cc_final: 0.8030 (tt0) REVERT: g 67 MET cc_start: 0.8776 (mmm) cc_final: 0.8486 (mmm) REVERT: g 130 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: g 195 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7865 (ttpp) REVERT: g 198 LYS cc_start: 0.8690 (tppp) cc_final: 0.8303 (mmpt) REVERT: g 334 MET cc_start: 0.8850 (ttp) cc_final: 0.8305 (ttt) REVERT: g 338 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.7334 (mpp-170) REVERT: h 93 ASN cc_start: 0.8148 (t0) cc_final: 0.7642 (t0) REVERT: h 191 LYS cc_start: 0.8420 (ptpt) cc_final: 0.7949 (pttp) REVERT: h 198 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8253 (mmpt) REVERT: h 201 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8236 (mt) REVERT: h 342 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7291 (ptp-170) REVERT: h 356 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6598 (mt0) REVERT: k 50 MET cc_start: 0.8804 (mtp) cc_final: 0.8574 (mtm) REVERT: k 122 GLU cc_start: 0.7385 (mp0) cc_final: 0.7109 (mp0) REVERT: k 175 ASP cc_start: 0.7448 (p0) cc_final: 0.7223 (p0) REVERT: k 195 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7940 (ttpp) REVERT: k 356 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6407 (mt0) REVERT: l 12 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8318 (mp) REVERT: l 71 MET cc_start: 0.9053 (mtm) cc_final: 0.8746 (mtp) REVERT: l 282 GLU cc_start: 0.6562 (pm20) cc_final: 0.6349 (pm20) outliers start: 182 outliers final: 65 residues processed: 881 average time/residue: 1.7095 time to fit residues: 1856.8739 Evaluate side-chains 820 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 711 time to evaluate : 5.090 ------------------------------------------------------------------------------- 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 195 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 12 LEU 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 39 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 356 GLN 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 12 LEU 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 201 LEU Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 356 GLN Chi-restraints excluded: chain G residue 363 ILE Chi-restraints excluded: chain H residue 12 LEU 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 123 ILE Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 198 LYS 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 336 GLU 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 120 THR Chi-restraints excluded: chain N residue 133 LYS 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 195 LYS Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 356 GLN Chi-restraints excluded: chain P residue 363 ILE Chi-restraints excluded: chain Q residue 12 LEU 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 142 MET Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 310 SER Chi-restraints excluded: chain S residue 356 GLN Chi-restraints excluded: chain T residue 12 LEU 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 142 MET Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 310 SER 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 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 32 SER Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 77 GLU Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 195 LYS Chi-restraints excluded: chain g residue 248 MET Chi-restraints excluded: chain g residue 363 ILE 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 39 ASP Chi-restraints excluded: chain k residue 195 LYS 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 97 VAL 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: 6.9990 chunk 402 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 528 optimal weight: 4.9990 chunk 292 optimal weight: 1.9990 chunk 605 optimal weight: 6.9990 chunk 490 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 362 optimal weight: 5.9990 chunk 636 optimal weight: 9.9990 chunk 179 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN B 192 ASN D 102 GLN D 192 ASN ** E 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 192 ASN K 192 ASN ** K 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN N 26 GLN N 45 ASN N 89 HIS N 356 GLN ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 192 ASN Q 192 ASN S 102 GLN S 192 ASN ** T 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 102 GLN c 192 ASN ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 192 ASN ** h 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 GLN l 26 GLN l 89 HIS l 356 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 61510 Z= 0.272 Angle : 0.560 13.218 83440 Z= 0.295 Chirality : 0.042 0.179 9560 Planarity : 0.004 0.038 10240 Dihedral : 11.145 73.993 10210 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.43 % Allowed : 15.00 % Favored : 81.57 % 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: 1.37 (0.10), residues: 7340 helix: 1.24 (0.07), residues: 4760 sheet: 0.51 (0.19), residues: 500 loop : 0.49 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP M 260 HIS 0.009 0.001 HIS k 225 PHE 0.014 0.002 PHE g 111 TYR 0.017 0.002 TYR S 135 ARG 0.011 0.001 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 951 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 740 time to evaluate : 5.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: A 198 LYS cc_start: 0.8230 (mmtm) cc_final: 0.7722 (mppt) REVERT: B 12 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8207 (tp) REVERT: B 71 MET cc_start: 0.9003 (mtm) cc_final: 0.8779 (mtp) REVERT: B 93 ASN cc_start: 0.8093 (t0) cc_final: 0.7807 (t0) REVERT: B 191 LYS cc_start: 0.8112 (ptpt) cc_final: 0.7799 (ptpp) REVERT: B 248 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8267 (mmm) REVERT: B 257 MET cc_start: 0.8776 (mmm) cc_final: 0.8442 (mmm) REVERT: B 336 GLU cc_start: 0.7342 (tm-30) cc_final: 0.7034 (tm-30) REVERT: D 71 MET cc_start: 0.9146 (mtm) cc_final: 0.8740 (mtm) REVERT: D 77 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: D 101 ARG cc_start: 0.8222 (ttm110) cc_final: 0.7852 (ttm110) REVERT: D 125 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8541 (mt) REVERT: D 142 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6258 (pp-130) REVERT: D 195 LYS cc_start: 0.8169 (mtmm) cc_final: 0.7774 (pttm) REVERT: D 198 LYS cc_start: 0.8248 (mmtm) cc_final: 0.7858 (mppt) REVERT: D 356 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6558 (mt0) REVERT: E 12 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8104 (mp) REVERT: E 15 ASP cc_start: 0.8554 (t70) cc_final: 0.8318 (t0) REVERT: E 67 MET cc_start: 0.8521 (mmp) cc_final: 0.8231 (mmm) REVERT: E 89 HIS cc_start: 0.7193 (t70) cc_final: 0.6791 (m-70) REVERT: E 93 ASN cc_start: 0.8061 (t0) cc_final: 0.7540 (t0) REVERT: E 359 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.5267 (mp0) REVERT: G 12 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8254 (tp) REVERT: G 67 MET cc_start: 0.8825 (mmm) cc_final: 0.8423 (mmm) REVERT: G 130 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: G 201 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7986 (mt) REVERT: H 12 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8193 (tp) REVERT: H 50 MET cc_start: 0.8194 (mtm) cc_final: 0.7916 (mtt) REVERT: H 93 ASN cc_start: 0.8155 (t0) cc_final: 0.7586 (t0) REVERT: H 126 ASN cc_start: 0.8720 (m-40) cc_final: 0.8518 (m-40) REVERT: J 12 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8135 (tp) REVERT: J 16 GLN cc_start: 0.8314 (tt0) cc_final: 0.8010 (tt0) REVERT: J 67 MET cc_start: 0.8796 (mmm) cc_final: 0.8521 (mmm) REVERT: J 123 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8070 (mp) REVERT: J 198 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8220 (mmpt) REVERT: J 334 MET cc_start: 0.8846 (ttp) cc_final: 0.8221 (ttt) REVERT: J 338 ARG cc_start: 0.7623 (mtm-85) cc_final: 0.7375 (mpp-170) REVERT: J 356 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6534 (mt0) REVERT: K 12 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8372 (tp) REVERT: K 93 ASN cc_start: 0.8101 (t0) cc_final: 0.7628 (t0) REVERT: K 142 MET cc_start: 0.5773 (OUTLIER) cc_final: 0.5486 (ptt) REVERT: K 191 LYS cc_start: 0.8313 (ptpt) cc_final: 0.7817 (pttp) REVERT: K 198 LYS cc_start: 0.8647 (mmtm) cc_final: 0.8318 (mmpt) REVERT: K 201 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8174 (mt) REVERT: K 282 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.6191 (tt0) REVERT: K 336 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: K 356 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6550 (mt0) REVERT: M 50 MET cc_start: 0.8833 (mtp) cc_final: 0.8604 (mtm) REVERT: M 122 GLU cc_start: 0.7371 (mp0) cc_final: 0.7088 (mp0) REVERT: M 338 ARG cc_start: 0.7600 (mtm180) cc_final: 0.7356 (mpp-170) REVERT: N 71 MET cc_start: 0.9031 (mtm) cc_final: 0.8749 (mtp) REVERT: N 93 ASN cc_start: 0.7975 (t0) cc_final: 0.7658 (t0) REVERT: P 77 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: P 101 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7956 (ttm110) REVERT: P 110 LYS cc_start: 0.8072 (tmtm) cc_final: 0.7853 (tmtm) REVERT: P 195 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7845 (pttp) REVERT: P 198 LYS cc_start: 0.8269 (mmtm) cc_final: 0.7730 (mppt) REVERT: Q 12 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8211 (tp) REVERT: Q 71 MET cc_start: 0.9002 (mtm) cc_final: 0.8774 (mtp) REVERT: Q 93 ASN cc_start: 0.8091 (t0) cc_final: 0.7809 (t0) REVERT: Q 101 ARG cc_start: 0.7889 (ttm110) cc_final: 0.7661 (ttm-80) REVERT: Q 110 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8280 (mtpp) REVERT: Q 191 LYS cc_start: 0.8101 (ptpt) cc_final: 0.7788 (ptpp) REVERT: Q 248 MET cc_start: 0.8524 (mmp) cc_final: 0.8318 (mmm) REVERT: Q 257 MET cc_start: 0.8778 (mmm) cc_final: 0.8444 (mmm) REVERT: Q 336 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7028 (tm-30) REVERT: S 71 MET cc_start: 0.9142 (mtm) cc_final: 0.8745 (mtm) REVERT: S 77 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: S 101 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7861 (ttm110) REVERT: S 125 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8542 (mt) REVERT: S 142 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6270 (pp-130) REVERT: S 195 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7772 (pttm) REVERT: S 198 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7857 (mppt) REVERT: S 356 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.6561 (mt0) REVERT: T 12 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8108 (mp) REVERT: T 15 ASP cc_start: 0.8556 (t70) cc_final: 0.8327 (t0) REVERT: T 67 MET cc_start: 0.8525 (mmp) cc_final: 0.8234 (mmm) REVERT: T 89 HIS cc_start: 0.7190 (t70) cc_final: 0.6798 (m-70) REVERT: T 359 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5265 (mp0) REVERT: c 12 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8255 (tp) REVERT: c 67 MET cc_start: 0.8823 (mmm) cc_final: 0.8418 (mmm) REVERT: c 130 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: c 201 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7985 (mt) REVERT: d 50 MET cc_start: 0.8194 (mtm) cc_final: 0.7916 (mtt) REVERT: d 93 ASN cc_start: 0.8201 (t0) cc_final: 0.7824 (t0) REVERT: g 12 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8159 (tp) REVERT: g 16 GLN cc_start: 0.8316 (tt0) cc_final: 0.8016 (tt0) REVERT: g 67 MET cc_start: 0.8799 (mmm) cc_final: 0.8529 (mmm) REVERT: g 130 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: g 138 MET cc_start: 0.7584 (tmm) cc_final: 0.7354 (tmt) REVERT: g 198 LYS cc_start: 0.8726 (tppp) cc_final: 0.8394 (mmpt) REVERT: g 334 MET cc_start: 0.8864 (ttp) cc_final: 0.8277 (ttt) REVERT: g 338 ARG cc_start: 0.7651 (mtm-85) cc_final: 0.7417 (mpp-170) REVERT: h 12 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8352 (tp) REVERT: h 33 ILE cc_start: 0.8653 (mm) cc_final: 0.8288 (mt) REVERT: h 93 ASN cc_start: 0.8122 (t0) cc_final: 0.7675 (t0) REVERT: h 142 MET cc_start: 0.5816 (OUTLIER) cc_final: 0.5508 (ptt) REVERT: h 191 LYS cc_start: 0.8308 (ptpt) cc_final: 0.7822 (pttp) REVERT: h 198 LYS cc_start: 0.8638 (mmtm) cc_final: 0.8249 (mmpt) REVERT: h 201 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8219 (mt) REVERT: h 282 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.6193 (tt0) REVERT: h 356 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6499 (mt0) REVERT: k 50 MET cc_start: 0.8836 (mtp) cc_final: 0.8606 (mtm) REVERT: k 122 GLU cc_start: 0.7332 (mp0) cc_final: 0.7096 (mp0) REVERT: k 195 LYS cc_start: 0.8129 (mtpm) cc_final: 0.7828 (pttm) REVERT: l 12 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8314 (mp) REVERT: l 67 MET cc_start: 0.8579 (mmp) cc_final: 0.8302 (mmm) REVERT: l 71 MET cc_start: 0.9030 (mtm) cc_final: 0.8750 (mtp) REVERT: l 93 ASN cc_start: 0.7987 (t0) cc_final: 0.7693 (t0) REVERT: l 282 GLU cc_start: 0.6487 (pm20) cc_final: 0.6277 (pm20) outliers start: 211 outliers final: 78 residues processed: 884 average time/residue: 1.7472 time to fit residues: 1900.8843 Evaluate side-chains 835 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 712 time to evaluate : 5.088 ------------------------------------------------------------------------------- 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 363 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 133 LYS 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 77 GLU Chi-restraints excluded: chain D residue 122 GLU 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 201 LEU Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 356 GLN 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 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 310 SER 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 191 LYS 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 123 ILE Chi-restraints excluded: chain J residue 198 LYS 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 120 THR Chi-restraints excluded: chain K residue 142 MET Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 282 GLU Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 356 GLN Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 363 ILE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 201 LEU 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 195 LYS Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 363 ILE Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 110 LYS Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 133 LYS 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 39 ASP Chi-restraints excluded: chain S residue 77 GLU 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 201 LEU Chi-restraints excluded: chain S residue 310 SER Chi-restraints excluded: chain S residue 356 GLN Chi-restraints excluded: chain T residue 12 LEU 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 310 SER Chi-restraints excluded: chain c residue 316 GLN Chi-restraints excluded: chain d residue 12 LEU 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 248 MET Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain h residue 142 MET Chi-restraints excluded: chain h residue 201 LEU Chi-restraints excluded: chain h residue 282 GLU Chi-restraints excluded: chain h residue 356 GLN Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 363 ILE Chi-restraints excluded: chain l residue 12 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 238 optimal weight: 0.2980 chunk 638 optimal weight: 8.9990 chunk 140 optimal weight: 0.9990 chunk 416 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 710 optimal weight: 5.9990 chunk 589 optimal weight: 5.9990 chunk 328 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 234 optimal weight: 3.9990 chunk 372 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN D 102 GLN D 192 ASN ** E 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 192 ASN G 356 GLN J 102 GLN ** K 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN M 356 GLN N 45 ASN ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 192 ASN S 102 GLN S 192 ASN ** T 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 102 GLN c 192 ASN c 356 GLN ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 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: 0.8034 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 61510 Z= 0.182 Angle : 0.516 12.054 83440 Z= 0.272 Chirality : 0.040 0.172 9560 Planarity : 0.003 0.056 10240 Dihedral : 11.049 73.784 10210 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.95 % Allowed : 15.93 % Favored : 81.12 % 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: 1.62 (0.10), residues: 7340 helix: 1.50 (0.08), residues: 4740 sheet: 0.33 (0.20), residues: 460 loop : 0.48 (0.14), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP c 260 HIS 0.006 0.001 HIS c 225 PHE 0.015 0.002 PHE J 111 TYR 0.015 0.001 TYR M 337 ARG 0.011 0.000 ARG G 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 940 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 758 time to evaluate : 5.102 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: 0.7380 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: A 101 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7930 (ttm110) REVERT: A 198 LYS cc_start: 0.8188 (mmtm) cc_final: 0.7706 (mppt) REVERT: A 357 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7599 (tt) REVERT: B 15 ASP cc_start: 0.8450 (t70) cc_final: 0.8182 (t70) REVERT: B 71 MET cc_start: 0.8989 (mtm) cc_final: 0.8759 (mtp) REVERT: B 93 ASN cc_start: 0.8069 (t0) cc_final: 0.7750 (t0) REVERT: B 191 LYS cc_start: 0.8075 (ptpt) cc_final: 0.7782 (ptpp) REVERT: B 248 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8305 (mmm) REVERT: B 257 MET cc_start: 0.8797 (mmm) cc_final: 0.8329 (mmm) REVERT: D 71 MET cc_start: 0.9147 (mtm) cc_final: 0.8730 (mtm) REVERT: D 77 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: D 93 ASN cc_start: 0.8396 (m-40) cc_final: 0.7799 (m-40) REVERT: D 101 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7834 (ttm110) REVERT: D 125 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8452 (mt) REVERT: D 142 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6155 (pp-130) REVERT: D 195 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7853 (pttp) REVERT: D 198 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7793 (mppt) REVERT: E 12 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8089 (mp) REVERT: E 15 ASP cc_start: 0.8453 (t70) cc_final: 0.8225 (t0) REVERT: E 67 MET cc_start: 0.8537 (mmp) cc_final: 0.8317 (mmm) REVERT: E 93 ASN cc_start: 0.7872 (t0) cc_final: 0.7330 (t0) REVERT: E 198 LYS cc_start: 0.8691 (mmpt) cc_final: 0.8478 (mmtt) REVERT: E 359 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.5352 (mp0) REVERT: G 12 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8252 (tp) REVERT: G 67 MET cc_start: 0.8777 (mmm) cc_final: 0.8370 (mmm) REVERT: G 130 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: G 201 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7834 (mt) REVERT: G 271 MET cc_start: 0.7134 (mmm) cc_final: 0.6915 (mmp) REVERT: H 12 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8210 (tp) REVERT: H 50 MET cc_start: 0.8160 (mtm) cc_final: 0.7885 (mtt) REVERT: H 93 ASN cc_start: 0.8136 (t0) cc_final: 0.7596 (t0) REVERT: H 126 ASN cc_start: 0.8735 (m-40) cc_final: 0.8526 (m-40) REVERT: H 359 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.5024 (mp0) REVERT: J 12 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8159 (tp) REVERT: J 16 GLN cc_start: 0.8299 (tt0) cc_final: 0.7999 (tt0) REVERT: J 67 MET cc_start: 0.8769 (mmm) cc_final: 0.8492 (mmm) REVERT: J 123 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8044 (mp) REVERT: J 130 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: J 198 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8239 (mmpt) REVERT: J 248 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8692 (mmm) REVERT: J 334 MET cc_start: 0.8861 (ttp) cc_final: 0.8301 (ttt) REVERT: J 356 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6550 (mt0) REVERT: K 12 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8358 (tp) REVERT: K 93 ASN cc_start: 0.7972 (t0) cc_final: 0.7454 (t0) REVERT: K 142 MET cc_start: 0.5621 (OUTLIER) cc_final: 0.5354 (ptt) REVERT: K 191 LYS cc_start: 0.8302 (ptpt) cc_final: 0.7820 (pttp) REVERT: K 198 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8366 (mmpt) REVERT: K 201 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8121 (mt) REVERT: K 257 MET cc_start: 0.8629 (mmt) cc_final: 0.8339 (mmm) REVERT: K 282 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.6135 (tt0) REVERT: K 336 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7430 (pt0) REVERT: K 356 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6547 (mt0) REVERT: M 50 MET cc_start: 0.8769 (mtp) cc_final: 0.8531 (mtm) REVERT: M 338 ARG cc_start: 0.7480 (mtm180) cc_final: 0.7222 (mpp-170) REVERT: N 67 MET cc_start: 0.8562 (mmp) cc_final: 0.8173 (mmm) REVERT: N 71 MET cc_start: 0.9030 (mtm) cc_final: 0.8770 (mtp) REVERT: N 93 ASN cc_start: 0.8004 (t0) cc_final: 0.7638 (t0) REVERT: P 77 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: P 101 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7985 (ttm110) REVERT: P 110 LYS cc_start: 0.8067 (tmtm) cc_final: 0.7796 (tmtm) REVERT: P 198 LYS cc_start: 0.8208 (mmtm) cc_final: 0.7722 (mppt) REVERT: P 357 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7600 (tt) REVERT: Q 15 ASP cc_start: 0.8455 (t70) cc_final: 0.8189 (t70) REVERT: Q 71 MET cc_start: 0.8991 (mtm) cc_final: 0.8760 (mtp) REVERT: Q 93 ASN cc_start: 0.8054 (t0) cc_final: 0.7778 (t0) REVERT: Q 257 MET cc_start: 0.8799 (mmm) cc_final: 0.8337 (mmm) REVERT: S 71 MET cc_start: 0.9140 (mtm) cc_final: 0.8735 (mtm) REVERT: S 77 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: S 93 ASN cc_start: 0.8397 (m-40) cc_final: 0.8183 (m110) REVERT: S 101 ARG cc_start: 0.8217 (ttm110) cc_final: 0.7832 (ttm110) REVERT: S 125 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8474 (mt) REVERT: S 142 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6354 (pp-130) REVERT: S 195 LYS cc_start: 0.8086 (mtmm) cc_final: 0.7849 (pttp) REVERT: S 198 LYS cc_start: 0.8151 (mmtm) cc_final: 0.7842 (mppt) REVERT: T 12 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8093 (mp) REVERT: T 15 ASP cc_start: 0.8450 (t70) cc_final: 0.8236 (t0) REVERT: T 67 MET cc_start: 0.8544 (mmp) cc_final: 0.8212 (mmm) REVERT: T 198 LYS cc_start: 0.8693 (mmpt) cc_final: 0.8483 (mmtt) REVERT: T 359 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.5355 (mp0) REVERT: c 12 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8241 (tp) REVERT: c 67 MET cc_start: 0.8773 (mmm) cc_final: 0.8364 (mmm) REVERT: c 130 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: c 201 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7849 (mt) REVERT: d 50 MET cc_start: 0.8161 (mtm) cc_final: 0.7888 (mtt) REVERT: d 93 ASN cc_start: 0.8176 (t0) cc_final: 0.7853 (t0) REVERT: g 12 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8166 (tp) REVERT: g 16 GLN cc_start: 0.8299 (tt0) cc_final: 0.8006 (tt0) REVERT: g 67 MET cc_start: 0.8770 (mmm) cc_final: 0.8502 (mmm) REVERT: g 130 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: g 198 LYS cc_start: 0.8619 (tppp) cc_final: 0.8357 (mmpt) REVERT: g 248 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8718 (mmm) REVERT: g 334 MET cc_start: 0.8863 (ttp) cc_final: 0.8348 (ttt) REVERT: h 12 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8345 (tp) REVERT: h 33 ILE cc_start: 0.8631 (mm) cc_final: 0.8256 (mt) REVERT: h 93 ASN cc_start: 0.8110 (t0) cc_final: 0.7525 (t0) REVERT: h 142 MET cc_start: 0.5777 (OUTLIER) cc_final: 0.5464 (ptt) REVERT: h 191 LYS cc_start: 0.8294 (ptpt) cc_final: 0.7887 (pttp) REVERT: h 198 LYS cc_start: 0.8664 (mmtm) cc_final: 0.8343 (mmpt) REVERT: h 201 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8161 (mt) REVERT: h 282 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.6130 (tt0) REVERT: k 50 MET cc_start: 0.8774 (mtp) cc_final: 0.8538 (mtm) REVERT: l 67 MET cc_start: 0.8590 (mmp) cc_final: 0.8328 (mmm) REVERT: l 71 MET cc_start: 0.9061 (mtm) cc_final: 0.8776 (mtp) REVERT: l 84 ARG cc_start: 0.7887 (mpt-90) cc_final: 0.7685 (mpt-90) REVERT: l 93 ASN cc_start: 0.7963 (t0) cc_final: 0.7605 (t0) REVERT: l 119 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8021 (mt) REVERT: l 281 MET cc_start: 0.8364 (mmm) cc_final: 0.8096 (tpp) REVERT: l 282 GLU cc_start: 0.6362 (pm20) cc_final: 0.6158 (pm20) outliers start: 182 outliers final: 72 residues processed: 879 average time/residue: 1.7267 time to fit residues: 1869.0901 Evaluate side-chains 825 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 708 time to evaluate : 5.217 ------------------------------------------------------------------------------- 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 201 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 133 LYS 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 77 GLU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 122 GLU 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 310 SER Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 201 LEU 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 310 SER 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 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 123 ILE Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 198 LYS 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 120 THR Chi-restraints excluded: chain K residue 142 MET Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 282 GLU Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 356 GLN Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 363 ILE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 120 THR 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 357 LEU Chi-restraints excluded: chain P residue 363 ILE Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 133 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 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 310 SER Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 201 LEU 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 310 SER Chi-restraints excluded: chain c residue 316 GLN Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 201 LEU 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 248 MET Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain h residue 142 MET Chi-restraints excluded: chain h residue 201 LEU Chi-restraints excluded: chain h residue 282 GLU Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 363 ILE 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 316 GLN 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: 3.9990 chunk 80 optimal weight: 10.0000 chunk 404 optimal weight: 0.9980 chunk 518 optimal weight: 7.9990 chunk 401 optimal weight: 7.9990 chunk 597 optimal weight: 2.9990 chunk 396 optimal weight: 0.7980 chunk 707 optimal weight: 8.9990 chunk 442 optimal weight: 7.9990 chunk 431 optimal weight: 6.9990 chunk 326 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 D 356 GLN G 102 GLN J 102 GLN M 16 GLN M 102 GLN N 45 ASN ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 102 GLN P 192 ASN Q 45 ASN S 102 GLN S 192 ASN S 356 GLN c 102 GLN ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 16 GLN k 102 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2843 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= 0.314 Angle : 0.587 12.407 83440 Z= 0.308 Chirality : 0.043 0.185 9560 Planarity : 0.004 0.058 10240 Dihedral : 11.161 74.062 10210 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.99 % Allowed : 16.59 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.10), residues: 7340 helix: 1.20 (0.07), residues: 4760 sheet: 0.34 (0.20), residues: 460 loop : 0.49 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 260 HIS 0.011 0.001 HIS M 225 PHE 0.018 0.002 PHE J 111 TYR 0.019 0.002 TYR K 365 ARG 0.013 0.001 ARG c 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 895 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 711 time to evaluate : 5.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: A 101 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.8004 (ttm110) REVERT: A 195 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7876 (pttp) REVERT: A 198 LYS cc_start: 0.8248 (mmtm) cc_final: 0.7705 (mppt) REVERT: B 71 MET cc_start: 0.8946 (mtm) cc_final: 0.8697 (mtp) REVERT: B 93 ASN cc_start: 0.8063 (t0) cc_final: 0.7766 (t0) REVERT: B 191 LYS cc_start: 0.8114 (ptpt) cc_final: 0.7794 (ptpp) REVERT: B 248 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8271 (mmm) REVERT: B 257 MET cc_start: 0.8744 (mmm) cc_final: 0.8438 (mmm) REVERT: D 71 MET cc_start: 0.9154 (mtm) cc_final: 0.8750 (mtm) REVERT: D 77 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: D 110 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7825 (ttpm) REVERT: D 125 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8601 (mt) REVERT: D 142 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6288 (pp-130) REVERT: D 195 LYS cc_start: 0.8096 (mtmm) cc_final: 0.7878 (pttp) REVERT: D 198 LYS cc_start: 0.8151 (mmtm) cc_final: 0.7884 (mppt) REVERT: E 12 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7903 (mp) REVERT: E 15 ASP cc_start: 0.8557 (t70) cc_final: 0.8293 (t0) REVERT: E 93 ASN cc_start: 0.8066 (t0) cc_final: 0.7524 (t0) REVERT: E 359 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.5503 (mp0) REVERT: G 12 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8262 (tp) REVERT: G 67 MET cc_start: 0.8820 (mmm) cc_final: 0.8422 (mmm) REVERT: G 130 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: G 201 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8068 (mt) REVERT: H 12 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8206 (tp) REVERT: H 50 MET cc_start: 0.8231 (mtm) cc_final: 0.7962 (mtt) REVERT: H 93 ASN cc_start: 0.8141 (t0) cc_final: 0.7572 (t0) REVERT: H 126 ASN cc_start: 0.8733 (m-40) cc_final: 0.8517 (m-40) REVERT: H 359 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5570 (mp0) REVERT: J 12 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8156 (tp) REVERT: J 16 GLN cc_start: 0.8314 (tt0) cc_final: 0.8020 (tt0) REVERT: J 67 MET cc_start: 0.8815 (mmm) cc_final: 0.8454 (mmm) REVERT: J 123 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8052 (mp) REVERT: J 130 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: J 138 MET cc_start: 0.7574 (tmm) cc_final: 0.7332 (tmt) REVERT: J 198 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8220 (mmpt) REVERT: J 334 MET cc_start: 0.8847 (ttp) cc_final: 0.8250 (ttt) REVERT: J 338 ARG cc_start: 0.7709 (mpp-170) cc_final: 0.7485 (mtm110) REVERT: J 356 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6517 (mt0) REVERT: K 12 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8384 (tp) REVERT: K 93 ASN cc_start: 0.7997 (t0) cc_final: 0.7538 (t0) REVERT: K 142 MET cc_start: 0.5672 (OUTLIER) cc_final: 0.5407 (ptt) REVERT: K 191 LYS cc_start: 0.8312 (ptpt) cc_final: 0.7812 (pttp) REVERT: K 198 LYS cc_start: 0.8653 (mmtm) cc_final: 0.8318 (mmpt) REVERT: K 201 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8188 (mt) REVERT: K 336 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7482 (pt0) REVERT: K 356 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6594 (mt0) REVERT: M 50 MET cc_start: 0.8862 (mtp) cc_final: 0.8602 (mtm) REVERT: M 338 ARG cc_start: 0.7576 (mtm180) cc_final: 0.7313 (mpp-170) REVERT: N 67 MET cc_start: 0.8668 (mmp) cc_final: 0.8301 (mmm) REVERT: N 71 MET cc_start: 0.9028 (mtm) cc_final: 0.8757 (mtp) REVERT: N 93 ASN cc_start: 0.7938 (t0) cc_final: 0.7631 (t0) REVERT: N 101 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7950 (tpp-160) REVERT: N 133 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8218 (ptmt) REVERT: P 77 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: P 101 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.8008 (ttm110) REVERT: P 110 LYS cc_start: 0.8082 (tmtm) cc_final: 0.7807 (tmtm) REVERT: P 198 LYS cc_start: 0.8263 (mmtm) cc_final: 0.7714 (mppt) REVERT: Q 71 MET cc_start: 0.9001 (mtm) cc_final: 0.8768 (mtp) REVERT: Q 93 ASN cc_start: 0.7993 (t0) cc_final: 0.7680 (t0) REVERT: Q 257 MET cc_start: 0.8746 (mmm) cc_final: 0.8494 (mmm) REVERT: S 71 MET cc_start: 0.9146 (mtm) cc_final: 0.8750 (mtm) REVERT: S 77 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: S 101 ARG cc_start: 0.8286 (ttm110) cc_final: 0.7886 (ttm110) REVERT: S 110 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7696 (ttpm) REVERT: S 125 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8578 (mt) REVERT: S 142 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6154 (pp-130) REVERT: S 195 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7873 (pttp) REVERT: S 198 LYS cc_start: 0.8156 (mmtm) cc_final: 0.7883 (mppt) REVERT: T 12 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7908 (mp) REVERT: T 15 ASP cc_start: 0.8565 (t70) cc_final: 0.8295 (t0) REVERT: T 359 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.5502 (mp0) REVERT: c 12 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8267 (tp) REVERT: c 67 MET cc_start: 0.8820 (mmm) cc_final: 0.8411 (mmm) REVERT: c 130 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: c 201 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8068 (mt) REVERT: d 50 MET cc_start: 0.8234 (mtm) cc_final: 0.7964 (mtt) REVERT: d 93 ASN cc_start: 0.8198 (t0) cc_final: 0.7825 (t0) REVERT: d 359 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.5600 (mp0) REVERT: g 12 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8154 (tp) REVERT: g 16 GLN cc_start: 0.8312 (tt0) cc_final: 0.8009 (tt0) REVERT: g 67 MET cc_start: 0.8817 (mmm) cc_final: 0.8460 (mmm) REVERT: g 130 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: g 138 MET cc_start: 0.7598 (tmm) cc_final: 0.7356 (tmt) REVERT: g 198 LYS cc_start: 0.8686 (tppp) cc_final: 0.8258 (mmpt) REVERT: g 334 MET cc_start: 0.8862 (ttp) cc_final: 0.8298 (ttt) REVERT: g 338 ARG cc_start: 0.7724 (mpp-170) cc_final: 0.7502 (mtm110) REVERT: h 12 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8372 (tp) REVERT: h 93 ASN cc_start: 0.8102 (t0) cc_final: 0.7567 (t0) REVERT: h 142 MET cc_start: 0.5788 (OUTLIER) cc_final: 0.5493 (ptt) REVERT: h 191 LYS cc_start: 0.8401 (ptpt) cc_final: 0.7906 (pttp) REVERT: h 198 LYS cc_start: 0.8643 (mmtm) cc_final: 0.8272 (mmpt) REVERT: h 201 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8276 (mt) REVERT: h 257 MET cc_start: 0.8710 (mmt) cc_final: 0.8236 (mmm) REVERT: k 50 MET cc_start: 0.8861 (mtp) cc_final: 0.8633 (mtm) REVERT: k 195 LYS cc_start: 0.8100 (mtpm) cc_final: 0.7839 (pttm) REVERT: l 12 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8328 (mp) REVERT: l 67 MET cc_start: 0.8645 (mmp) cc_final: 0.8294 (mmm) REVERT: l 71 MET cc_start: 0.9040 (mtm) cc_final: 0.8753 (mtp) REVERT: l 93 ASN cc_start: 0.8027 (t0) cc_final: 0.7698 (t0) REVERT: l 119 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8108 (mt) REVERT: l 137 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8305 (ttpp) REVERT: l 282 GLU cc_start: 0.6546 (pm20) cc_final: 0.6329 (pm20) outliers start: 184 outliers final: 84 residues processed: 836 average time/residue: 1.6984 time to fit residues: 1757.6883 Evaluate side-chains 814 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 683 time to evaluate : 5.027 ------------------------------------------------------------------------------- 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 109 MET Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 133 LYS 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 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 122 GLU 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 310 SER Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 201 LEU 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 129 ILE 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 191 LYS Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 310 SER 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 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 123 ILE Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 198 LYS 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 120 THR Chi-restraints excluded: chain K residue 142 MET Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 356 GLN Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 363 ILE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 101 ARG Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 201 LEU 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 109 MET Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 363 ILE Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 133 LYS 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 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 310 SER Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 201 LEU 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 129 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 c residue 191 LYS Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 310 SER Chi-restraints excluded: chain c residue 316 GLN Chi-restraints excluded: chain d residue 12 LEU 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 248 MET Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain h residue 142 MET Chi-restraints excluded: chain h residue 201 LEU Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 363 ILE Chi-restraints excluded: chain l residue 12 LEU 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 316 GLN 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: 0.8980 chunk 282 optimal weight: 2.9990 chunk 422 optimal weight: 8.9990 chunk 213 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 449 optimal weight: 0.8980 chunk 481 optimal weight: 0.9990 chunk 349 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 556 optimal weight: 0.0470 overall best weight: 0.6880 ------------------------------------------------------------------------------- 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 102 GLN J 102 GLN ** K 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN M 102 GLN N 45 ASN ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 102 GLN P 192 ASN Q 45 ASN S 102 GLN S 192 ASN c 102 GLN ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 16 GLN k 102 GLN l 45 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 61510 Z= 0.144 Angle : 0.507 11.271 83440 Z= 0.264 Chirality : 0.039 0.176 9560 Planarity : 0.003 0.055 10240 Dihedral : 11.009 73.649 10210 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.27 % Allowed : 17.76 % Favored : 79.97 % 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: 1.79 (0.10), residues: 7340 helix: 1.62 (0.08), residues: 4740 sheet: 0.32 (0.21), residues: 440 loop : 0.59 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 260 HIS 0.005 0.001 HIS c 225 PHE 0.012 0.001 PHE J 111 TYR 0.015 0.001 TYR M 337 ARG 0.013 0.000 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 877 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 737 time to evaluate : 5.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6784 (mp0) REVERT: A 101 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7912 (ttm110) REVERT: A 198 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7691 (mppt) REVERT: B 15 ASP cc_start: 0.8287 (t70) cc_final: 0.8044 (t70) REVERT: B 71 MET cc_start: 0.9006 (mtm) cc_final: 0.8772 (mtp) REVERT: B 89 HIS cc_start: 0.7214 (t70) cc_final: 0.6731 (t-90) REVERT: B 93 ASN cc_start: 0.7915 (t0) cc_final: 0.7598 (t0) REVERT: B 248 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8373 (mmm) REVERT: B 257 MET cc_start: 0.8790 (mmm) cc_final: 0.8327 (mmm) REVERT: D 71 MET cc_start: 0.9091 (mtm) cc_final: 0.8765 (mtm) REVERT: D 110 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7718 (ttpm) REVERT: D 125 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8402 (mt) REVERT: D 142 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6276 (pp-130) REVERT: D 195 LYS cc_start: 0.8090 (mtmm) cc_final: 0.7847 (pttp) REVERT: D 198 LYS cc_start: 0.8039 (mmtm) cc_final: 0.7830 (mppt) REVERT: D 310 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7971 (t) REVERT: E 12 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8049 (mp) REVERT: E 15 ASP cc_start: 0.8323 (t70) cc_final: 0.8108 (t70) REVERT: E 93 ASN cc_start: 0.7900 (t0) cc_final: 0.7361 (t0) REVERT: E 359 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.5385 (mp0) REVERT: G 46 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8005 (mtmm) REVERT: G 67 MET cc_start: 0.8761 (mmm) cc_final: 0.8366 (mmm) REVERT: G 91 LYS cc_start: 0.7296 (tmtm) cc_final: 0.6851 (tmtm) REVERT: G 130 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: G 201 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7735 (mt) REVERT: G 334 MET cc_start: 0.8887 (ttp) cc_final: 0.8592 (ttp) REVERT: H 12 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8210 (tp) REVERT: H 50 MET cc_start: 0.8184 (mtm) cc_final: 0.7906 (mtt) REVERT: H 93 ASN cc_start: 0.8170 (t0) cc_final: 0.7722 (t0) REVERT: H 126 ASN cc_start: 0.8722 (m-40) cc_final: 0.8498 (m-40) REVERT: J 16 GLN cc_start: 0.8288 (tt0) cc_final: 0.7916 (tt0) REVERT: J 67 MET cc_start: 0.8756 (mmm) cc_final: 0.8482 (mmm) REVERT: J 123 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8113 (mp) REVERT: J 130 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: J 198 LYS cc_start: 0.8521 (tppp) cc_final: 0.8237 (mmpt) REVERT: J 334 MET cc_start: 0.8814 (ttp) cc_final: 0.8293 (ttt) REVERT: J 356 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6503 (mt0) REVERT: K 93 ASN cc_start: 0.7857 (t0) cc_final: 0.7468 (t0) REVERT: K 142 MET cc_start: 0.5679 (OUTLIER) cc_final: 0.5447 (ptt) REVERT: K 191 LYS cc_start: 0.8275 (ptpt) cc_final: 0.7899 (pttp) REVERT: K 198 LYS cc_start: 0.8653 (mmtm) cc_final: 0.8316 (mmpt) REVERT: K 201 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8087 (mt) REVERT: M 50 MET cc_start: 0.8733 (mtp) cc_final: 0.8508 (mtm) REVERT: M 338 ARG cc_start: 0.7445 (mtm180) cc_final: 0.7186 (mpp-170) REVERT: N 67 MET cc_start: 0.8577 (mmp) cc_final: 0.8280 (mmm) REVERT: N 71 MET cc_start: 0.9050 (mtm) cc_final: 0.8813 (mtp) REVERT: N 93 ASN cc_start: 0.7889 (t0) cc_final: 0.7645 (t0) REVERT: N 101 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7111 (tpp-160) REVERT: N 142 MET cc_start: 0.5247 (pp-130) cc_final: 0.4970 (tmm) REVERT: P 77 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: P 132 ARG cc_start: 0.7482 (mtm-85) cc_final: 0.7250 (mtm-85) REVERT: P 198 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7743 (mppt) REVERT: Q 15 ASP cc_start: 0.8292 (t70) cc_final: 0.8051 (t70) REVERT: Q 71 MET cc_start: 0.9001 (mtm) cc_final: 0.8742 (mtp) REVERT: Q 89 HIS cc_start: 0.7213 (t70) cc_final: 0.6741 (t-90) REVERT: Q 93 ASN cc_start: 0.7908 (t0) cc_final: 0.7644 (t0) REVERT: Q 257 MET cc_start: 0.8790 (mmm) cc_final: 0.8337 (mmm) REVERT: S 71 MET cc_start: 0.9083 (mtm) cc_final: 0.8771 (mtm) REVERT: S 101 ARG cc_start: 0.8218 (ttm110) cc_final: 0.7823 (ttm110) REVERT: S 110 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7584 (ttpm) REVERT: S 125 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8427 (mt) REVERT: S 142 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.6426 (pp-130) REVERT: S 195 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7844 (pttp) REVERT: S 198 LYS cc_start: 0.8046 (mmtm) cc_final: 0.7845 (mppt) REVERT: S 310 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7975 (t) REVERT: S 334 MET cc_start: 0.8788 (ttp) cc_final: 0.8238 (ttt) REVERT: T 12 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8072 (mp) REVERT: T 15 ASP cc_start: 0.8321 (t70) cc_final: 0.8103 (t70) REVERT: T 359 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5379 (mp0) REVERT: c 46 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8000 (mtmm) REVERT: c 67 MET cc_start: 0.8757 (mmm) cc_final: 0.8354 (mmm) REVERT: c 91 LYS cc_start: 0.7226 (tmtm) cc_final: 0.6787 (tmtm) REVERT: c 130 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: c 201 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7731 (mt) REVERT: c 334 MET cc_start: 0.8900 (ttp) cc_final: 0.8604 (ttp) REVERT: d 50 MET cc_start: 0.8186 (mtm) cc_final: 0.7908 (mtt) REVERT: d 93 ASN cc_start: 0.8229 (t0) cc_final: 0.7932 (t0) REVERT: g 16 GLN cc_start: 0.8296 (tt0) cc_final: 0.7926 (tt0) REVERT: g 67 MET cc_start: 0.8757 (mmm) cc_final: 0.8492 (mmm) REVERT: g 101 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8078 (ttm110) REVERT: g 130 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: g 198 LYS cc_start: 0.8493 (tppp) cc_final: 0.8270 (mmpt) REVERT: g 334 MET cc_start: 0.8851 (ttp) cc_final: 0.8289 (ttt) REVERT: h 93 ASN cc_start: 0.7932 (t0) cc_final: 0.7476 (t0) REVERT: h 191 LYS cc_start: 0.8264 (ptpt) cc_final: 0.7885 (pttp) REVERT: h 198 LYS cc_start: 0.8660 (mmtm) cc_final: 0.8322 (mmpt) REVERT: k 50 MET cc_start: 0.8738 (mtp) cc_final: 0.8522 (mtm) REVERT: k 195 LYS cc_start: 0.8115 (mtpm) cc_final: 0.7906 (pttm) REVERT: l 67 MET cc_start: 0.8548 (mmp) cc_final: 0.8342 (mmm) REVERT: l 71 MET cc_start: 0.9063 (mtm) cc_final: 0.8838 (mtp) REVERT: l 93 ASN cc_start: 0.7940 (t0) cc_final: 0.7690 (t0) REVERT: l 119 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8019 (mt) REVERT: l 142 MET cc_start: 0.5224 (pp-130) cc_final: 0.4946 (tmm) outliers start: 140 outliers final: 51 residues processed: 829 average time/residue: 1.7215 time to fit residues: 1762.6769 Evaluate side-chains 795 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 712 time to evaluate : 5.087 ------------------------------------------------------------------------------- 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 109 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 133 LYS 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 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 310 SER Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 362 VAL 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 310 SER Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain H residue 12 LEU 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 123 ILE Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 356 GLN Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 125 ILE Chi-restraints excluded: chain K residue 142 MET Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain N residue 89 HIS Chi-restraints excluded: chain N residue 101 ARG 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 101 ARG Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 133 LYS 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 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 310 SER Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 359 GLU Chi-restraints excluded: chain T residue 362 VAL 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 310 SER Chi-restraints excluded: chain c residue 316 GLN Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain g residue 32 SER Chi-restraints excluded: chain g residue 101 ARG Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain k residue 109 MET 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: 0.0670 chunk 677 optimal weight: 2.9990 chunk 618 optimal weight: 1.9990 chunk 659 optimal weight: 3.9990 chunk 396 optimal weight: 1.9990 chunk 287 optimal weight: 5.9990 chunk 517 optimal weight: 0.9980 chunk 202 optimal weight: 0.1980 chunk 595 optimal weight: 0.9980 chunk 623 optimal weight: 0.9980 chunk 656 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 192 ASN D 93 ASN D 102 GLN D 192 ASN ** E 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 192 ASN J 45 ASN J 102 GLN ** K 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN M 102 GLN ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 ASN P 102 GLN P 151 HIS P 192 ASN S 93 ASN S 102 GLN S 192 ASN c 102 GLN c 192 ASN g 45 ASN ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 16 GLN k 102 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 61510 Z= 0.141 Angle : 0.509 10.839 83440 Z= 0.264 Chirality : 0.038 0.167 9560 Planarity : 0.003 0.058 10240 Dihedral : 10.922 73.668 10210 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.09 % Allowed : 18.38 % Favored : 79.53 % 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: 1.97 (0.10), residues: 7340 helix: 1.78 (0.08), residues: 4740 sheet: 0.30 (0.21), residues: 440 loop : 0.66 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 260 HIS 0.005 0.001 HIS k 225 PHE 0.013 0.001 PHE J 111 TYR 0.015 0.001 TYR S 135 ARG 0.014 0.000 ARG c 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 871 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 742 time to evaluate : 5.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: A 93 ASN cc_start: 0.8207 (m-40) cc_final: 0.7845 (m-40) REVERT: A 198 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7720 (mppt) REVERT: A 357 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7256 (tt) REVERT: B 15 ASP cc_start: 0.8268 (t70) cc_final: 0.8028 (t70) REVERT: B 71 MET cc_start: 0.9004 (mtm) cc_final: 0.8781 (mtp) REVERT: B 89 HIS cc_start: 0.7217 (t70) cc_final: 0.6768 (t-90) REVERT: B 93 ASN cc_start: 0.7841 (t0) cc_final: 0.7553 (t0) REVERT: B 248 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8359 (mmm) REVERT: B 257 MET cc_start: 0.8761 (mmm) cc_final: 0.8298 (mmm) REVERT: D 71 MET cc_start: 0.9095 (mtm) cc_final: 0.8713 (mtm) REVERT: D 93 ASN cc_start: 0.8431 (m-40) cc_final: 0.8015 (m-40) REVERT: D 110 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7729 (ttpm) REVERT: D 125 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8398 (mt) REVERT: D 138 MET cc_start: 0.7447 (tmm) cc_final: 0.7179 (tmt) REVERT: D 142 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6421 (pp-130) REVERT: D 195 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7860 (pttp) REVERT: D 257 MET cc_start: 0.8247 (mmt) cc_final: 0.7979 (mmm) REVERT: D 310 SER cc_start: 0.8207 (OUTLIER) cc_final: 0.7986 (t) REVERT: D 334 MET cc_start: 0.8774 (ttp) cc_final: 0.8239 (ttt) REVERT: E 12 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8057 (mp) REVERT: E 93 ASN cc_start: 0.7763 (t0) cc_final: 0.7240 (t0) REVERT: E 359 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5318 (mp0) REVERT: G 46 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8027 (mtmm) REVERT: G 67 MET cc_start: 0.8743 (mmm) cc_final: 0.8341 (mmm) REVERT: G 91 LYS cc_start: 0.7197 (tmtm) cc_final: 0.6605 (tmtm) REVERT: G 93 ASN cc_start: 0.8116 (m-40) cc_final: 0.7727 (m-40) REVERT: G 130 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: G 201 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7712 (mt) REVERT: G 334 MET cc_start: 0.8852 (ttp) cc_final: 0.8550 (ttp) REVERT: H 12 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8199 (tp) REVERT: H 50 MET cc_start: 0.8192 (mtm) cc_final: 0.7897 (mtt) REVERT: H 93 ASN cc_start: 0.8129 (t0) cc_final: 0.7727 (t0) REVERT: H 126 ASN cc_start: 0.8784 (m-40) cc_final: 0.8554 (m-40) REVERT: J 16 GLN cc_start: 0.8231 (tt0) cc_final: 0.7951 (tt0) REVERT: J 67 MET cc_start: 0.8747 (mmm) cc_final: 0.8446 (mmm) REVERT: J 123 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8174 (mp) REVERT: J 130 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: J 198 LYS cc_start: 0.8374 (tppp) cc_final: 0.8159 (mmpt) REVERT: J 201 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7691 (mt) REVERT: J 334 MET cc_start: 0.8799 (ttp) cc_final: 0.8343 (ttt) REVERT: J 356 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6600 (mt0) REVERT: K 12 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8425 (tp) REVERT: K 93 ASN cc_start: 0.7800 (t0) cc_final: 0.7421 (t0) REVERT: K 191 LYS cc_start: 0.8389 (ptpt) cc_final: 0.8047 (pttp) REVERT: K 198 LYS cc_start: 0.8637 (mmtm) cc_final: 0.8300 (mmpt) REVERT: K 201 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8070 (mt) REVERT: M 50 MET cc_start: 0.8731 (mtp) cc_final: 0.8486 (mtm) REVERT: M 142 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7078 (ptt) REVERT: M 338 ARG cc_start: 0.7427 (mtm180) cc_final: 0.7167 (mpp-170) REVERT: N 67 MET cc_start: 0.8606 (mmp) cc_final: 0.8302 (mmm) REVERT: N 71 MET cc_start: 0.9008 (mtm) cc_final: 0.8754 (mtp) REVERT: N 93 ASN cc_start: 0.7825 (t0) cc_final: 0.7580 (t0) REVERT: N 110 LYS cc_start: 0.8272 (tppp) cc_final: 0.7614 (tppp) REVERT: P 77 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: P 101 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7922 (ttm110) REVERT: P 110 LYS cc_start: 0.8128 (tttm) cc_final: 0.7727 (tttp) REVERT: P 198 LYS cc_start: 0.8122 (mmtm) cc_final: 0.7749 (mppt) REVERT: P 357 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7284 (tt) REVERT: Q 15 ASP cc_start: 0.8269 (t70) cc_final: 0.8035 (t70) REVERT: Q 71 MET cc_start: 0.9038 (mtm) cc_final: 0.8781 (mtp) REVERT: Q 89 HIS cc_start: 0.7212 (t70) cc_final: 0.6760 (t-90) REVERT: Q 93 ASN cc_start: 0.7898 (t0) cc_final: 0.7641 (t0) REVERT: Q 257 MET cc_start: 0.8758 (mmm) cc_final: 0.8307 (mmm) REVERT: S 71 MET cc_start: 0.9089 (mtm) cc_final: 0.8692 (mtm) REVERT: S 93 ASN cc_start: 0.8403 (m-40) cc_final: 0.8027 (m-40) REVERT: S 101 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7820 (ttm110) REVERT: S 110 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7593 (ttpm) REVERT: S 125 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8407 (mt) REVERT: S 138 MET cc_start: 0.7419 (tmm) cc_final: 0.7104 (tmt) REVERT: S 142 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6487 (pp-130) REVERT: S 257 MET cc_start: 0.8250 (mmt) cc_final: 0.7986 (mmm) REVERT: S 310 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7989 (t) REVERT: T 12 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8095 (mp) REVERT: T 359 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.5373 (mp0) REVERT: c 46 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8027 (mtmm) REVERT: c 67 MET cc_start: 0.8742 (mmm) cc_final: 0.8333 (mmm) REVERT: c 91 LYS cc_start: 0.7219 (tmtm) cc_final: 0.6583 (tmtm) REVERT: c 93 ASN cc_start: 0.8237 (m-40) cc_final: 0.7803 (m-40) REVERT: c 130 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: c 201 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7710 (mt) REVERT: c 334 MET cc_start: 0.8863 (ttp) cc_final: 0.8560 (ttp) REVERT: d 50 MET cc_start: 0.8193 (mtm) cc_final: 0.7898 (mtt) REVERT: d 93 ASN cc_start: 0.8181 (t0) cc_final: 0.7956 (t0) REVERT: g 16 GLN cc_start: 0.8248 (tt0) cc_final: 0.7977 (tt0) REVERT: g 67 MET cc_start: 0.8748 (mmm) cc_final: 0.8450 (mmm) REVERT: g 101 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.8023 (ttm110) REVERT: g 130 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: g 198 LYS cc_start: 0.8444 (tppp) cc_final: 0.8235 (mmpt) REVERT: h 12 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8395 (tp) REVERT: h 93 ASN cc_start: 0.7853 (t0) cc_final: 0.7453 (t0) REVERT: h 191 LYS cc_start: 0.8373 (ptpt) cc_final: 0.8031 (pttp) REVERT: h 198 LYS cc_start: 0.8649 (mmtm) cc_final: 0.8315 (mmpt) REVERT: h 201 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8113 (mt) REVERT: k 50 MET cc_start: 0.8737 (mtp) cc_final: 0.8501 (mtm) REVERT: k 195 LYS cc_start: 0.8036 (mtpm) cc_final: 0.7825 (pttm) REVERT: l 55 GLU cc_start: 0.8123 (tp30) cc_final: 0.7921 (tp30) REVERT: l 67 MET cc_start: 0.8553 (mmp) cc_final: 0.8246 (mmm) REVERT: l 71 MET cc_start: 0.9079 (mtm) cc_final: 0.8836 (mtp) REVERT: l 119 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8043 (mt) outliers start: 129 outliers final: 49 residues processed: 830 average time/residue: 1.6885 time to fit residues: 1733.6463 Evaluate side-chains 790 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 704 time to evaluate : 5.103 ------------------------------------------------------------------------------- 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 109 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 357 LEU 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 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 310 SER Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 362 VAL 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 310 SER Chi-restraints excluded: chain H residue 12 LEU 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 123 ILE Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 356 GLN Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 125 ILE Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain M residue 142 MET Chi-restraints excluded: chain M residue 248 MET Chi-restraints excluded: chain N residue 89 HIS 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 357 LEU 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 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 310 SER Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 359 GLU Chi-restraints excluded: chain T residue 362 VAL 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 310 SER Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain g residue 32 SER Chi-restraints excluded: chain g residue 101 ARG Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain h residue 201 LEU Chi-restraints excluded: chain k residue 109 MET Chi-restraints excluded: chain l residue 89 HIS 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: 0.9990 chunk 697 optimal weight: 4.9990 chunk 425 optimal weight: 7.9990 chunk 330 optimal weight: 3.9990 chunk 484 optimal weight: 7.9990 chunk 731 optimal weight: 6.9990 chunk 673 optimal weight: 0.9980 chunk 582 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 449 optimal weight: 4.9990 chunk 357 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 G 192 ASN J 45 ASN J 102 GLN M 16 GLN M 102 GLN N 100 HIS ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 ASN P 102 GLN P 192 ASN S 102 GLN S 192 ASN c 102 GLN g 45 ASN ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 26 GLN ** h 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 16 GLN k 102 GLN k 192 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 61510 Z= 0.221 Angle : 0.553 11.377 83440 Z= 0.287 Chirality : 0.041 0.172 9560 Planarity : 0.003 0.037 10240 Dihedral : 10.958 73.895 10210 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.14 % Allowed : 18.39 % Favored : 79.46 % 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: 1.77 (0.10), residues: 7340 helix: 1.60 (0.08), residues: 4740 sheet: 0.29 (0.21), residues: 440 loop : 0.63 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 260 HIS 0.008 0.001 HIS M 225 PHE 0.018 0.002 PHE J 111 TYR 0.014 0.001 TYR K 365 ARG 0.008 0.000 ARG c 338 ********************** 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 831 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 699 time to evaluate : 5.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: A 195 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7859 (pttp) REVERT: A 198 LYS cc_start: 0.8165 (mmtm) cc_final: 0.7772 (mppt) REVERT: B 15 ASP cc_start: 0.8352 (t70) cc_final: 0.8086 (t70) REVERT: B 71 MET cc_start: 0.8989 (mtm) cc_final: 0.8734 (mtp) REVERT: B 89 HIS cc_start: 0.7221 (t70) cc_final: 0.6752 (t-90) REVERT: B 93 ASN cc_start: 0.7903 (t0) cc_final: 0.7576 (t0) REVERT: B 248 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8268 (mmm) REVERT: B 257 MET cc_start: 0.8787 (mmm) cc_final: 0.8340 (mmm) REVERT: D 71 MET cc_start: 0.9106 (mtm) cc_final: 0.8717 (mtm) REVERT: D 93 ASN cc_start: 0.8444 (m-40) cc_final: 0.8016 (m-40) REVERT: D 110 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7730 (ttpm) REVERT: D 125 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8536 (mt) REVERT: D 142 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.6371 (pp-130) REVERT: D 195 LYS cc_start: 0.8142 (mtmm) cc_final: 0.7924 (pttp) REVERT: E 12 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8087 (mp) REVERT: E 93 ASN cc_start: 0.7853 (t0) cc_final: 0.7291 (t0) REVERT: E 132 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.8104 (mtm-85) REVERT: E 359 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5345 (mp0) REVERT: G 46 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8017 (mtmm) REVERT: G 67 MET cc_start: 0.8763 (mmm) cc_final: 0.8395 (mmm) REVERT: G 130 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: G 138 MET cc_start: 0.7435 (tmm) cc_final: 0.7050 (tmt) REVERT: G 201 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7892 (mt) REVERT: H 12 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8188 (tp) REVERT: H 50 MET cc_start: 0.8224 (mtm) cc_final: 0.7948 (mtt) REVERT: H 93 ASN cc_start: 0.8186 (t0) cc_final: 0.7733 (t0) REVERT: H 126 ASN cc_start: 0.8778 (m-40) cc_final: 0.8516 (m-40) REVERT: H 359 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5548 (mp0) REVERT: J 16 GLN cc_start: 0.8257 (tt0) cc_final: 0.7976 (tt0) REVERT: J 67 MET cc_start: 0.8792 (mmm) cc_final: 0.8411 (mmm) REVERT: J 123 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8125 (mp) REVERT: J 130 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: J 138 MET cc_start: 0.7445 (tmm) cc_final: 0.7164 (tmt) REVERT: J 198 LYS cc_start: 0.8552 (tppp) cc_final: 0.8251 (mmpt) REVERT: J 201 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7850 (mt) REVERT: J 334 MET cc_start: 0.8802 (ttp) cc_final: 0.8177 (ttt) REVERT: J 356 GLN cc_start: 0.6847 (OUTLIER) cc_final: 0.6585 (mt0) REVERT: K 12 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8442 (tp) REVERT: K 93 ASN cc_start: 0.7857 (t0) cc_final: 0.7496 (t0) REVERT: K 191 LYS cc_start: 0.8397 (ptpt) cc_final: 0.8034 (pttp) REVERT: K 198 LYS cc_start: 0.8648 (mmtm) cc_final: 0.8317 (mmpt) REVERT: K 201 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8125 (mt) REVERT: M 50 MET cc_start: 0.8808 (mtp) cc_final: 0.8582 (mtm) REVERT: M 338 ARG cc_start: 0.7505 (mtm180) cc_final: 0.7260 (mpp-170) REVERT: N 67 MET cc_start: 0.8670 (mmp) cc_final: 0.8238 (mmm) REVERT: N 71 MET cc_start: 0.9055 (mtm) cc_final: 0.8761 (mtp) REVERT: N 93 ASN cc_start: 0.7833 (t0) cc_final: 0.7562 (t0) REVERT: P 77 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: P 101 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7959 (ttm110) REVERT: P 138 MET cc_start: 0.7531 (tmm) cc_final: 0.7218 (tmt) REVERT: P 195 LYS cc_start: 0.8183 (mtpm) cc_final: 0.7795 (pttp) REVERT: P 198 LYS cc_start: 0.8194 (mmtm) cc_final: 0.7798 (mppt) REVERT: Q 15 ASP cc_start: 0.8355 (t70) cc_final: 0.8092 (t70) REVERT: Q 71 MET cc_start: 0.8968 (mtm) cc_final: 0.8700 (mtp) REVERT: Q 89 HIS cc_start: 0.7244 (t70) cc_final: 0.6774 (t-90) REVERT: Q 93 ASN cc_start: 0.7885 (t0) cc_final: 0.7577 (t0) REVERT: Q 257 MET cc_start: 0.8792 (mmm) cc_final: 0.8345 (mmm) REVERT: S 71 MET cc_start: 0.9097 (mtm) cc_final: 0.8722 (mtm) REVERT: S 93 ASN cc_start: 0.8410 (m-40) cc_final: 0.8101 (m-40) REVERT: S 110 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7627 (ttpm) REVERT: S 125 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8519 (mt) REVERT: S 142 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6318 (pp-130) REVERT: T 12 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8133 (mp) REVERT: T 132 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.8114 (mtm-85) REVERT: T 359 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.5449 (mp0) REVERT: c 67 MET cc_start: 0.8761 (mmm) cc_final: 0.8387 (mmm) REVERT: c 130 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: c 138 MET cc_start: 0.7428 (tmm) cc_final: 0.7043 (tmt) REVERT: c 201 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7890 (mt) REVERT: d 50 MET cc_start: 0.8220 (mtm) cc_final: 0.7946 (mtt) REVERT: d 93 ASN cc_start: 0.8223 (t0) cc_final: 0.7930 (t0) REVERT: d 359 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.5653 (mp0) REVERT: g 16 GLN cc_start: 0.8262 (tt0) cc_final: 0.7982 (tt0) REVERT: g 67 MET cc_start: 0.8790 (mmm) cc_final: 0.8413 (mmm) REVERT: g 130 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: g 138 MET cc_start: 0.7405 (tmm) cc_final: 0.7047 (tmt) REVERT: g 198 LYS cc_start: 0.8571 (tppp) cc_final: 0.8220 (mmpt) REVERT: g 201 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7871 (mt) REVERT: g 334 MET cc_start: 0.8660 (ttp) cc_final: 0.8243 (ttt) REVERT: h 12 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8429 (tp) REVERT: h 93 ASN cc_start: 0.7885 (t0) cc_final: 0.7507 (t0) REVERT: h 191 LYS cc_start: 0.8378 (ptpt) cc_final: 0.8017 (pttp) REVERT: h 198 LYS cc_start: 0.8653 (mmtm) cc_final: 0.8290 (mmpt) REVERT: h 201 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8141 (mt) REVERT: k 50 MET cc_start: 0.8809 (mtp) cc_final: 0.8588 (mtm) REVERT: k 138 MET cc_start: 0.7155 (tmm) cc_final: 0.6882 (tmt) REVERT: l 67 MET cc_start: 0.8648 (mmp) cc_final: 0.8234 (mmm) REVERT: l 71 MET cc_start: 0.9059 (mtm) cc_final: 0.8781 (mtp) REVERT: l 110 LYS cc_start: 0.8546 (mmmm) cc_final: 0.8231 (tppp) REVERT: l 119 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8049 (mt) outliers start: 132 outliers final: 66 residues processed: 791 average time/residue: 1.7075 time to fit residues: 1671.1645 Evaluate side-chains 791 residues out of total 6160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 691 time to evaluate : 5.428 ------------------------------------------------------------------------------- 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 195 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 39 ASP 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 310 SER Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 362 VAL 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 310 SER Chi-restraints excluded: chain H residue 12 LEU 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 123 ILE Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 201 LEU 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 120 THR Chi-restraints excluded: chain K residue 125 ILE 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 89 HIS Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 248 MET 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 109 MET Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 310 SER Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 316 GLN 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 310 SER Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 56 ASP Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 359 GLU Chi-restraints excluded: chain T residue 362 VAL Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 130 GLU 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 201 LEU Chi-restraints excluded: chain c residue 310 SER 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 32 SER Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain h residue 201 LEU Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 109 MET Chi-restraints excluded: chain k residue 248 MET Chi-restraints excluded: chain l residue 89 HIS 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 248 MET Chi-restraints excluded: chain l residue 316 GLN 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: 0.7980 chunk 620 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 536 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 583 optimal weight: 1.9990 chunk 244 optimal weight: 0.3980 chunk 598 optimal weight: 0.0870 chunk 73 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 G 192 ASN ** H 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN J 102 GLN M 16 GLN M 102 GLN ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 ASN P 102 GLN P 151 HIS P 192 ASN S 102 GLN S 192 ASN ** T 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 102 GLN ** d 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 45 ASN ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 16 GLN k 102 GLN k 192 ASN ** l 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.159243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121214 restraints weight = 67072.464| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.43 r_work: 0.3265 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 61510 Z= 0.137 Angle : 0.512 10.912 83440 Z= 0.266 Chirality : 0.038 0.179 9560 Planarity : 0.003 0.050 10240 Dihedral : 10.912 73.650 10210 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.82 % Allowed : 18.91 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.10), residues: 7340 helix: 1.80 (0.08), residues: 4740 sheet: 0.20 (0.21), residues: 440 loop : 0.71 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP k 260 HIS 0.005 0.001 HIS G 225 PHE 0.012 0.001 PHE g 111 TYR 0.018 0.001 TYR S 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: 26224.07 seconds wall clock time: 448 minutes 7.10 seconds (26887.10 seconds total)