Starting phenix.real_space_refine on Mon Dec 30 00:00:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8op2_17038/12_2024/8op2_17038.cif Found real_map, /net/cci-nas-00/data/ceres_data/8op2_17038/12_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/cci-nas-00/data/ceres_data/8op2_17038/12_2024/8op2_17038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8op2_17038/12_2024/8op2_17038.map" model { file = "/net/cci-nas-00/data/ceres_data/8op2_17038/12_2024/8op2_17038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8op2_17038/12_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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 24.53, per 1000 atoms: 0.41 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: 10.95 Conformation dependent library (CDL) restraints added in 5.9 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: 15.13 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: 23.11 Time building geometry restraints manager: 13.09 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: 5.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 1.650 Check model and map are aligned: 0.330 Set scattering table: 0.420 Process input model: 110.550 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.820 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 320 poor density : 1153 time to evaluate : 4.917 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: 1.7338 time to fit residues: 2769.0863 Evaluate side-chains 773 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 732 time to evaluate : 4.996 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 200 poor density : 890 time to evaluate : 5.165 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: 1.6984 time to fit residues: 2050.6722 Evaluate side-chains 816 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 746 time to evaluate : 4.883 ------------------------------------------------------------------------------- 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: 0.5980 chunk 453 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 667 optimal weight: 5.9990 chunk 721 optimal weight: 10.0000 chunk 594 optimal weight: 4.9990 chunk 662 optimal weight: 0.9980 chunk 227 optimal weight: 0.5980 chunk 535 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 ** H 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 ** d 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 61510 Z= 0.221 Angle : 0.530 5.842 83440 Z= 0.284 Chirality : 0.041 0.173 9560 Planarity : 0.003 0.034 10240 Dihedral : 11.166 73.859 10214 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.00 % Allowed : 12.66 % Favored : 84.33 % 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: 1.52 (0.10), residues: 7340 helix: 1.41 (0.08), residues: 4760 sheet: 0.65 (0.20), residues: 500 loop : 0.36 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP c 260 HIS 0.007 0.001 HIS c 225 PHE 0.012 0.002 PHE g 226 TYR 0.018 0.001 TYR J 135 ARG 0.009 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 998 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 813 time to evaluate : 5.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: A 195 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7771 (pttp) REVERT: A 198 LYS cc_start: 0.8233 (mmtm) cc_final: 0.7277 (mppt) REVERT: A 356 GLN cc_start: 0.6361 (OUTLIER) cc_final: 0.6113 (mt0) REVERT: B 15 ASP cc_start: 0.8529 (t70) cc_final: 0.8163 (t70) REVERT: B 71 MET cc_start: 0.9027 (mtm) cc_final: 0.8778 (mtp) REVERT: B 93 ASN cc_start: 0.8071 (t0) cc_final: 0.7819 (t0) REVERT: B 110 LYS cc_start: 0.8559 (mtpp) cc_final: 0.8357 (mtpp) REVERT: B 191 LYS cc_start: 0.8102 (ptpt) cc_final: 0.7844 (ptpp) REVERT: B 248 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8287 (mmm) REVERT: B 257 MET cc_start: 0.8796 (mmm) cc_final: 0.8376 (mmm) REVERT: D 24 THR cc_start: 0.8661 (p) cc_final: 0.8458 (p) REVERT: D 71 MET cc_start: 0.9159 (mtm) cc_final: 0.8811 (mtm) REVERT: D 112 GLU cc_start: 0.7171 (tt0) cc_final: 0.6952 (mt-10) REVERT: D 142 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6172 (tmm) REVERT: D 195 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7848 (pttm) REVERT: D 198 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7578 (mppt) REVERT: D 334 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8276 (ttp) REVERT: D 356 GLN cc_start: 0.6644 (mp10) cc_final: 0.6342 (mt0) REVERT: E 12 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7887 (mp) REVERT: E 67 MET cc_start: 0.8383 (mmm) cc_final: 0.8129 (mmm) REVERT: E 93 ASN cc_start: 0.8018 (t0) cc_final: 0.7648 (t0) REVERT: E 138 MET cc_start: 0.7952 (tmm) cc_final: 0.7727 (ppp) REVERT: E 359 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.5023 (mp0) REVERT: G 12 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8258 (tp) REVERT: G 67 MET cc_start: 0.8803 (mmm) cc_final: 0.8472 (mmm) REVERT: G 93 ASN cc_start: 0.8253 (m-40) cc_final: 0.7818 (m-40) REVERT: G 101 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7471 (ttm110) REVERT: G 130 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7618 (mp0) REVERT: G 198 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7851 (tppt) REVERT: G 201 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7935 (mt) REVERT: G 356 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.6215 (mt0) REVERT: H 12 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8226 (tp) REVERT: H 50 MET cc_start: 0.8194 (mtm) cc_final: 0.7893 (mtt) REVERT: H 93 ASN cc_start: 0.8156 (t0) cc_final: 0.7646 (t0) REVERT: H 334 MET cc_start: 0.8883 (ttp) cc_final: 0.8565 (ttt) REVERT: H 336 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: J 12 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8125 (tp) REVERT: J 16 GLN cc_start: 0.8278 (tt0) cc_final: 0.8001 (tt0) REVERT: J 24 THR cc_start: 0.8715 (p) cc_final: 0.8494 (p) REVERT: J 93 ASN cc_start: 0.8279 (m-40) cc_final: 0.7691 (m110) REVERT: J 130 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: J 198 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7930 (mtmm) REVERT: J 334 MET cc_start: 0.8829 (ttp) cc_final: 0.8220 (ttt) REVERT: J 338 ARG cc_start: 0.7483 (mtm-85) cc_final: 0.7251 (mpp-170) REVERT: J 356 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6555 (mt0) REVERT: K 12 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8383 (tp) REVERT: K 93 ASN cc_start: 0.8116 (t0) cc_final: 0.7652 (t0) REVERT: K 191 LYS cc_start: 0.8418 (ptpt) cc_final: 0.8070 (pttp) REVERT: K 257 MET cc_start: 0.8670 (mmm) cc_final: 0.8451 (mmt) REVERT: K 336 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7417 (pt0) REVERT: K 342 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7275 (ptp-170) REVERT: K 356 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6561 (mt0) REVERT: M 50 MET cc_start: 0.8752 (mtp) cc_final: 0.8488 (mtm) REVERT: M 98 THR cc_start: 0.8554 (p) cc_final: 0.8033 (t) REVERT: M 122 GLU cc_start: 0.7400 (mp0) cc_final: 0.7033 (mp0) REVERT: M 338 ARG cc_start: 0.7659 (mtm180) cc_final: 0.7384 (mpp-170) REVERT: M 356 GLN cc_start: 0.6642 (OUTLIER) cc_final: 0.6308 (mt0) REVERT: N 71 MET cc_start: 0.9095 (mtm) cc_final: 0.8797 (mtp) REVERT: N 282 GLU cc_start: 0.6344 (mp0) cc_final: 0.6139 (pm20) REVERT: P 77 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: P 122 GLU cc_start: 0.7661 (mp0) cc_final: 0.7450 (pm20) REVERT: P 195 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7792 (pttp) REVERT: P 198 LYS cc_start: 0.8238 (mmtm) cc_final: 0.7276 (mppt) REVERT: P 356 GLN cc_start: 0.6350 (OUTLIER) cc_final: 0.6114 (mt0) REVERT: Q 15 ASP cc_start: 0.8533 (t70) cc_final: 0.8161 (t70) REVERT: Q 71 MET cc_start: 0.9027 (mtm) cc_final: 0.8774 (mtp) REVERT: Q 93 ASN cc_start: 0.8075 (t0) cc_final: 0.7817 (t0) REVERT: Q 101 ARG cc_start: 0.8139 (ttm110) cc_final: 0.7776 (ttm110) REVERT: Q 191 LYS cc_start: 0.8103 (ptpt) cc_final: 0.7831 (ptpp) REVERT: Q 248 MET cc_start: 0.8411 (mmm) cc_final: 0.8147 (mmp) REVERT: Q 257 MET cc_start: 0.8802 (mmm) cc_final: 0.8379 (mmm) REVERT: S 24 THR cc_start: 0.8655 (p) cc_final: 0.8452 (p) REVERT: S 71 MET cc_start: 0.9152 (mtm) cc_final: 0.8813 (mtm) REVERT: S 123 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8500 (mt) REVERT: S 142 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.6175 (tmm) REVERT: S 195 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7841 (pttm) REVERT: S 198 LYS cc_start: 0.8173 (mmtm) cc_final: 0.7604 (mppt) REVERT: S 334 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8261 (ttp) REVERT: S 356 GLN cc_start: 0.6658 (mp10) cc_final: 0.6349 (mt0) REVERT: T 12 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7904 (mp) REVERT: T 138 MET cc_start: 0.7948 (tmm) cc_final: 0.7727 (ppp) REVERT: T 336 GLU cc_start: 0.7745 (pt0) cc_final: 0.6922 (tm-30) REVERT: T 359 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5022 (mp0) REVERT: c 12 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8256 (tp) REVERT: c 67 MET cc_start: 0.8796 (mmm) cc_final: 0.8464 (mmm) REVERT: c 93 ASN cc_start: 0.8255 (m-40) cc_final: 0.7837 (m-40) REVERT: c 130 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7609 (mp0) REVERT: c 198 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7848 (tppt) REVERT: c 201 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7935 (mt) REVERT: c 356 GLN cc_start: 0.6697 (OUTLIER) cc_final: 0.6165 (mt0) REVERT: d 50 MET cc_start: 0.8194 (mtm) cc_final: 0.7889 (mtt) REVERT: d 93 ASN cc_start: 0.8189 (t0) cc_final: 0.7858 (t0) REVERT: d 334 MET cc_start: 0.8890 (ttp) cc_final: 0.8642 (ttt) REVERT: d 336 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7310 (tm-30) REVERT: g 12 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8155 (tp) REVERT: g 16 GLN cc_start: 0.8301 (tt0) cc_final: 0.8024 (tt0) REVERT: g 24 THR cc_start: 0.8702 (p) cc_final: 0.8467 (p) REVERT: g 93 ASN cc_start: 0.8188 (m-40) cc_final: 0.7621 (m-40) REVERT: g 195 LYS cc_start: 0.8160 (mtpm) cc_final: 0.7856 (ttpp) REVERT: g 198 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7906 (mtmm) REVERT: g 334 MET cc_start: 0.8828 (ttp) cc_final: 0.8203 (ttt) REVERT: h 12 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8375 (tp) REVERT: h 93 ASN cc_start: 0.8220 (t0) cc_final: 0.7608 (t0) REVERT: h 191 LYS cc_start: 0.8408 (ptpt) cc_final: 0.8067 (pttp) REVERT: h 201 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8237 (mt) REVERT: h 257 MET cc_start: 0.8673 (mmm) cc_final: 0.8456 (mmt) REVERT: h 342 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7278 (ptp-170) REVERT: h 356 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6558 (mt0) REVERT: k 50 MET cc_start: 0.8754 (mtp) cc_final: 0.8493 (mtm) REVERT: k 98 THR cc_start: 0.8561 (p) cc_final: 0.8031 (t) REVERT: k 122 GLU cc_start: 0.7397 (mp0) cc_final: 0.7029 (mp0) REVERT: k 356 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.6352 (mt0) REVERT: l 12 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8331 (mp) REVERT: l 71 MET cc_start: 0.9152 (mtm) cc_final: 0.8863 (mtp) REVERT: l 281 MET cc_start: 0.8401 (mmm) cc_final: 0.8044 (tpp) outliers start: 185 outliers final: 58 residues processed: 926 average time/residue: 1.6719 time to fit residues: 1908.6506 Evaluate side-chains 859 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 756 time to evaluate : 4.982 ------------------------------------------------------------------------------- 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 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 D residue 334 MET Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 101 ARG 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 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 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 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 S residue 334 MET 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 198 LYS 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 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: 2.9990 chunk 502 optimal weight: 0.7980 chunk 346 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 318 optimal weight: 1.9990 chunk 448 optimal weight: 0.8980 chunk 670 optimal weight: 5.9990 chunk 709 optimal weight: 7.9990 chunk 350 optimal weight: 0.9980 chunk 635 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 192 ASN D 93 ASN D 102 GLN D 192 ASN ** E 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 ASN ** H 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN N 26 GLN ** N 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 192 ASN Q 192 ASN S 93 ASN S 192 ASN ** T 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 192 ASN ** d 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 GLN l 26 GLN ** l 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 61510 Z= 0.168 Angle : 0.494 12.051 83440 Z= 0.264 Chirality : 0.039 0.176 9560 Planarity : 0.003 0.053 10240 Dihedral : 11.042 73.765 10210 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.50 % Allowed : 14.40 % Favored : 83.10 % 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: 1.72 (0.10), residues: 7340 helix: 1.60 (0.08), residues: 4760 sheet: 0.32 (0.19), residues: 460 loop : 0.46 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 260 HIS 0.014 0.001 HIS l 89 PHE 0.012 0.001 PHE J 111 TYR 0.014 0.001 TYR k 135 ARG 0.010 0.000 ARG N 132 *********************** 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 941 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 787 time to evaluate : 4.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: A 110 LYS cc_start: 0.8151 (tmtm) cc_final: 0.7924 (tmtm) REVERT: A 198 LYS cc_start: 0.8242 (mmtm) cc_final: 0.7270 (mppt) REVERT: A 356 GLN cc_start: 0.6261 (OUTLIER) cc_final: 0.5940 (mt0) REVERT: B 15 ASP cc_start: 0.8436 (t70) cc_final: 0.8172 (t70) REVERT: B 71 MET cc_start: 0.9004 (mtm) cc_final: 0.8777 (mtp) REVERT: B 93 ASN cc_start: 0.8052 (t0) cc_final: 0.7824 (t0) REVERT: B 191 LYS cc_start: 0.8124 (ptpt) cc_final: 0.7859 (ptpp) REVERT: B 248 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8301 (mmm) REVERT: B 257 MET cc_start: 0.8814 (mmm) cc_final: 0.8360 (mmm) REVERT: D 71 MET cc_start: 0.9156 (mtm) cc_final: 0.8790 (mtm) REVERT: D 77 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: D 93 ASN cc_start: 0.8443 (m-40) cc_final: 0.7865 (m-40) REVERT: D 101 ARG cc_start: 0.8049 (ttm110) cc_final: 0.7701 (ttm110) REVERT: D 142 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6059 (pp-130) REVERT: D 195 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7823 (pttm) REVERT: D 198 LYS cc_start: 0.8173 (mmtm) cc_final: 0.7676 (mppt) REVERT: D 334 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8265 (ttp) REVERT: D 356 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6509 (mt0) REVERT: E 12 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8099 (mp) REVERT: E 93 ASN cc_start: 0.7875 (t0) cc_final: 0.7391 (t0) REVERT: E 359 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5089 (mp0) REVERT: G 46 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7795 (mtpt) REVERT: G 67 MET cc_start: 0.8794 (mmm) cc_final: 0.8363 (mmm) REVERT: G 93 ASN cc_start: 0.8233 (m-40) cc_final: 0.7780 (m-40) REVERT: G 101 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7607 (ttm110) REVERT: G 198 LYS cc_start: 0.8090 (tppp) cc_final: 0.7806 (tppt) REVERT: G 201 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7842 (mt) REVERT: G 356 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.6245 (mt0) REVERT: H 12 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8212 (tp) REVERT: H 50 MET cc_start: 0.8162 (mtm) cc_final: 0.7855 (mtt) REVERT: H 93 ASN cc_start: 0.8131 (t0) cc_final: 0.7630 (t0) REVERT: H 334 MET cc_start: 0.8883 (ttp) cc_final: 0.8523 (ttt) REVERT: J 12 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8113 (tp) REVERT: J 16 GLN cc_start: 0.8293 (tt0) cc_final: 0.7997 (tt0) REVERT: J 24 THR cc_start: 0.8755 (p) cc_final: 0.8517 (p) REVERT: J 67 MET cc_start: 0.8717 (mmm) cc_final: 0.8439 (mmm) REVERT: J 93 ASN cc_start: 0.8267 (m-40) cc_final: 0.7689 (m110) REVERT: J 130 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: J 195 LYS cc_start: 0.8281 (mtmm) cc_final: 0.8062 (ttpp) REVERT: J 198 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8010 (mmpt) REVERT: J 334 MET cc_start: 0.8792 (ttp) cc_final: 0.8310 (ttp) REVERT: J 356 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6433 (mt0) REVERT: K 93 ASN cc_start: 0.8091 (t0) cc_final: 0.7626 (t0) REVERT: K 191 LYS cc_start: 0.8411 (ptpt) cc_final: 0.8080 (pttp) REVERT: K 198 LYS cc_start: 0.8574 (mmtm) cc_final: 0.8257 (mmpt) REVERT: K 201 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8119 (mt) REVERT: K 257 MET cc_start: 0.8681 (mmm) cc_final: 0.8474 (mmt) REVERT: K 336 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7408 (pt0) REVERT: K 342 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7262 (ptp-170) REVERT: K 356 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6604 (mt0) REVERT: M 50 MET cc_start: 0.8720 (mtp) cc_final: 0.8483 (mtm) REVERT: M 71 MET cc_start: 0.9148 (mtm) cc_final: 0.8867 (mtp) REVERT: M 98 THR cc_start: 0.8591 (p) cc_final: 0.7955 (t) REVERT: M 122 GLU cc_start: 0.7316 (mp0) cc_final: 0.7085 (mp0) REVERT: M 338 ARG cc_start: 0.7612 (mtm180) cc_final: 0.7361 (mpp-170) REVERT: M 356 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.6391 (mt0) REVERT: N 71 MET cc_start: 0.9033 (mtm) cc_final: 0.8746 (mtp) REVERT: N 142 MET cc_start: 0.5456 (pp-130) cc_final: 0.5113 (tmm) REVERT: P 77 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: P 198 LYS cc_start: 0.8232 (mmtm) cc_final: 0.7551 (mppt) REVERT: P 356 GLN cc_start: 0.6256 (OUTLIER) cc_final: 0.6023 (mt0) REVERT: Q 15 ASP cc_start: 0.8440 (t70) cc_final: 0.8177 (t70) REVERT: Q 71 MET cc_start: 0.9000 (mtm) cc_final: 0.8778 (mtp) REVERT: Q 93 ASN cc_start: 0.8063 (t0) cc_final: 0.7812 (t0) REVERT: Q 110 LYS cc_start: 0.8627 (mtpp) cc_final: 0.8407 (mtpp) REVERT: Q 191 LYS cc_start: 0.8124 (ptpt) cc_final: 0.7865 (ptpp) REVERT: Q 257 MET cc_start: 0.8822 (mmm) cc_final: 0.8364 (mmm) REVERT: S 24 THR cc_start: 0.8669 (p) cc_final: 0.8469 (p) REVERT: S 71 MET cc_start: 0.9152 (mtm) cc_final: 0.8790 (mtm) REVERT: S 93 ASN cc_start: 0.8405 (m-40) cc_final: 0.7833 (m-40) REVERT: S 101 ARG cc_start: 0.8148 (ttm110) cc_final: 0.7692 (ttm110) REVERT: S 122 GLU cc_start: 0.7480 (mp0) cc_final: 0.7277 (pm20) REVERT: S 142 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6058 (pp-130) REVERT: S 195 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7819 (pttm) REVERT: S 198 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7676 (mppt) REVERT: S 334 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8249 (ttp) REVERT: S 356 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6378 (mt0) REVERT: T 12 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8114 (mp) REVERT: T 67 MET cc_start: 0.8578 (mmt) cc_final: 0.8221 (mmm) REVERT: T 359 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5081 (mp0) REVERT: c 46 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7795 (mtpt) REVERT: c 67 MET cc_start: 0.8790 (mmm) cc_final: 0.8354 (mmm) REVERT: c 93 ASN cc_start: 0.8228 (m-40) cc_final: 0.7785 (m-40) REVERT: c 198 LYS cc_start: 0.8119 (tppp) cc_final: 0.7828 (tppt) REVERT: c 201 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7839 (mt) REVERT: c 356 GLN cc_start: 0.6696 (OUTLIER) cc_final: 0.6324 (mt0) REVERT: d 50 MET cc_start: 0.8164 (mtm) cc_final: 0.7853 (mtt) REVERT: d 93 ASN cc_start: 0.8164 (t0) cc_final: 0.7875 (t0) REVERT: d 334 MET cc_start: 0.8890 (ttp) cc_final: 0.8527 (ttt) REVERT: g 12 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8155 (tp) REVERT: g 16 GLN cc_start: 0.8286 (tt0) cc_final: 0.8002 (tt0) REVERT: g 24 THR cc_start: 0.8752 (p) cc_final: 0.8516 (p) REVERT: g 67 MET cc_start: 0.8724 (mmm) cc_final: 0.8458 (mmm) REVERT: g 130 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: g 195 LYS cc_start: 0.8140 (mtpm) cc_final: 0.7879 (ttpp) REVERT: g 198 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7880 (tppt) REVERT: g 201 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7786 (mt) REVERT: g 248 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8738 (mmm) REVERT: g 334 MET cc_start: 0.8804 (ttp) cc_final: 0.8226 (ttp) REVERT: g 338 ARG cc_start: 0.7623 (mtm180) cc_final: 0.7360 (mpp-170) REVERT: h 93 ASN cc_start: 0.8138 (t0) cc_final: 0.7625 (t0) REVERT: h 191 LYS cc_start: 0.8403 (ptpt) cc_final: 0.8080 (pttp) REVERT: h 198 LYS cc_start: 0.8600 (mmtm) cc_final: 0.8296 (mmpt) REVERT: h 201 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8206 (mt) REVERT: h 257 MET cc_start: 0.8682 (mmm) cc_final: 0.8475 (mmt) REVERT: h 342 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7269 (ptp-170) REVERT: h 356 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6592 (mt0) REVERT: k 50 MET cc_start: 0.8721 (mtp) cc_final: 0.8484 (mtm) REVERT: k 71 MET cc_start: 0.9156 (mtm) cc_final: 0.8884 (mtp) REVERT: k 122 GLU cc_start: 0.7317 (mp0) cc_final: 0.7083 (mp0) REVERT: k 356 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.6395 (mt0) REVERT: l 12 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8320 (mp) REVERT: l 71 MET cc_start: 0.9135 (mtm) cc_final: 0.8846 (mtp) REVERT: l 281 MET cc_start: 0.8398 (mmm) cc_final: 0.8178 (tpp) outliers start: 154 outliers final: 48 residues processed: 884 average time/residue: 1.6123 time to fit residues: 1765.1847 Evaluate side-chains 841 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 750 time to evaluate : 4.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 356 GLN Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 101 ARG 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 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 362 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 198 LYS Chi-restraints excluded: chain J residue 356 GLN Chi-restraints excluded: chain J residue 363 ILE 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 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 201 LEU Chi-restraints excluded: chain P residue 356 GLN Chi-restraints excluded: chain P residue 363 ILE Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 142 MET Chi-restraints excluded: chain S residue 310 SER Chi-restraints excluded: chain S residue 334 MET Chi-restraints excluded: chain S residue 356 GLN Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 359 GLU Chi-restraints excluded: chain T residue 362 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain c residue 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 c residue 363 ILE 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 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 198 LYS Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain g residue 248 MET Chi-restraints excluded: chain g residue 363 ILE 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 22 LYS 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 316 GLN Chi-restraints excluded: chain l residue 359 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 590 optimal weight: 7.9990 chunk 402 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 528 optimal weight: 8.9990 chunk 292 optimal weight: 3.9990 chunk 605 optimal weight: 6.9990 chunk 490 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 362 optimal weight: 2.9990 chunk 636 optimal weight: 40.0000 chunk 179 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 ** H 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 ASN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 356 GLN P 192 ASN Q 45 ASN Q 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 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 16 GLN k 102 GLN ** l 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 356 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 61510 Z= 0.308 Angle : 0.571 11.754 83440 Z= 0.303 Chirality : 0.043 0.184 9560 Planarity : 0.004 0.056 10240 Dihedral : 11.158 74.070 10210 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.23 % Allowed : 14.64 % Favored : 82.13 % 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: 1.42 (0.10), residues: 7340 helix: 1.30 (0.07), residues: 4760 sheet: 0.48 (0.19), residues: 500 loop : 0.48 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP c 260 HIS 0.010 0.001 HIS M 225 PHE 0.014 0.002 PHE J 111 TYR 0.020 0.002 TYR d 365 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 to be fit. rotamer outliers: 199 poor density : 752 time to evaluate : 4.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: A 101 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7973 (ttm110) REVERT: A 110 LYS cc_start: 0.8178 (tmtm) cc_final: 0.7946 (tmtm) REVERT: A 195 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7873 (pttp) REVERT: A 198 LYS cc_start: 0.8270 (mmtm) cc_final: 0.7709 (mppt) REVERT: A 356 GLN cc_start: 0.6305 (OUTLIER) cc_final: 0.5928 (mt0) REVERT: B 12 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8188 (tp) REVERT: B 71 MET cc_start: 0.8997 (mtm) cc_final: 0.8762 (mtp) REVERT: B 93 ASN cc_start: 0.8087 (t0) cc_final: 0.7792 (t0) REVERT: B 191 LYS cc_start: 0.8118 (ptpt) cc_final: 0.7812 (ptpp) REVERT: B 248 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8267 (mmm) REVERT: B 257 MET cc_start: 0.8744 (mmm) cc_final: 0.8406 (mmm) REVERT: D 71 MET cc_start: 0.9155 (mtm) cc_final: 0.8778 (mtm) REVERT: D 77 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: D 101 ARG cc_start: 0.8251 (ttm110) cc_final: 0.7903 (ttm110) REVERT: D 125 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8542 (mt) REVERT: D 142 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6374 (pp-130) REVERT: D 195 LYS cc_start: 0.8159 (mtmm) cc_final: 0.7759 (pttm) REVERT: D 198 LYS cc_start: 0.8272 (mmtm) cc_final: 0.7839 (mppt) REVERT: D 334 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8224 (ttp) REVERT: D 356 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6519 (mt0) REVERT: E 12 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7918 (mp) REVERT: E 67 MET cc_start: 0.8289 (mmm) cc_final: 0.7733 (mmt) REVERT: E 93 ASN cc_start: 0.8071 (t0) cc_final: 0.7554 (t0) REVERT: E 359 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.5215 (mp0) REVERT: G 12 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8260 (tp) REVERT: G 67 MET cc_start: 0.8797 (mmm) cc_final: 0.8468 (mmm) REVERT: G 101 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7807 (ttm110) REVERT: G 198 LYS cc_start: 0.8260 (tppp) cc_final: 0.8059 (mmpt) REVERT: G 201 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8050 (mt) REVERT: G 356 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.6502 (mt0) REVERT: H 12 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8194 (tp) REVERT: H 50 MET cc_start: 0.8219 (mtm) cc_final: 0.7944 (mtt) REVERT: H 93 ASN cc_start: 0.8154 (t0) cc_final: 0.7614 (t0) REVERT: H 126 ASN cc_start: 0.8747 (m-40) cc_final: 0.8547 (m-40) REVERT: H 334 MET cc_start: 0.8933 (ttp) cc_final: 0.8653 (ttp) REVERT: J 12 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8126 (tp) REVERT: J 16 GLN cc_start: 0.8311 (tt0) cc_final: 0.8020 (tt0) REVERT: J 24 THR cc_start: 0.8818 (p) cc_final: 0.8613 (p) REVERT: J 67 MET cc_start: 0.8797 (mmm) cc_final: 0.8429 (mmm) REVERT: J 130 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: J 195 LYS cc_start: 0.8270 (mtmm) cc_final: 0.8013 (ttpp) REVERT: J 198 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8070 (mmpt) REVERT: J 334 MET cc_start: 0.8834 (ttp) cc_final: 0.8259 (ttt) REVERT: J 356 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6529 (mt0) REVERT: K 12 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8358 (tp) REVERT: K 93 ASN cc_start: 0.8124 (t0) cc_final: 0.7645 (t0) REVERT: K 142 MET cc_start: 0.5752 (OUTLIER) cc_final: 0.5458 (ptt) REVERT: K 191 LYS cc_start: 0.8431 (ptpt) cc_final: 0.7868 (pttp) REVERT: K 195 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7421 (mtmt) REVERT: K 198 LYS cc_start: 0.8626 (mmtm) cc_final: 0.8295 (mmpt) REVERT: K 201 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8135 (mt) REVERT: K 336 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7433 (pt0) REVERT: K 356 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6557 (mt0) REVERT: M 50 MET cc_start: 0.8852 (mtp) cc_final: 0.8632 (mtm) REVERT: M 109 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6980 (mtp) REVERT: M 122 GLU cc_start: 0.7358 (mp0) cc_final: 0.7116 (mp0) REVERT: M 142 MET cc_start: 0.7216 (tmm) cc_final: 0.6891 (ptt) REVERT: M 338 ARG cc_start: 0.7565 (mtm180) cc_final: 0.7334 (mpp-170) REVERT: M 356 GLN cc_start: 0.6660 (OUTLIER) cc_final: 0.6417 (mt0) REVERT: N 71 MET cc_start: 0.9036 (mtm) cc_final: 0.8750 (mtp) REVERT: N 93 ASN cc_start: 0.8017 (t0) cc_final: 0.7663 (t0) REVERT: N 101 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7929 (tpp-160) REVERT: P 77 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: P 101 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7931 (ttm110) REVERT: P 195 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7858 (pttp) REVERT: P 198 LYS cc_start: 0.8272 (mmtm) cc_final: 0.7729 (mppt) REVERT: P 356 GLN cc_start: 0.6306 (OUTLIER) cc_final: 0.6005 (mt0) REVERT: Q 12 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8195 (tp) REVERT: Q 71 MET cc_start: 0.8997 (mtm) cc_final: 0.8759 (mtp) REVERT: Q 93 ASN cc_start: 0.8092 (t0) cc_final: 0.7797 (t0) REVERT: Q 110 LYS cc_start: 0.8633 (mtpp) cc_final: 0.8380 (mtpp) REVERT: Q 191 LYS cc_start: 0.8148 (ptpt) cc_final: 0.7812 (ptpp) REVERT: Q 248 MET cc_start: 0.8587 (mmp) cc_final: 0.8378 (mmm) REVERT: Q 257 MET cc_start: 0.8747 (mmm) cc_final: 0.8406 (mmm) REVERT: S 71 MET cc_start: 0.9148 (mtm) cc_final: 0.8780 (mtm) REVERT: S 77 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: S 142 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6363 (pp-130) REVERT: S 195 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7750 (pttm) REVERT: S 198 LYS cc_start: 0.8265 (mmtm) cc_final: 0.7837 (mppt) REVERT: S 334 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8212 (ttp) REVERT: S 356 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6522 (mt0) REVERT: T 12 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7923 (mp) REVERT: T 67 MET cc_start: 0.8566 (mmp) cc_final: 0.8241 (mmm) REVERT: T 359 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.5267 (mp0) REVERT: c 12 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8262 (tp) REVERT: c 67 MET cc_start: 0.8795 (mmm) cc_final: 0.8460 (mmm) REVERT: c 198 LYS cc_start: 0.8265 (tppp) cc_final: 0.8056 (mmpt) REVERT: c 201 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8052 (mt) REVERT: c 356 GLN cc_start: 0.6801 (OUTLIER) cc_final: 0.6587 (mt0) REVERT: d 50 MET cc_start: 0.8222 (mtm) cc_final: 0.7945 (mtt) REVERT: d 93 ASN cc_start: 0.8209 (t0) cc_final: 0.7838 (t0) REVERT: d 334 MET cc_start: 0.8934 (ttp) cc_final: 0.8652 (ttp) REVERT: g 12 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8149 (tp) REVERT: g 16 GLN cc_start: 0.8316 (tt0) cc_final: 0.8029 (tt0) REVERT: g 24 THR cc_start: 0.8815 (p) cc_final: 0.8609 (p) REVERT: g 67 MET cc_start: 0.8803 (mmm) cc_final: 0.8441 (mmm) REVERT: g 130 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: g 195 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7967 (ttpp) REVERT: g 198 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8061 (mmpt) REVERT: g 334 MET cc_start: 0.8845 (ttp) cc_final: 0.8237 (ttt) REVERT: g 338 ARG cc_start: 0.7812 (mtm180) cc_final: 0.7559 (mpp-170) REVERT: h 12 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8352 (tp) REVERT: h 33 ILE cc_start: 0.8649 (mm) cc_final: 0.8255 (mt) REVERT: h 93 ASN cc_start: 0.8125 (t0) cc_final: 0.7662 (t0) REVERT: h 142 MET cc_start: 0.5705 (OUTLIER) cc_final: 0.5406 (ptt) REVERT: h 191 LYS cc_start: 0.8422 (ptpt) cc_final: 0.7948 (pttp) REVERT: h 198 LYS cc_start: 0.8640 (mmtm) cc_final: 0.8279 (mmpt) REVERT: h 201 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8334 (mt) REVERT: h 356 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6540 (mt0) REVERT: k 50 MET cc_start: 0.8853 (mtp) cc_final: 0.8632 (mtm) REVERT: k 109 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.6952 (mtp) REVERT: k 122 GLU cc_start: 0.7354 (mp0) cc_final: 0.7110 (mp0) REVERT: k 142 MET cc_start: 0.7358 (tmm) cc_final: 0.6935 (ptt) REVERT: k 195 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7884 (pttm) REVERT: k 356 GLN cc_start: 0.6646 (OUTLIER) cc_final: 0.6405 (mt0) REVERT: l 12 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8313 (mp) REVERT: l 71 MET cc_start: 0.9046 (mtm) cc_final: 0.8753 (mtp) REVERT: l 93 ASN cc_start: 0.7992 (t0) cc_final: 0.7650 (t0) outliers start: 199 outliers final: 72 residues processed: 883 average time/residue: 1.6625 time to fit residues: 1813.6920 Evaluate side-chains 836 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 707 time to evaluate : 4.920 ------------------------------------------------------------------------------- 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 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 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 D residue 334 MET Chi-restraints excluded: chain D residue 356 GLN Chi-restraints excluded: chain D residue 363 ILE 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 101 ARG Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 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 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 130 GLU Chi-restraints excluded: chain J residue 198 LYS 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 195 LYS 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 109 MET 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 101 ARG 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 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 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 142 MET Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain S residue 310 SER Chi-restraints excluded: chain S residue 334 MET Chi-restraints excluded: chain S residue 356 GLN Chi-restraints excluded: chain S residue 363 ILE 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 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 c residue 316 GLN Chi-restraints excluded: chain c residue 356 GLN Chi-restraints excluded: chain c residue 363 ILE 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 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 195 LYS Chi-restraints excluded: chain g residue 198 LYS 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 142 MET Chi-restraints excluded: chain h residue 201 LEU Chi-restraints excluded: chain h residue 356 GLN Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 109 MET 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 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: 3.9990 chunk 638 optimal weight: 8.9990 chunk 140 optimal weight: 0.7980 chunk 416 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 710 optimal weight: 0.9990 chunk 589 optimal weight: 5.9990 chunk 328 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 372 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 192 ASN D 102 GLN D 192 ASN ** E 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN ** H 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 ASN N 356 GLN P 192 ASN Q 45 ASN Q 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** ** h 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 GLN ** l 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 356 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 61510 Z= 0.152 Angle : 0.498 12.512 83440 Z= 0.263 Chirality : 0.039 0.176 9560 Planarity : 0.003 0.058 10240 Dihedral : 11.013 73.690 10210 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.81 % Allowed : 15.63 % Favored : 81.56 % 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: 1.80 (0.10), residues: 7340 helix: 1.65 (0.08), residues: 4740 sheet: 0.29 (0.20), residues: 440 loop : 0.54 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 260 HIS 0.005 0.001 HIS c 225 PHE 0.014 0.001 PHE g 111 TYR 0.014 0.001 TYR A 135 ARG 0.011 0.000 ARG c 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 753 time to evaluate : 4.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: A 101 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7859 (ttm110) REVERT: A 110 LYS cc_start: 0.8063 (tmtm) cc_final: 0.7750 (tmtm) REVERT: A 198 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7666 (mppt) REVERT: A 356 GLN cc_start: 0.6298 (OUTLIER) cc_final: 0.6077 (mt0) REVERT: B 15 ASP cc_start: 0.8341 (t70) cc_final: 0.8078 (t70) REVERT: B 71 MET cc_start: 0.9003 (mtm) cc_final: 0.8761 (mtp) REVERT: B 93 ASN cc_start: 0.8043 (t0) cc_final: 0.7794 (t0) REVERT: B 191 LYS cc_start: 0.8095 (ptpt) cc_final: 0.7819 (ptpp) REVERT: B 248 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8329 (mmm) REVERT: B 257 MET cc_start: 0.8799 (mmm) cc_final: 0.8399 (mmm) REVERT: D 12 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8207 (mp) REVERT: D 71 MET cc_start: 0.9149 (mtm) cc_final: 0.8775 (mtm) REVERT: D 77 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: D 93 ASN cc_start: 0.8423 (m-40) cc_final: 0.7854 (m-40) REVERT: D 101 ARG cc_start: 0.8165 (ttm110) cc_final: 0.7765 (ttm110) REVERT: D 110 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7752 (ttpm) REVERT: D 142 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6101 (pp-130) REVERT: D 195 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7858 (pttm) REVERT: D 198 LYS cc_start: 0.8120 (mmtm) cc_final: 0.7764 (mppt) REVERT: D 334 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8201 (ttt) REVERT: D 356 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6661 (mt0) REVERT: E 12 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8056 (mp) REVERT: E 93 ASN cc_start: 0.7790 (t0) cc_final: 0.7253 (t0) REVERT: E 359 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.5348 (mp0) REVERT: G 46 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8002 (mtmm) REVERT: G 67 MET cc_start: 0.8775 (mmm) cc_final: 0.8339 (mmm) REVERT: G 93 ASN cc_start: 0.8221 (m-40) cc_final: 0.7760 (m-40) REVERT: G 201 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7790 (mt) REVERT: H 12 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8188 (tp) REVERT: H 50 MET cc_start: 0.8177 (mtm) cc_final: 0.7909 (mtt) REVERT: H 93 ASN cc_start: 0.8200 (t0) cc_final: 0.7730 (t0) REVERT: H 126 ASN cc_start: 0.8736 (m-40) cc_final: 0.8528 (m-40) REVERT: H 334 MET cc_start: 0.8929 (ttp) cc_final: 0.8706 (ttp) REVERT: J 16 GLN cc_start: 0.8292 (tt0) cc_final: 0.8016 (tt0) REVERT: J 24 THR cc_start: 0.8774 (p) cc_final: 0.8542 (p) REVERT: J 67 MET cc_start: 0.8761 (mmm) cc_final: 0.8405 (mmm) REVERT: J 130 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: J 334 MET cc_start: 0.8823 (ttp) cc_final: 0.8269 (ttt) REVERT: J 338 ARG cc_start: 0.7624 (mpp-170) cc_final: 0.7415 (mtm110) REVERT: J 356 GLN cc_start: 0.6941 (OUTLIER) cc_final: 0.6537 (mt0) REVERT: K 93 ASN cc_start: 0.8016 (t0) cc_final: 0.7443 (t0) REVERT: K 142 MET cc_start: 0.5676 (OUTLIER) cc_final: 0.5380 (ptt) REVERT: K 191 LYS cc_start: 0.8287 (ptpt) cc_final: 0.7915 (pttp) REVERT: K 198 LYS cc_start: 0.8654 (mmtm) cc_final: 0.8330 (mmpt) REVERT: K 201 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8095 (mt) REVERT: K 336 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7393 (pt0) REVERT: K 356 GLN cc_start: 0.6867 (OUTLIER) cc_final: 0.6531 (mt0) REVERT: M 50 MET cc_start: 0.8744 (mtp) cc_final: 0.8516 (mtm) REVERT: M 71 MET cc_start: 0.9146 (mtm) cc_final: 0.8869 (mtp) REVERT: M 109 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7050 (mtp) REVERT: M 122 GLU cc_start: 0.7299 (mp0) cc_final: 0.7086 (mp0) REVERT: M 338 ARG cc_start: 0.7470 (mtm180) cc_final: 0.7211 (mpp-170) REVERT: N 67 MET cc_start: 0.8545 (mmp) cc_final: 0.8313 (mmm) REVERT: N 71 MET cc_start: 0.9023 (mtm) cc_final: 0.8744 (mtp) REVERT: N 101 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7766 (tpp-160) REVERT: P 77 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: P 101 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7896 (ttm110) REVERT: P 198 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7672 (mppt) REVERT: Q 15 ASP cc_start: 0.8345 (t70) cc_final: 0.8085 (t70) REVERT: Q 71 MET cc_start: 0.9004 (mtm) cc_final: 0.8750 (mtp) REVERT: Q 93 ASN cc_start: 0.8044 (t0) cc_final: 0.7794 (t0) REVERT: Q 101 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.7340 (ttm110) REVERT: Q 257 MET cc_start: 0.8804 (mmm) cc_final: 0.8399 (mmm) REVERT: S 12 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8209 (mp) REVERT: S 71 MET cc_start: 0.9141 (mtm) cc_final: 0.8768 (mtm) REVERT: S 93 ASN cc_start: 0.8433 (m-40) cc_final: 0.8204 (m110) REVERT: S 110 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7739 (ttpm) REVERT: S 125 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8410 (mt) REVERT: S 142 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6067 (pp-130) REVERT: S 195 LYS cc_start: 0.8046 (mtmm) cc_final: 0.7756 (pttm) REVERT: S 198 LYS cc_start: 0.8123 (mmtm) cc_final: 0.7765 (mppt) REVERT: S 334 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8187 (ttt) REVERT: S 356 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6691 (mt0) REVERT: T 12 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8055 (mp) REVERT: T 359 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.5320 (mp0) REVERT: c 46 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7999 (mtmm) REVERT: c 67 MET cc_start: 0.8775 (mmm) cc_final: 0.8334 (mmm) REVERT: c 93 ASN cc_start: 0.8222 (m-40) cc_final: 0.7786 (m-40) REVERT: c 201 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7789 (mt) REVERT: d 50 MET cc_start: 0.8177 (mtm) cc_final: 0.7910 (mtt) REVERT: d 93 ASN cc_start: 0.8240 (t0) cc_final: 0.7942 (t0) REVERT: d 126 ASN cc_start: 0.8728 (m-40) cc_final: 0.8520 (m-40) REVERT: d 334 MET cc_start: 0.8932 (ttp) cc_final: 0.8602 (ttp) REVERT: g 16 GLN cc_start: 0.8299 (tt0) cc_final: 0.8026 (tt0) REVERT: g 24 THR cc_start: 0.8752 (p) cc_final: 0.8515 (p) REVERT: g 67 MET cc_start: 0.8762 (mmm) cc_final: 0.8419 (mmm) REVERT: g 130 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: g 195 LYS cc_start: 0.8165 (mtpm) cc_final: 0.7952 (ttpp) REVERT: g 334 MET cc_start: 0.8869 (ttp) cc_final: 0.8244 (ttt) REVERT: g 338 ARG cc_start: 0.7608 (mtm180) cc_final: 0.7333 (mpp-170) REVERT: h 12 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8424 (tp) REVERT: h 93 ASN cc_start: 0.8118 (t0) cc_final: 0.7504 (t0) REVERT: h 142 MET cc_start: 0.5773 (OUTLIER) cc_final: 0.5476 (ptt) REVERT: h 191 LYS cc_start: 0.8286 (ptpt) cc_final: 0.7915 (pttp) REVERT: h 198 LYS cc_start: 0.8660 (mmtm) cc_final: 0.8339 (mmpt) REVERT: h 201 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8113 (mt) REVERT: h 282 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.6047 (tt0) REVERT: k 50 MET cc_start: 0.8746 (mtp) cc_final: 0.8519 (mtm) REVERT: k 109 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7045 (mtp) REVERT: k 122 GLU cc_start: 0.7297 (mp0) cc_final: 0.7069 (mp0) REVERT: l 67 MET cc_start: 0.8577 (mmp) cc_final: 0.8334 (mmm) REVERT: l 71 MET cc_start: 0.9077 (mtm) cc_final: 0.8827 (mtp) REVERT: l 137 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8234 (ttpp) REVERT: l 281 MET cc_start: 0.8362 (mmm) cc_final: 0.8109 (tpp) outliers start: 173 outliers final: 63 residues processed: 868 average time/residue: 1.6356 time to fit residues: 1759.0426 Evaluate side-chains 816 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 711 time to evaluate : 5.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 356 GLN 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 77 GLU Chi-restraints excluded: chain D residue 110 LYS 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 D residue 334 MET Chi-restraints excluded: chain D residue 356 GLN Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 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 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 H residue 12 LEU Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 362 VAL Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 356 GLN Chi-restraints excluded: chain J residue 363 ILE 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 109 MET 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 101 ARG Chi-restraints excluded: chain N residue 120 THR 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 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 12 LEU 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 S residue 334 MET Chi-restraints excluded: chain S residue 356 GLN Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 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 39 ASP Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain c residue 189 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 310 SER Chi-restraints excluded: chain c residue 316 GLN Chi-restraints excluded: chain d residue 110 LYS Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain g residue 22 LYS Chi-restraints excluded: chain g residue 32 SER 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 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 109 MET Chi-restraints excluded: chain k residue 363 ILE Chi-restraints excluded: chain l residue 89 HIS Chi-restraints excluded: chain l residue 120 THR Chi-restraints excluded: chain l residue 137 LYS 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: 2.9990 chunk 80 optimal weight: 10.0000 chunk 404 optimal weight: 1.9990 chunk 518 optimal weight: 7.9990 chunk 401 optimal weight: 0.8980 chunk 597 optimal weight: 3.9990 chunk 396 optimal weight: 0.6980 chunk 707 optimal weight: 10.0000 chunk 442 optimal weight: 0.9990 chunk 431 optimal weight: 6.9990 chunk 326 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 192 ASN D 102 GLN D 192 ASN ** E 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 356 GLN J 102 GLN ** K 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN M 356 GLN ** N 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 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 ** l 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 61510 Z= 0.210 Angle : 0.531 12.088 83440 Z= 0.277 Chirality : 0.040 0.169 9560 Planarity : 0.003 0.057 10240 Dihedral : 11.015 73.864 10210 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.97 % Allowed : 16.27 % Favored : 80.76 % 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: 1.73 (0.10), residues: 7340 helix: 1.58 (0.08), residues: 4740 sheet: 0.32 (0.21), residues: 440 loop : 0.55 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 260 HIS 0.008 0.001 HIS k 225 PHE 0.015 0.002 PHE J 111 TYR 0.016 0.001 TYR S 135 ARG 0.012 0.000 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 902 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 719 time to evaluate : 5.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: A 101 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7911 (ttm110) REVERT: A 110 LYS cc_start: 0.8067 (tmtm) cc_final: 0.7812 (tmtm) REVERT: A 198 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7726 (mppt) REVERT: B 12 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8178 (tp) REVERT: B 15 ASP cc_start: 0.8409 (t70) cc_final: 0.8140 (t70) REVERT: B 71 MET cc_start: 0.8988 (mtm) cc_final: 0.8749 (mtp) REVERT: B 93 ASN cc_start: 0.8055 (t0) cc_final: 0.7740 (t0) REVERT: B 248 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8260 (mmm) REVERT: B 257 MET cc_start: 0.8787 (mmm) cc_final: 0.8344 (mmm) REVERT: D 12 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8199 (mp) REVERT: D 71 MET cc_start: 0.9146 (mtm) cc_final: 0.8722 (mtm) REVERT: D 77 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: D 93 ASN cc_start: 0.8405 (m-40) cc_final: 0.8150 (m110) REVERT: D 101 ARG cc_start: 0.8238 (ttm110) cc_final: 0.7825 (ttm110) REVERT: D 110 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7771 (ttpm) REVERT: D 125 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8493 (mt) REVERT: D 142 MET cc_start: 0.6794 (OUTLIER) cc_final: 0.6325 (pp-130) REVERT: D 195 LYS cc_start: 0.8069 (mtmm) cc_final: 0.7847 (pttp) REVERT: D 198 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7871 (mppt) REVERT: D 334 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8252 (ttp) REVERT: E 12 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8100 (mp) REVERT: E 67 MET cc_start: 0.8213 (mmm) cc_final: 0.7967 (mmp) REVERT: E 93 ASN cc_start: 0.7872 (t0) cc_final: 0.7323 (t0) REVERT: E 359 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.5332 (mp0) REVERT: G 12 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8228 (tp) REVERT: G 67 MET cc_start: 0.8774 (mmm) cc_final: 0.8342 (mmm) REVERT: G 130 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: G 201 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7917 (mt) REVERT: H 12 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8197 (tp) REVERT: H 50 MET cc_start: 0.8193 (mtm) cc_final: 0.7904 (mtt) REVERT: H 84 ARG cc_start: 0.7829 (mpt-90) cc_final: 0.7627 (mpt-90) REVERT: H 93 ASN cc_start: 0.8198 (t0) cc_final: 0.7688 (t0) REVERT: H 126 ASN cc_start: 0.8734 (m-40) cc_final: 0.8515 (m-40) REVERT: H 334 MET cc_start: 0.8925 (ttp) cc_final: 0.8706 (ttp) REVERT: J 12 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8130 (tp) REVERT: J 16 GLN cc_start: 0.8318 (tt0) cc_final: 0.8040 (tt0) REVERT: J 24 THR cc_start: 0.8772 (p) cc_final: 0.8523 (p) REVERT: J 67 MET cc_start: 0.8776 (mmm) cc_final: 0.8415 (mmm) REVERT: J 334 MET cc_start: 0.8852 (ttp) cc_final: 0.8274 (ttt) REVERT: J 338 ARG cc_start: 0.7659 (mpp-170) cc_final: 0.7433 (mtm110) REVERT: J 356 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6593 (mt0) REVERT: K 93 ASN cc_start: 0.7995 (t0) cc_final: 0.7448 (t0) REVERT: K 142 MET cc_start: 0.5782 (OUTLIER) cc_final: 0.5483 (ptt) REVERT: K 191 LYS cc_start: 0.8306 (ptpt) cc_final: 0.7933 (pttp) REVERT: K 198 LYS cc_start: 0.8660 (mmtm) cc_final: 0.8334 (mmpt) REVERT: K 201 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8136 (mt) REVERT: K 336 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7423 (pt0) REVERT: K 356 GLN cc_start: 0.6902 (OUTLIER) cc_final: 0.6604 (mt0) REVERT: M 50 MET cc_start: 0.8786 (mtp) cc_final: 0.8546 (mtm) REVERT: M 109 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7110 (mtp) REVERT: M 195 LYS cc_start: 0.8213 (ttpp) cc_final: 0.7957 (mtpm) REVERT: M 338 ARG cc_start: 0.7470 (mtm180) cc_final: 0.7247 (mpp-170) REVERT: N 67 MET cc_start: 0.8626 (mmp) cc_final: 0.8304 (mmm) REVERT: N 71 MET cc_start: 0.9031 (mtm) cc_final: 0.8748 (mtp) REVERT: N 93 ASN cc_start: 0.7969 (t0) cc_final: 0.7701 (t0) REVERT: N 101 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7297 (tpp-160) REVERT: P 77 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: P 101 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7940 (ttm110) REVERT: P 129 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7968 (mp) REVERT: P 198 LYS cc_start: 0.8200 (mmtm) cc_final: 0.7729 (mppt) REVERT: Q 12 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8181 (tp) REVERT: Q 15 ASP cc_start: 0.8454 (t70) cc_final: 0.8194 (t70) REVERT: Q 71 MET cc_start: 0.9005 (mtm) cc_final: 0.8765 (mtp) REVERT: Q 93 ASN cc_start: 0.7957 (t0) cc_final: 0.7663 (t0) REVERT: Q 257 MET cc_start: 0.8794 (mmm) cc_final: 0.8346 (mmm) REVERT: S 12 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8203 (mp) REVERT: S 71 MET cc_start: 0.9140 (mtm) cc_final: 0.8733 (mtm) REVERT: S 93 ASN cc_start: 0.8442 (m-40) cc_final: 0.7868 (m-40) REVERT: S 110 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7815 (ttpm) REVERT: S 125 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8517 (mt) REVERT: S 142 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6216 (pp-130) REVERT: S 195 LYS cc_start: 0.8055 (mtmm) cc_final: 0.7822 (pttp) REVERT: S 198 LYS cc_start: 0.8142 (mmtm) cc_final: 0.7870 (mppt) REVERT: S 334 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8259 (ttt) REVERT: T 12 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8106 (mp) REVERT: T 359 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.5349 (mp0) REVERT: c 12 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8235 (tp) REVERT: c 67 MET cc_start: 0.8770 (mmm) cc_final: 0.8333 (mmm) REVERT: c 130 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: c 201 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7901 (mt) REVERT: d 50 MET cc_start: 0.8197 (mtm) cc_final: 0.7906 (mtt) REVERT: d 93 ASN cc_start: 0.8262 (t0) cc_final: 0.7930 (t0) REVERT: d 126 ASN cc_start: 0.8724 (m-40) cc_final: 0.8505 (m-40) REVERT: d 334 MET cc_start: 0.8930 (ttp) cc_final: 0.8708 (ttp) REVERT: d 359 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.5202 (mp0) REVERT: g 12 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8139 (tp) REVERT: g 16 GLN cc_start: 0.8324 (tt0) cc_final: 0.8049 (tt0) REVERT: g 24 THR cc_start: 0.8765 (p) cc_final: 0.8519 (p) REVERT: g 67 MET cc_start: 0.8779 (mmm) cc_final: 0.8429 (mmm) REVERT: g 130 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: g 195 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7981 (ttpp) REVERT: g 334 MET cc_start: 0.8844 (ttp) cc_final: 0.8339 (ttt) REVERT: g 338 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7325 (mpp-170) REVERT: h 93 ASN cc_start: 0.8049 (t0) cc_final: 0.7504 (t0) REVERT: h 142 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.5456 (ptt) REVERT: h 191 LYS cc_start: 0.8397 (ptpt) cc_final: 0.8030 (pttp) REVERT: h 198 LYS cc_start: 0.8660 (mmtm) cc_final: 0.8345 (mmpt) REVERT: h 282 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.6184 (tt0) REVERT: k 50 MET cc_start: 0.8794 (mtp) cc_final: 0.8550 (mtm) REVERT: k 109 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7109 (mtp) REVERT: l 67 MET cc_start: 0.8660 (mmp) cc_final: 0.8311 (mmm) REVERT: l 71 MET cc_start: 0.9059 (mtm) cc_final: 0.8767 (mtp) REVERT: l 93 ASN cc_start: 0.7955 (t0) cc_final: 0.7693 (t0) REVERT: l 281 MET cc_start: 0.8468 (mmm) cc_final: 0.8134 (tpp) outliers start: 183 outliers final: 77 residues processed: 837 average time/residue: 1.6426 time to fit residues: 1701.4826 Evaluate side-chains 820 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 698 time to evaluate : 4.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 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 39 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 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 131 SER 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 110 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 356 GLN Chi-restraints excluded: chain J residue 363 ILE 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 109 MET 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 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 129 ILE 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 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 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 S residue 334 MET 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 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 c residue 316 GLN Chi-restraints excluded: chain c residue 363 ILE Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 110 LYS 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 195 LYS Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 142 MET Chi-restraints excluded: chain h residue 282 GLU Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 109 MET Chi-restraints excluded: chain k residue 363 ILE Chi-restraints excluded: chain l residue 120 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 437 optimal weight: 7.9990 chunk 282 optimal weight: 4.9990 chunk 422 optimal weight: 9.9990 chunk 213 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 449 optimal weight: 0.5980 chunk 481 optimal weight: 1.9990 chunk 349 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 556 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 D 356 GLN ** E 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN J 102 GLN ** K 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 151 HIS P 192 ASN Q 45 ASN S 102 GLN S 192 ASN S 356 GLN T 26 GLN ** T 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 102 GLN ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 GLN ** l 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 61510 Z= 0.248 Angle : 0.558 12.368 83440 Z= 0.291 Chirality : 0.041 0.174 9560 Planarity : 0.003 0.054 10240 Dihedral : 11.057 73.936 10210 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.92 % Allowed : 16.56 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.10), residues: 7340 helix: 1.47 (0.08), residues: 4740 sheet: 0.31 (0.21), residues: 440 loop : 0.54 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 260 HIS 0.009 0.001 HIS M 225 PHE 0.016 0.002 PHE J 111 TYR 0.015 0.002 TYR h 365 ARG 0.014 0.001 ARG c 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 707 time to evaluate : 5.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: A 101 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7954 (ttm110) REVERT: A 110 LYS cc_start: 0.8091 (tmtm) cc_final: 0.7798 (tmtm) REVERT: A 129 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7974 (mp) REVERT: A 198 LYS cc_start: 0.8221 (mmtm) cc_final: 0.7736 (mppt) REVERT: B 12 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8185 (tp) REVERT: B 15 ASP cc_start: 0.8469 (t70) cc_final: 0.8207 (t70) REVERT: B 71 MET cc_start: 0.8997 (mtm) cc_final: 0.8772 (mtp) REVERT: B 89 HIS cc_start: 0.7266 (t70) cc_final: 0.6739 (t-90) REVERT: B 93 ASN cc_start: 0.8047 (t0) cc_final: 0.7704 (t0) REVERT: B 248 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8228 (mmm) REVERT: B 257 MET cc_start: 0.8780 (mmm) cc_final: 0.8398 (mmm) REVERT: D 12 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8208 (mp) REVERT: D 71 MET cc_start: 0.9149 (mtm) cc_final: 0.8757 (mtm) REVERT: D 77 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: D 110 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7801 (ttpm) REVERT: D 125 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8543 (mt) REVERT: D 142 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6199 (pp-130) REVERT: D 195 LYS cc_start: 0.8069 (mtmm) cc_final: 0.7856 (pttp) REVERT: D 198 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7888 (mppt) REVERT: D 334 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8239 (ttp) REVERT: E 12 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8105 (mp) REVERT: E 55 GLU cc_start: 0.7740 (pm20) cc_final: 0.7450 (pm20) REVERT: E 67 MET cc_start: 0.8225 (mmm) cc_final: 0.7877 (mmp) REVERT: E 93 ASN cc_start: 0.7928 (t0) cc_final: 0.7374 (t0) REVERT: E 359 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.5387 (mp0) REVERT: G 12 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8247 (tp) REVERT: G 67 MET cc_start: 0.8789 (mmm) cc_final: 0.8360 (mmm) REVERT: G 130 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: G 201 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7932 (mt) REVERT: H 12 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8178 (tp) REVERT: H 50 MET cc_start: 0.8228 (mtm) cc_final: 0.7948 (mtt) REVERT: H 93 ASN cc_start: 0.8194 (t0) cc_final: 0.7668 (t0) REVERT: H 126 ASN cc_start: 0.8756 (m-40) cc_final: 0.8523 (m-40) REVERT: H 359 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.5244 (mp0) REVERT: J 12 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8165 (tp) REVERT: J 16 GLN cc_start: 0.8315 (tt0) cc_final: 0.8021 (tt0) REVERT: J 24 THR cc_start: 0.8823 (p) cc_final: 0.8604 (p) REVERT: J 67 MET cc_start: 0.8797 (mmm) cc_final: 0.8450 (mmm) REVERT: J 130 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: J 334 MET cc_start: 0.8840 (ttp) cc_final: 0.8251 (ttt) REVERT: J 338 ARG cc_start: 0.7648 (mpp-170) cc_final: 0.7410 (mtm110) REVERT: J 356 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6560 (mt0) REVERT: K 12 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8391 (tp) REVERT: K 93 ASN cc_start: 0.7899 (t0) cc_final: 0.7410 (t0) REVERT: K 191 LYS cc_start: 0.8313 (ptpt) cc_final: 0.7918 (pttp) REVERT: K 198 LYS cc_start: 0.8658 (mmtm) cc_final: 0.8329 (mmpt) REVERT: K 201 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8126 (mt) REVERT: K 336 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7481 (pt0) REVERT: K 356 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6481 (mt0) REVERT: M 50 MET cc_start: 0.8815 (mtp) cc_final: 0.8602 (mtm) REVERT: M 109 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7115 (mtp) REVERT: M 195 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7741 (mtpm) REVERT: M 338 ARG cc_start: 0.7478 (mtm180) cc_final: 0.7278 (mpp-170) REVERT: N 67 MET cc_start: 0.8644 (mmp) cc_final: 0.8317 (mmm) REVERT: N 71 MET cc_start: 0.9035 (mtm) cc_final: 0.8746 (mtp) REVERT: N 93 ASN cc_start: 0.8030 (t0) cc_final: 0.7688 (t0) REVERT: N 110 LYS cc_start: 0.8248 (tppp) cc_final: 0.7647 (tppp) REVERT: N 119 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8046 (mt) REVERT: N 142 MET cc_start: 0.5154 (pp-130) cc_final: 0.4923 (tmm) REVERT: N 198 LYS cc_start: 0.8652 (mmpt) cc_final: 0.8445 (mmtm) REVERT: P 77 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: P 101 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7987 (ttm110) REVERT: P 129 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7979 (mp) REVERT: P 198 LYS cc_start: 0.8221 (mmtm) cc_final: 0.7743 (mppt) REVERT: Q 12 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8189 (tp) REVERT: Q 15 ASP cc_start: 0.8474 (t70) cc_final: 0.8215 (t70) REVERT: Q 71 MET cc_start: 0.8993 (mtm) cc_final: 0.8756 (mtp) REVERT: Q 89 HIS cc_start: 0.7290 (t70) cc_final: 0.6772 (t-90) REVERT: Q 93 ASN cc_start: 0.7928 (t0) cc_final: 0.7610 (t0) REVERT: Q 138 MET cc_start: 0.7947 (tmm) cc_final: 0.7585 (ppp) REVERT: Q 257 MET cc_start: 0.8780 (mmm) cc_final: 0.8397 (mmm) REVERT: S 12 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8210 (mp) REVERT: S 71 MET cc_start: 0.9145 (mtm) cc_final: 0.8742 (mtm) REVERT: S 77 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: S 110 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7816 (ttpm) REVERT: S 125 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8543 (mt) REVERT: S 142 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6282 (pp-130) REVERT: S 195 LYS cc_start: 0.8073 (mtmm) cc_final: 0.7848 (pttp) REVERT: S 198 LYS cc_start: 0.8134 (mmtm) cc_final: 0.7892 (mppt) REVERT: S 334 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8255 (ttt) REVERT: T 12 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8118 (mp) REVERT: T 132 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.8105 (mtm-85) REVERT: T 359 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.5480 (mp0) REVERT: c 12 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8239 (tp) REVERT: c 67 MET cc_start: 0.8788 (mmm) cc_final: 0.8351 (mmm) REVERT: c 130 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: c 201 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7933 (mt) REVERT: d 50 MET cc_start: 0.8236 (mtm) cc_final: 0.7951 (mtt) REVERT: d 84 ARG cc_start: 0.7840 (mpt-90) cc_final: 0.7636 (mpt-90) REVERT: d 93 ASN cc_start: 0.8261 (t0) cc_final: 0.7924 (t0) REVERT: d 126 ASN cc_start: 0.8748 (m-40) cc_final: 0.8517 (m-40) REVERT: d 359 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5255 (mp0) REVERT: g 12 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8160 (tp) REVERT: g 16 GLN cc_start: 0.8323 (tt0) cc_final: 0.8034 (tt0) REVERT: g 24 THR cc_start: 0.8816 (p) cc_final: 0.8598 (p) REVERT: g 67 MET cc_start: 0.8801 (mmm) cc_final: 0.8463 (mmm) REVERT: g 130 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: g 195 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7987 (ttpp) REVERT: g 334 MET cc_start: 0.8847 (ttp) cc_final: 0.8317 (ttt) REVERT: h 93 ASN cc_start: 0.7979 (t0) cc_final: 0.7542 (t0) REVERT: h 142 MET cc_start: 0.5726 (OUTLIER) cc_final: 0.5475 (ptt) REVERT: h 191 LYS cc_start: 0.8405 (ptpt) cc_final: 0.8008 (pttp) REVERT: h 198 LYS cc_start: 0.8672 (mmtm) cc_final: 0.8307 (mmpt) REVERT: h 201 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8152 (mt) REVERT: k 50 MET cc_start: 0.8814 (mtp) cc_final: 0.8603 (mtm) REVERT: k 109 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7112 (mtp) REVERT: k 195 LYS cc_start: 0.8074 (ttpp) cc_final: 0.7753 (mtpm) REVERT: l 12 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8327 (mp) REVERT: l 67 MET cc_start: 0.8670 (mmp) cc_final: 0.8310 (mmm) REVERT: l 71 MET cc_start: 0.9039 (mtm) cc_final: 0.8751 (mtp) REVERT: l 93 ASN cc_start: 0.8024 (t0) cc_final: 0.7747 (t0) REVERT: l 281 MET cc_start: 0.8490 (mmm) cc_final: 0.8129 (tpp) outliers start: 180 outliers final: 84 residues processed: 822 average time/residue: 1.6809 time to fit residues: 1703.7276 Evaluate side-chains 830 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 696 time to evaluate : 4.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 129 ILE 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 248 MET Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 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 131 SER 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 110 LYS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 359 GLU Chi-restraints excluded: chain H residue 362 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 195 LYS 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 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 109 MET 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 119 LEU Chi-restraints excluded: chain N residue 120 THR 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 129 ILE Chi-restraints excluded: chain P residue 131 SER Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 363 ILE Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 120 THR Chi-restraints excluded: chain Q residue 133 LYS Chi-restraints excluded: chain Q residue 316 GLN 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 122 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 310 SER Chi-restraints excluded: chain S residue 334 MET Chi-restraints excluded: chain S residue 363 ILE Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 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 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 c residue 316 GLN Chi-restraints excluded: chain c residue 363 ILE Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 110 LYS 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 360 ASN 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 195 LYS Chi-restraints excluded: chain g residue 363 ILE 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 109 MET 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 201 LEU Chi-restraints excluded: chain l residue 316 GLN 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: 7.9990 chunk 677 optimal weight: 6.9990 chunk 618 optimal weight: 1.9990 chunk 659 optimal weight: 5.9990 chunk 396 optimal weight: 0.7980 chunk 287 optimal weight: 4.9990 chunk 517 optimal weight: 0.8980 chunk 202 optimal weight: 7.9990 chunk 595 optimal weight: 2.9990 chunk 623 optimal weight: 3.9990 chunk 656 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 102 GLN ** N 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 ** g 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 45 ASN ** h 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 GLN ** l 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 61510 Z= 0.274 Angle : 0.576 12.106 83440 Z= 0.300 Chirality : 0.042 0.176 9560 Planarity : 0.003 0.056 10240 Dihedral : 11.090 73.978 10210 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.89 % Allowed : 17.00 % Favored : 80.11 % 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: 1.47 (0.10), residues: 7340 helix: 1.35 (0.07), residues: 4740 sheet: 0.27 (0.20), residues: 440 loop : 0.52 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP P 260 HIS 0.009 0.001 HIS M 225 PHE 0.017 0.002 PHE g 111 TYR 0.016 0.002 TYR K 365 ARG 0.014 0.001 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 864 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 686 time to evaluate : 5.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6755 (mp0) REVERT: A 101 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7979 (ttm110) REVERT: A 110 LYS cc_start: 0.8071 (tmtm) cc_final: 0.7750 (tmtm) REVERT: A 129 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8008 (mp) REVERT: A 195 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7854 (pttp) REVERT: A 198 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7707 (mppt) REVERT: B 12 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8170 (tp) REVERT: B 71 MET cc_start: 0.9000 (mtm) cc_final: 0.8761 (mtp) REVERT: B 93 ASN cc_start: 0.8070 (t0) cc_final: 0.7695 (t0) REVERT: B 248 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8277 (mmm) REVERT: B 257 MET cc_start: 0.8768 (mmm) cc_final: 0.8359 (mmm) REVERT: D 71 MET cc_start: 0.9152 (mtm) cc_final: 0.8770 (mtm) REVERT: D 77 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: D 110 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7799 (ttpm) REVERT: D 125 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8566 (mt) REVERT: D 142 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6325 (pp-130) REVERT: D 195 LYS cc_start: 0.8090 (mtmm) cc_final: 0.7876 (pttp) REVERT: D 198 LYS cc_start: 0.8122 (mmtm) cc_final: 0.7904 (mppt) REVERT: D 334 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8253 (ttt) REVERT: E 12 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8118 (mp) REVERT: E 93 ASN cc_start: 0.8048 (t0) cc_final: 0.7486 (t0) REVERT: E 198 LYS cc_start: 0.8767 (mmpt) cc_final: 0.8550 (mmtt) REVERT: E 359 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.5465 (mp0) REVERT: G 12 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8246 (tp) REVERT: G 67 MET cc_start: 0.8799 (mmm) cc_final: 0.8377 (mmm) REVERT: G 130 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: G 201 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7985 (mt) REVERT: H 12 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8182 (tp) REVERT: H 50 MET cc_start: 0.8241 (mtm) cc_final: 0.7963 (mtt) REVERT: H 93 ASN cc_start: 0.8123 (t0) cc_final: 0.7569 (t0) REVERT: H 126 ASN cc_start: 0.8779 (m-40) cc_final: 0.8553 (m-40) REVERT: H 359 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.5251 (mp0) REVERT: J 12 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8165 (tp) REVERT: J 16 GLN cc_start: 0.8325 (tt0) cc_final: 0.8027 (tt0) REVERT: J 24 THR cc_start: 0.8791 (p) cc_final: 0.8544 (p) REVERT: J 67 MET cc_start: 0.8810 (mmm) cc_final: 0.8460 (mmm) REVERT: J 130 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: J 138 MET cc_start: 0.7233 (tmm) cc_final: 0.6845 (tmt) REVERT: J 334 MET cc_start: 0.8842 (ttp) cc_final: 0.8256 (ttt) REVERT: J 356 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6556 (mt0) REVERT: K 12 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8367 (tp) REVERT: K 93 ASN cc_start: 0.7959 (t0) cc_final: 0.7488 (t0) REVERT: K 191 LYS cc_start: 0.8307 (ptpt) cc_final: 0.7822 (pttp) REVERT: K 198 LYS cc_start: 0.8658 (mmtm) cc_final: 0.8330 (mmpt) REVERT: K 201 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8155 (mt) REVERT: K 336 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7478 (pt0) REVERT: K 356 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6484 (mt0) REVERT: M 50 MET cc_start: 0.8826 (mtp) cc_final: 0.8588 (mtm) REVERT: M 138 MET cc_start: 0.7219 (tmm) cc_final: 0.7005 (tmt) REVERT: M 195 LYS cc_start: 0.8087 (ttpp) cc_final: 0.7737 (mtpm) REVERT: M 338 ARG cc_start: 0.7493 (mtm180) cc_final: 0.7288 (mpp-170) REVERT: N 67 MET cc_start: 0.8631 (mmp) cc_final: 0.8201 (mmm) REVERT: N 71 MET cc_start: 0.9023 (mtm) cc_final: 0.8733 (mtp) REVERT: N 93 ASN cc_start: 0.8027 (t0) cc_final: 0.7683 (t0) REVERT: N 119 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8077 (mt) REVERT: P 77 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: P 98 THR cc_start: 0.8543 (p) cc_final: 0.7995 (t) REVERT: P 129 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7894 (mp) REVERT: P 195 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7836 (pttp) REVERT: P 198 LYS cc_start: 0.8243 (mmtm) cc_final: 0.7722 (mppt) REVERT: Q 12 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8174 (tp) REVERT: Q 71 MET cc_start: 0.9006 (mtm) cc_final: 0.8767 (mtp) REVERT: Q 93 ASN cc_start: 0.7967 (t0) cc_final: 0.7624 (t0) REVERT: Q 257 MET cc_start: 0.8767 (mmm) cc_final: 0.8360 (mmm) REVERT: S 71 MET cc_start: 0.9147 (mtm) cc_final: 0.8778 (mtm) REVERT: S 77 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: S 110 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7754 (ttpm) REVERT: S 125 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8561 (mt) REVERT: S 138 MET cc_start: 0.7393 (tmm) cc_final: 0.7114 (tmt) REVERT: S 142 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6535 (pp-130) REVERT: S 195 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7864 (pttp) REVERT: S 198 LYS cc_start: 0.8116 (mmtm) cc_final: 0.7910 (mppt) REVERT: S 334 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8234 (ttt) REVERT: T 12 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8129 (mp) REVERT: T 198 LYS cc_start: 0.8758 (mmpt) cc_final: 0.8527 (mmtt) REVERT: T 359 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.5486 (mp0) REVERT: c 12 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8240 (tp) REVERT: c 67 MET cc_start: 0.8798 (mmm) cc_final: 0.8370 (mmm) REVERT: c 130 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: c 201 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7986 (mt) REVERT: d 50 MET cc_start: 0.8215 (mtm) cc_final: 0.7942 (mtt) REVERT: d 93 ASN cc_start: 0.8174 (t0) cc_final: 0.7828 (t0) REVERT: d 126 ASN cc_start: 0.8781 (m-40) cc_final: 0.8547 (m-40) REVERT: d 359 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.5254 (mp0) REVERT: g 12 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8160 (tp) REVERT: g 16 GLN cc_start: 0.8329 (tt0) cc_final: 0.8037 (tt0) REVERT: g 24 THR cc_start: 0.8788 (p) cc_final: 0.8544 (p) REVERT: g 67 MET cc_start: 0.8816 (mmm) cc_final: 0.8475 (mmm) REVERT: g 130 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: g 138 MET cc_start: 0.7350 (tmm) cc_final: 0.7069 (tmt) REVERT: g 195 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7914 (ttpp) REVERT: g 334 MET cc_start: 0.8836 (ttp) cc_final: 0.8303 (ttt) REVERT: h 12 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8369 (tp) REVERT: h 93 ASN cc_start: 0.7992 (t0) cc_final: 0.7538 (t0) REVERT: h 191 LYS cc_start: 0.8399 (ptpt) cc_final: 0.7916 (pttp) REVERT: h 198 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8346 (mmpt) REVERT: h 201 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8155 (mt) REVERT: h 282 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.6212 (tt0) REVERT: k 50 MET cc_start: 0.8826 (mtp) cc_final: 0.8589 (mtm) REVERT: k 138 MET cc_start: 0.7218 (tmm) cc_final: 0.7003 (tmt) REVERT: k 195 LYS cc_start: 0.8086 (ttpp) cc_final: 0.7743 (mtpm) REVERT: l 12 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8330 (mp) REVERT: l 71 MET cc_start: 0.9033 (mtm) cc_final: 0.8749 (mtp) REVERT: l 93 ASN cc_start: 0.8031 (t0) cc_final: 0.7681 (t0) outliers start: 178 outliers final: 91 residues processed: 805 average time/residue: 1.6950 time to fit residues: 1681.0741 Evaluate side-chains 815 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 676 time to evaluate : 4.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 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 39 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 110 LYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 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 109 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain G residue 363 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 359 GLU Chi-restraints excluded: chain H residue 362 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 195 LYS Chi-restraints excluded: chain J residue 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 201 LEU Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 356 GLN Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain M residue 363 ILE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 89 HIS Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 120 THR 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 55 GLU Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain P residue 131 SER Chi-restraints excluded: chain P residue 195 LYS Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain 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 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 122 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 310 SER Chi-restraints excluded: chain S residue 334 MET Chi-restraints excluded: chain S residue 363 ILE Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 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 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 c residue 363 ILE Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 110 LYS Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 359 GLU Chi-restraints excluded: chain d residue 360 ASN 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 130 GLU Chi-restraints excluded: chain g residue 195 LYS Chi-restraints excluded: chain g residue 363 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 201 LEU Chi-restraints excluded: chain h residue 282 GLU Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 39 ASP Chi-restraints excluded: chain k residue 109 MET Chi-restraints excluded: chain k residue 363 ILE Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 89 HIS 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 432 optimal weight: 0.9990 chunk 697 optimal weight: 5.9990 chunk 425 optimal weight: 4.9990 chunk 330 optimal weight: 1.9990 chunk 484 optimal weight: 7.9990 chunk 731 optimal weight: 7.9990 chunk 673 optimal weight: 0.3980 chunk 582 optimal weight: 4.9990 chunk 60 optimal weight: 0.0000 chunk 449 optimal weight: 3.9990 chunk 357 optimal weight: 0.0020 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 151 HIS A 192 ASN B 45 ASN D 102 GLN D 192 ASN ** E 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN J 102 GLN ** K 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN N 26 GLN P 151 HIS P 192 ASN Q 45 ASN S 102 GLN S 192 ASN ** T 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 102 GLN h 45 ASN ** h 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 GLN l 26 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 61510 Z= 0.149 Angle : 0.519 11.495 83440 Z= 0.270 Chirality : 0.039 0.175 9560 Planarity : 0.003 0.062 10240 Dihedral : 10.968 73.649 10210 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.06 % Allowed : 17.94 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.10), residues: 7340 helix: 1.69 (0.08), residues: 4740 sheet: 0.27 (0.21), residues: 440 loop : 0.65 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 260 HIS 0.004 0.001 HIS c 225 PHE 0.013 0.001 PHE J 111 TYR 0.014 0.001 TYR M 135 ARG 0.014 0.000 ARG c 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14680 Ramachandran restraints generated. 7340 Oldfield, 0 Emsley, 7340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 719 time to evaluate : 5.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: A 198 LYS cc_start: 0.8162 (mmtm) cc_final: 0.7714 (mppt) REVERT: B 15 ASP cc_start: 0.8281 (t70) cc_final: 0.8044 (t70) REVERT: B 71 MET cc_start: 0.9002 (mtm) cc_final: 0.8753 (mtp) REVERT: B 89 HIS cc_start: 0.7175 (t70) cc_final: 0.6662 (t-90) REVERT: B 93 ASN cc_start: 0.7913 (t0) cc_final: 0.7572 (t0) REVERT: B 248 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8348 (mmm) REVERT: B 257 MET cc_start: 0.8787 (mmm) cc_final: 0.8331 (mmm) REVERT: D 71 MET cc_start: 0.9089 (mtm) cc_final: 0.8752 (mtm) REVERT: D 93 ASN cc_start: 0.8423 (m-40) cc_final: 0.8214 (m110) REVERT: D 138 MET cc_start: 0.7477 (tmm) cc_final: 0.7168 (tmt) REVERT: D 142 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6500 (pp-130) REVERT: D 195 LYS cc_start: 0.8017 (mtmm) cc_final: 0.7803 (pttp) REVERT: D 310 SER cc_start: 0.8209 (OUTLIER) cc_final: 0.7969 (t) REVERT: D 334 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8265 (ttt) REVERT: E 12 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8052 (mp) REVERT: E 93 ASN cc_start: 0.7803 (t0) cc_final: 0.7262 (t0) REVERT: E 359 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5340 (mp0) REVERT: G 46 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8030 (mtmm) REVERT: G 67 MET cc_start: 0.8766 (mmm) cc_final: 0.8351 (mmm) REVERT: G 93 ASN cc_start: 0.8087 (m-40) cc_final: 0.7653 (m-40) REVERT: G 138 MET cc_start: 0.7442 (tmm) cc_final: 0.7111 (tmt) REVERT: G 201 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7739 (mt) REVERT: H 12 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8196 (tp) REVERT: H 50 MET cc_start: 0.8238 (mtm) cc_final: 0.7961 (mtt) REVERT: H 93 ASN cc_start: 0.8144 (t0) cc_final: 0.7701 (t0) REVERT: H 126 ASN cc_start: 0.8745 (m-40) cc_final: 0.8505 (m-40) REVERT: H 359 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.5314 (mp0) REVERT: J 16 GLN cc_start: 0.8297 (tt0) cc_final: 0.7918 (tt0) REVERT: J 24 THR cc_start: 0.8757 (p) cc_final: 0.8509 (p) REVERT: J 67 MET cc_start: 0.8757 (mmm) cc_final: 0.8406 (mmm) REVERT: J 138 MET cc_start: 0.7447 (tmm) cc_final: 0.7104 (tmt) REVERT: J 198 LYS cc_start: 0.8300 (mmpt) cc_final: 0.8051 (mppt) REVERT: J 334 MET cc_start: 0.8801 (ttp) cc_final: 0.8273 (ttt) REVERT: J 338 ARG cc_start: 0.7624 (mpp-170) cc_final: 0.7416 (mtm110) REVERT: J 356 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6581 (mt0) REVERT: K 12 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8397 (tp) REVERT: K 93 ASN cc_start: 0.7831 (t0) cc_final: 0.7429 (t0) REVERT: K 191 LYS cc_start: 0.8273 (ptpt) cc_final: 0.7909 (pttp) REVERT: K 198 LYS cc_start: 0.8637 (mmtm) cc_final: 0.8303 (mmpt) REVERT: K 201 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8077 (mt) REVERT: M 50 MET cc_start: 0.8718 (mtp) cc_final: 0.8488 (mtm) REVERT: M 195 LYS cc_start: 0.8050 (ttpp) cc_final: 0.7734 (mtpm) REVERT: M 338 ARG cc_start: 0.7439 (mtm180) cc_final: 0.7190 (mpp-170) REVERT: N 67 MET cc_start: 0.8589 (mmp) cc_final: 0.8350 (mmm) REVERT: N 71 MET cc_start: 0.9033 (mtm) cc_final: 0.8781 (mtp) REVERT: N 93 ASN cc_start: 0.7941 (t0) cc_final: 0.7605 (t0) REVERT: P 77 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: P 98 THR cc_start: 0.8524 (p) cc_final: 0.8049 (t) REVERT: P 132 ARG cc_start: 0.7582 (mtm-85) cc_final: 0.7370 (mtm-85) REVERT: P 198 LYS cc_start: 0.8165 (mmtm) cc_final: 0.7740 (mppt) REVERT: Q 15 ASP cc_start: 0.8288 (t70) cc_final: 0.8049 (t70) REVERT: Q 71 MET cc_start: 0.8999 (mtm) cc_final: 0.8732 (mtp) REVERT: Q 89 HIS cc_start: 0.7206 (t70) cc_final: 0.6712 (t-90) REVERT: Q 93 ASN cc_start: 0.7898 (t0) cc_final: 0.7566 (t0) REVERT: Q 257 MET cc_start: 0.8784 (mmm) cc_final: 0.8331 (mmm) REVERT: S 71 MET cc_start: 0.9084 (mtm) cc_final: 0.8760 (mtm) REVERT: S 110 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7716 (ttpm) REVERT: S 125 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8431 (mt) REVERT: S 138 MET cc_start: 0.7446 (tmm) cc_final: 0.7171 (tmt) REVERT: S 142 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6516 (pp-130) REVERT: S 310 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7974 (t) REVERT: S 334 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8252 (ttt) REVERT: T 12 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8070 (mp) REVERT: T 359 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.5343 (mp0) REVERT: c 46 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8031 (mtmm) REVERT: c 67 MET cc_start: 0.8765 (mmm) cc_final: 0.8346 (mmm) REVERT: c 93 ASN cc_start: 0.8230 (m-40) cc_final: 0.7769 (m-40) REVERT: c 101 ARG cc_start: 0.8201 (ttm110) cc_final: 0.7872 (mtm-85) REVERT: c 138 MET cc_start: 0.7458 (tmm) cc_final: 0.7137 (tmt) REVERT: c 201 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7729 (mt) REVERT: d 50 MET cc_start: 0.8241 (mtm) cc_final: 0.7956 (mtt) REVERT: d 93 ASN cc_start: 0.8213 (t0) cc_final: 0.7926 (t0) REVERT: d 126 ASN cc_start: 0.8729 (m-40) cc_final: 0.8490 (m-40) REVERT: d 359 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.5329 (mp0) REVERT: g 16 GLN cc_start: 0.8310 (tt0) cc_final: 0.7946 (tt0) REVERT: g 24 THR cc_start: 0.8755 (p) cc_final: 0.8508 (p) REVERT: g 67 MET cc_start: 0.8757 (mmm) cc_final: 0.8424 (mmm) REVERT: g 130 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: g 198 LYS cc_start: 0.8314 (mmpt) cc_final: 0.8061 (mppt) REVERT: g 334 MET cc_start: 0.8849 (ttp) cc_final: 0.8313 (ttt) REVERT: h 93 ASN cc_start: 0.7866 (t0) cc_final: 0.7474 (t0) REVERT: h 191 LYS cc_start: 0.8263 (ptpt) cc_final: 0.7894 (pttp) REVERT: h 198 LYS cc_start: 0.8665 (mmtm) cc_final: 0.8338 (mmpt) REVERT: h 201 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8125 (mt) REVERT: h 282 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.6080 (tt0) REVERT: k 50 MET cc_start: 0.8722 (mtp) cc_final: 0.8495 (mtm) REVERT: k 195 LYS cc_start: 0.8146 (ttpp) cc_final: 0.7858 (mtpm) REVERT: l 67 MET cc_start: 0.8593 (mmp) cc_final: 0.8319 (mmm) REVERT: l 71 MET cc_start: 0.9067 (mtm) cc_final: 0.8843 (mtp) REVERT: l 93 ASN cc_start: 0.7972 (t0) cc_final: 0.7595 (t0) REVERT: l 198 LYS cc_start: 0.8543 (mmpt) cc_final: 0.8253 (mmpt) outliers start: 127 outliers final: 59 residues processed: 801 average time/residue: 1.6325 time to fit residues: 1621.7684 Evaluate side-chains 776 residues out of total 6160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 689 time to evaluate : 4.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 201 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 39 ASP Chi-restraints excluded: chain D residue 109 MET 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 D residue 334 MET Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 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 131 SER 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 110 LYS 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 200 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 201 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 89 HIS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 359 GLU Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 362 VAL 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 39 ASP Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain S residue 110 LYS Chi-restraints excluded: chain S residue 122 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 310 SER Chi-restraints excluded: chain S residue 334 MET 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 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 12 LEU Chi-restraints excluded: chain d residue 110 LYS 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 h residue 201 LEU Chi-restraints excluded: chain h residue 282 GLU Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 109 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 462 optimal weight: 0.6980 chunk 620 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 536 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 583 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 chunk 598 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 J 102 GLN ** K 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN M 102 GLN P 151 HIS P 192 ASN S 93 ASN S 102 GLN S 192 ASN c 102 GLN c 192 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.156326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118136 restraints weight = 66894.509| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.37 r_work: 0.3212 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 61510 Z= 0.198 Angle : 0.539 11.559 83440 Z= 0.280 Chirality : 0.040 0.170 9560 Planarity : 0.003 0.056 10240 Dihedral : 10.953 73.844 10210 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.03 % Allowed : 18.21 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.10), residues: 7340 helix: 1.63 (0.08), residues: 4740 sheet: 0.24 (0.21), residues: 440 loop : 0.64 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 260 HIS 0.007 0.001 HIS c 225 PHE 0.016 0.002 PHE J 111 TYR 0.015 0.001 TYR J 135 ARG 0.014 0.000 ARG c 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23706.79 seconds wall clock time: 409 minutes 50.61 seconds (24590.61 seconds total)