Starting phenix.real_space_refine on Sun Feb 18 05:10:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8due_27719/02_2024/8due_27719_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8due_27719/02_2024/8due_27719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8due_27719/02_2024/8due_27719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8due_27719/02_2024/8due_27719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8due_27719/02_2024/8due_27719_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8due_27719/02_2024/8due_27719_updated.pdb" } resolution = 2.9 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 25 5.49 5 Mg 5 5.21 5 S 119 5.16 5 C 13224 2.51 5 N 3465 2.21 5 O 4066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "F PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20904 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "M" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.12, per 1000 atoms: 0.53 Number of scatterers: 20904 At special positions: 0 Unit cell: (115.92, 135.792, 154.836, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 119 16.00 P 25 15.00 Mg 5 11.99 O 4066 8.00 N 3465 7.00 C 13224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.91 Conformation dependent library (CDL) restraints added in 3.7 seconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 117 helices and 9 sheets defined 47.3% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.47 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 14 through 18 Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 67 through 79 removed outlier: 3.735A pdb=" N LYS A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 118 Processing helix chain 'A' and resid 131 through 142 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 204 through 217 Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 259 through 267 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 331 through 346 Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 377 through 380 No H-bonds generated for 'chain 'A' and resid 377 through 380' Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 13 through 19 Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 67 through 78 removed outlier: 3.567A pdb=" N GLY B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 118 Processing helix chain 'B' and resid 131 through 142 removed outlier: 3.634A pdb=" N ILE B 134 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 177 through 183 Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 230 through 241 Processing helix chain 'B' and resid 246 through 249 No H-bonds generated for 'chain 'B' and resid 246 through 249' Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 287 through 300 Processing helix chain 'B' and resid 328 through 346 Processing helix chain 'B' and resid 358 through 362 removed outlier: 4.099A pdb=" N ASP B 362 " --> pdb=" O GLN B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 377 through 380 No H-bonds generated for 'chain 'B' and resid 377 through 380' Processing helix chain 'B' and resid 391 through 395 Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 14 through 18 Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 53 through 62 Processing helix chain 'C' and resid 67 through 78 removed outlier: 3.757A pdb=" N SER C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 117 Processing helix chain 'C' and resid 121 through 123 No H-bonds generated for 'chain 'C' and resid 121 through 123' Processing helix chain 'C' and resid 131 through 142 Proline residue: C 135 - end of helix Processing helix chain 'C' and resid 158 through 166 Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 230 through 241 Processing helix chain 'C' and resid 246 through 250 removed outlier: 3.744A pdb=" N ASP C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 246 through 250' Processing helix chain 'C' and resid 256 through 268 Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.604A pdb=" N LEU C 293 " --> pdb=" O THR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 328 through 346 Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 376 through 380 Processing helix chain 'C' and resid 391 through 395 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 14 through 18 Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 32 through 47 Processing helix chain 'D' and resid 53 through 61 Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 87 through 118 Processing helix chain 'D' and resid 131 through 142 Proline residue: D 135 - end of helix removed outlier: 3.876A pdb=" N GLN D 140 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA D 141 " --> pdb=" O MET D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 167 Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'D' and resid 246 through 251 removed outlier: 3.664A pdb=" N ASP D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 267 Processing helix chain 'D' and resid 287 through 300 Processing helix chain 'D' and resid 328 through 346 Processing helix chain 'D' and resid 368 through 370 No H-bonds generated for 'chain 'D' and resid 368 through 370' Processing helix chain 'D' and resid 376 through 380 Processing helix chain 'D' and resid 391 through 395 Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 14 through 17 No H-bonds generated for 'chain 'E' and resid 14 through 17' Processing helix chain 'E' and resid 25 through 28 No H-bonds generated for 'chain 'E' and resid 25 through 28' Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 53 through 62 Processing helix chain 'E' and resid 67 through 76 Processing helix chain 'E' and resid 87 through 118 removed outlier: 3.588A pdb=" N GLU E 118 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 123 No H-bonds generated for 'chain 'E' and resid 121 through 123' Processing helix chain 'E' and resid 131 through 142 removed outlier: 3.685A pdb=" N ILE E 134 " --> pdb=" O VAL E 131 " (cutoff:3.500A) Proline residue: E 135 - end of helix Processing helix chain 'E' and resid 158 through 165 Processing helix chain 'E' and resid 177 through 183 Processing helix chain 'E' and resid 203 through 217 Processing helix chain 'E' and resid 230 through 242 Processing helix chain 'E' and resid 246 through 250 Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 328 through 346 removed outlier: 5.768A pdb=" N LYS E 333 " --> pdb=" O TYR E 329 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA E 334 " --> pdb=" O THR E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 391 through 396 Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 14 through 18 Processing helix chain 'F' and resid 32 through 47 Processing helix chain 'F' and resid 53 through 62 Processing helix chain 'F' and resid 67 through 79 Processing helix chain 'F' and resid 90 through 118 removed outlier: 4.022A pdb=" N ASN F 116 " --> pdb=" O GLU F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 143 Proline residue: F 135 - end of helix Processing helix chain 'F' and resid 155 through 167 removed outlier: 4.934A pdb=" N GLU F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG F 161 " --> pdb=" O TYR F 158 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TRP F 162 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN F 167 " --> pdb=" O SER F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 182 Processing helix chain 'F' and resid 203 through 217 Processing helix chain 'F' and resid 230 through 242 Processing helix chain 'F' and resid 246 through 250 Processing helix chain 'F' and resid 256 through 268 Processing helix chain 'F' and resid 287 through 299 Processing helix chain 'F' and resid 328 through 346 Processing helix chain 'F' and resid 358 through 360 No H-bonds generated for 'chain 'F' and resid 358 through 360' Processing helix chain 'F' and resid 368 through 370 No H-bonds generated for 'chain 'F' and resid 368 through 370' Processing helix chain 'F' and resid 376 through 380 Processing sheet with id= A, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.737A pdb=" N LEU A 350 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N LEU A 195 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR A 352 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ALA A 197 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA A 354 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA A 353 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 417 through 419 removed outlier: 3.507A pdb=" N PHE B 383 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU B 350 " --> pdb=" O ASN B 193 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N LEU B 195 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR B 352 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA B 353 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 420 through 422 Processing sheet with id= D, first strand: chain 'C' and resid 427 through 430 removed outlier: 6.519A pdb=" N MET C 384 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU C 350 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU C 195 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR C 352 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ALA C 197 " --> pdb=" O THR C 352 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA C 354 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA C 353 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG C 274 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N TYR C 223 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE C 276 " --> pdb=" O TYR C 223 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER C 225 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS C 278 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 427 through 430 removed outlier: 3.635A pdb=" N LYS D 427 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 404 " --> pdb=" O MET D 384 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET D 384 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE D 383 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU D 350 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LEU D 195 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR D 352 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA D 353 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 427 through 430 removed outlier: 3.783A pdb=" N PHE E 383 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E 197 " --> pdb=" O ALA E 354 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG E 274 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR E 223 " --> pdb=" O ARG E 274 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE E 276 " --> pdb=" O TYR E 223 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N SER E 225 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS E 278 " --> pdb=" O SER E 225 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 350 through 355 Processing sheet with id= H, first strand: chain 'F' and resid 221 through 225 Processing sheet with id= I, first strand: chain 'F' and resid 420 through 422 886 hydrogen bonds defined for protein. 2493 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.73 Time building geometry restraints manager: 9.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6754 1.36 - 1.51: 5720 1.51 - 1.65: 8641 1.65 - 1.80: 137 1.80 - 1.95: 72 Bond restraints: 21324 Sorted by residual: bond pdb=" N VAL C 304 " pdb=" CA VAL C 304 " ideal model delta sigma weight residual 1.457 1.492 -0.035 9.00e-03 1.23e+04 1.54e+01 bond pdb=" N VAL B 19 " pdb=" CA VAL B 19 " ideal model delta sigma weight residual 1.460 1.492 -0.032 8.60e-03 1.35e+04 1.39e+01 bond pdb=" N LYS C 301 " pdb=" CA LYS C 301 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.22e-02 6.72e+03 9.42e+00 bond pdb=" N SER C 292 " pdb=" CA SER C 292 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.08e+00 bond pdb=" N VAL E 232 " pdb=" CA VAL E 232 " ideal model delta sigma weight residual 1.460 1.494 -0.033 1.19e-02 7.06e+03 7.90e+00 ... (remaining 21319 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.25: 521 106.25 - 113.20: 11807 113.20 - 120.15: 7352 120.15 - 127.10: 8966 127.10 - 134.04: 252 Bond angle restraints: 28898 Sorted by residual: angle pdb=" N LYS C 298 " pdb=" CA LYS C 298 " pdb=" C LYS C 298 " ideal model delta sigma weight residual 111.28 105.70 5.58 1.09e+00 8.42e-01 2.62e+01 angle pdb=" N PHE B 16 " pdb=" CA PHE B 16 " pdb=" C PHE B 16 " ideal model delta sigma weight residual 111.71 107.14 4.57 1.15e+00 7.56e-01 1.58e+01 angle pdb=" N ASP E 382 " pdb=" CA ASP E 382 " pdb=" C ASP E 382 " ideal model delta sigma weight residual 114.56 109.64 4.92 1.27e+00 6.20e-01 1.50e+01 angle pdb=" N SER F 30 " pdb=" CA SER F 30 " pdb=" C SER F 30 " ideal model delta sigma weight residual 113.01 108.60 4.41 1.20e+00 6.94e-01 1.35e+01 angle pdb=" N MET E 226 " pdb=" CA MET E 226 " pdb=" C MET E 226 " ideal model delta sigma weight residual 113.50 109.04 4.46 1.23e+00 6.61e-01 1.31e+01 ... (remaining 28893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 12670 35.99 - 71.99: 231 71.99 - 107.98: 6 107.98 - 143.97: 2 143.97 - 179.97: 2 Dihedral angle restraints: 12911 sinusoidal: 5297 harmonic: 7614 Sorted by residual: dihedral pdb=" CA VAL E 19 " pdb=" C VAL E 19 " pdb=" N TRP E 20 " pdb=" CA TRP E 20 " ideal model delta harmonic sigma weight residual 180.00 153.47 26.53 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL C 19 " pdb=" C VAL C 19 " pdb=" N TRP C 20 " pdb=" CA TRP C 20 " ideal model delta harmonic sigma weight residual 180.00 156.56 23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" O1A AGS D 501 " pdb=" O3A AGS D 501 " pdb=" PA AGS D 501 " pdb=" PB AGS D 501 " ideal model delta sinusoidal sigma weight residual -67.73 112.24 -179.97 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2345 0.039 - 0.079: 639 0.079 - 0.118: 232 0.118 - 0.158: 16 0.158 - 0.197: 6 Chirality restraints: 3238 Sorted by residual: chirality pdb=" CA VAL F 150 " pdb=" N VAL F 150 " pdb=" C VAL F 150 " pdb=" CB VAL F 150 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA LEU C 294 " pdb=" N LEU C 294 " pdb=" C LEU C 294 " pdb=" CB LEU C 294 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CA LEU C 299 " pdb=" N LEU C 299 " pdb=" C LEU C 299 " pdb=" CB LEU C 299 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 3235 not shown) Planarity restraints: 3597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 225 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C SER E 225 " 0.069 2.00e-02 2.50e+03 pdb=" O SER E 225 " -0.026 2.00e-02 2.50e+03 pdb=" N MET E 226 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 227 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.06e+00 pdb=" C GLU E 227 " 0.046 2.00e-02 2.50e+03 pdb=" O GLU E 227 " -0.017 2.00e-02 2.50e+03 pdb=" N MET E 228 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 16 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C PHE B 16 " 0.028 2.00e-02 2.50e+03 pdb=" O PHE B 16 " -0.011 2.00e-02 2.50e+03 pdb=" N SER B 17 " -0.010 2.00e-02 2.50e+03 ... (remaining 3594 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 216 2.52 - 3.12: 16587 3.12 - 3.71: 34182 3.71 - 4.31: 47143 4.31 - 4.90: 77991 Nonbonded interactions: 176119 Sorted by model distance: nonbonded pdb=" O2B AGS D 501 " pdb="MG MG D 502 " model vdw 1.926 2.170 nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.963 2.170 nonbonded pdb=" O3B AGS D 501 " pdb="MG MG D 502 " model vdw 1.972 2.170 nonbonded pdb=" O3A AGS C 501 " pdb="MG MG C 502 " model vdw 1.990 2.170 nonbonded pdb=" O1A AGS C 501 " pdb="MG MG C 502 " model vdw 1.998 2.170 ... (remaining 176114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 432) selection = (chain 'C' and resid 1 through 432) selection = (chain 'D' and resid 1 through 432) selection = (chain 'E' and resid 1 through 432) selection = (chain 'F' and resid 1 through 432) } 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: 1.620 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: 0.010 Extract box with map and model: 8.310 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 57.550 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.130 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:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 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 : 0.003 0.037 21324 Z= 0.199 Angle : 0.535 5.720 28898 Z= 0.325 Chirality : 0.041 0.197 3238 Planarity : 0.003 0.040 3597 Dihedral : 13.298 179.966 7991 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.40 % Allowed : 8.98 % Favored : 87.62 % 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: 0.26 (0.17), residues: 2580 helix: 1.55 (0.15), residues: 1274 sheet: -0.32 (0.31), residues: 307 loop : -1.51 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 162 HIS 0.002 0.001 HIS E 8 PHE 0.013 0.001 PHE F 417 TYR 0.009 0.001 TYR E 15 ARG 0.002 0.000 ARG F 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 446 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.3989 (pm20) cc_final: 0.3118 (pt0) REVERT: A 138 MET cc_start: 0.4909 (mpp) cc_final: 0.4433 (mpt) REVERT: A 155 MET cc_start: 0.6678 (tmm) cc_final: 0.6384 (tmm) REVERT: A 228 MET cc_start: 0.1530 (tpp) cc_final: 0.0638 (mtm) REVERT: A 241 MET cc_start: 0.1594 (mtm) cc_final: 0.1324 (mtm) REVERT: A 296 GLU cc_start: 0.2610 (OUTLIER) cc_final: 0.2379 (pt0) REVERT: A 298 LYS cc_start: 0.4106 (tptp) cc_final: 0.3714 (mtpm) REVERT: A 312 TYR cc_start: 0.2929 (OUTLIER) cc_final: 0.2699 (m-10) REVERT: A 315 ILE cc_start: 0.5531 (pt) cc_final: 0.5127 (pt) REVERT: A 325 SER cc_start: 0.4461 (t) cc_final: 0.4172 (p) REVERT: A 329 TYR cc_start: 0.3597 (m-80) cc_final: 0.3392 (m-80) REVERT: A 355 GLN cc_start: 0.5519 (mm110) cc_final: 0.5252 (mm-40) REVERT: A 411 LYS cc_start: 0.4861 (ttmm) cc_final: 0.4516 (ttpp) REVERT: A 431 ILE cc_start: 0.4374 (tp) cc_final: 0.4039 (pt) REVERT: B 13 GLN cc_start: 0.5098 (tm-30) cc_final: 0.4744 (tp-100) REVERT: B 70 TYR cc_start: 0.6180 (t80) cc_final: 0.5711 (t80) REVERT: B 76 LEU cc_start: 0.5828 (mp) cc_final: 0.5518 (tt) REVERT: B 138 MET cc_start: 0.3359 (mtt) cc_final: 0.3149 (mtt) REVERT: B 177 ARG cc_start: 0.4499 (mtm110) cc_final: 0.3706 (tpp-160) REVERT: B 241 MET cc_start: 0.4009 (ptp) cc_final: 0.2631 (mtp) REVERT: B 249 ILE cc_start: 0.6041 (mm) cc_final: 0.5695 (mt) REVERT: B 265 LYS cc_start: 0.5955 (pttp) cc_final: 0.5745 (ptpt) REVERT: B 267 ARG cc_start: 0.6511 (ttp-110) cc_final: 0.5456 (mmt-90) REVERT: B 304 VAL cc_start: 0.7196 (OUTLIER) cc_final: 0.6995 (p) REVERT: B 348 THR cc_start: 0.8075 (p) cc_final: 0.7594 (t) REVERT: B 384 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7064 (mtt) REVERT: C 1 MET cc_start: 0.7077 (ptm) cc_final: 0.6786 (ptm) REVERT: C 29 GLU cc_start: 0.6497 (tp30) cc_final: 0.6134 (mt-10) REVERT: C 93 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7215 (mm-30) REVERT: C 103 MET cc_start: 0.6971 (tpp) cc_final: 0.6075 (tpp) REVERT: C 113 ILE cc_start: 0.6473 (mt) cc_final: 0.6253 (mp) REVERT: C 235 LYS cc_start: 0.6264 (tttt) cc_final: 0.5687 (ttmt) REVERT: C 243 ASP cc_start: 0.6115 (t0) cc_final: 0.5888 (t0) REVERT: C 247 ASP cc_start: 0.4178 (OUTLIER) cc_final: 0.3701 (m-30) REVERT: C 274 ARG cc_start: 0.3695 (mpp-170) cc_final: 0.3283 (ttm170) REVERT: C 293 LEU cc_start: 0.3922 (OUTLIER) cc_final: 0.2685 (mt) REVERT: C 308 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7072 (mt) REVERT: C 326 GLU cc_start: 0.5049 (tt0) cc_final: 0.4839 (mp0) REVERT: C 356 VAL cc_start: 0.7535 (m) cc_final: 0.7298 (p) REVERT: C 368 MET cc_start: 0.5758 (ttm) cc_final: 0.5473 (ttp) REVERT: D 36 THR cc_start: 0.7595 (t) cc_final: 0.7349 (m) REVERT: D 92 LYS cc_start: 0.6759 (tmmt) cc_final: 0.6192 (mmmt) REVERT: D 93 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6085 (tp30) REVERT: D 139 ARG cc_start: 0.5877 (ptp90) cc_final: 0.5313 (ptt-90) REVERT: D 140 GLN cc_start: 0.6385 (mt0) cc_final: 0.5848 (pt0) REVERT: D 177 ARG cc_start: 0.7168 (mtm110) cc_final: 0.6764 (mtp-110) REVERT: D 184 LYS cc_start: 0.7569 (mmtp) cc_final: 0.7001 (mtpt) REVERT: D 231 GLU cc_start: 0.6390 (mp0) cc_final: 0.6114 (mp0) REVERT: D 288 ASN cc_start: 0.6166 (m-40) cc_final: 0.5762 (m-40) REVERT: D 295 ASN cc_start: 0.5535 (m110) cc_final: 0.5327 (m110) REVERT: D 347 GLU cc_start: 0.6661 (mm-30) cc_final: 0.6374 (mm-30) REVERT: D 364 SER cc_start: 0.6473 (p) cc_final: 0.5998 (t) REVERT: D 387 VAL cc_start: 0.6553 (t) cc_final: 0.6344 (t) REVERT: E 86 ASP cc_start: 0.7200 (t0) cc_final: 0.6718 (t0) REVERT: E 92 LYS cc_start: 0.6422 (ttmt) cc_final: 0.5685 (mptp) REVERT: E 95 GLU cc_start: 0.6458 (tt0) cc_final: 0.6156 (tt0) REVERT: E 104 PHE cc_start: 0.6821 (t80) cc_final: 0.6385 (t80) REVERT: E 128 MET cc_start: 0.3086 (tmt) cc_final: 0.1513 (mtp) REVERT: E 156 ASP cc_start: 0.6572 (m-30) cc_final: 0.5998 (t0) REVERT: E 166 MET cc_start: 0.6687 (ptp) cc_final: 0.6363 (ptt) REVERT: E 226 MET cc_start: 0.6666 (mmm) cc_final: 0.5426 (mpp) REVERT: E 292 SER cc_start: 0.7576 (t) cc_final: 0.7072 (p) REVERT: E 323 VAL cc_start: 0.3218 (OUTLIER) cc_final: 0.2805 (t) REVERT: E 373 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6459 (mt-10) REVERT: E 384 MET cc_start: 0.7874 (mtm) cc_final: 0.7524 (mtt) REVERT: E 389 GLU cc_start: 0.5406 (tt0) cc_final: 0.5063 (tp30) REVERT: F 1 MET cc_start: 0.2564 (tmm) cc_final: 0.1742 (mmt) REVERT: F 114 GLN cc_start: 0.4700 (OUTLIER) cc_final: 0.4477 (mt0) REVERT: F 123 LYS cc_start: 0.3431 (OUTLIER) cc_final: 0.3151 (ptpt) REVERT: F 155 MET cc_start: 0.1937 (OUTLIER) cc_final: 0.1465 (ttp) REVERT: F 184 LYS cc_start: 0.7105 (mmtp) cc_final: 0.6674 (mtmm) REVERT: F 226 MET cc_start: 0.6595 (mmt) cc_final: 0.5973 (mmt) REVERT: F 265 LYS cc_start: 0.6706 (ttmm) cc_final: 0.6387 (ttmt) REVERT: F 279 GLN cc_start: 0.6854 (tt0) cc_final: 0.6542 (tt0) REVERT: F 312 TYR cc_start: 0.5321 (OUTLIER) cc_final: 0.3232 (m-80) REVERT: F 313 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.6035 (tt) REVERT: F 338 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6493 (mp0) REVERT: F 368 MET cc_start: 0.5453 (tpt) cc_final: 0.5021 (tmm) REVERT: F 384 MET cc_start: 0.6275 (mtm) cc_final: 0.5710 (ttm) REVERT: F 407 ARG cc_start: 0.7002 (tmm-80) cc_final: 0.6709 (ttt180) REVERT: F 427 LYS cc_start: 0.6338 (ttpt) cc_final: 0.6105 (ttmt) outliers start: 76 outliers final: 12 residues processed: 497 average time/residue: 1.2519 time to fit residues: 708.7902 Evaluate side-chains 296 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 271 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 312 TYR Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 316 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 67 optimal weight: 0.0970 chunk 132 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 123 optimal weight: 0.8980 chunk 151 optimal weight: 6.9990 chunk 235 optimal weight: 10.0000 overall best weight: 2.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 355 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 HIS B 295 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN C 279 GLN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN E 253 HIS E 398 GLN F 288 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 399 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21324 Z= 0.245 Angle : 0.575 10.194 28898 Z= 0.304 Chirality : 0.043 0.252 3238 Planarity : 0.004 0.039 3597 Dihedral : 11.372 179.407 3022 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 5.27 % Allowed : 14.79 % Favored : 79.94 % 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: 0.06 (0.17), residues: 2580 helix: 1.24 (0.15), residues: 1271 sheet: -0.57 (0.30), residues: 333 loop : -1.33 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 20 HIS 0.005 0.001 HIS E 219 PHE 0.022 0.002 PHE F 417 TYR 0.029 0.002 TYR F 312 ARG 0.006 0.001 ARG C 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 284 time to evaluate : 2.395 Fit side-chains revert: symmetry clash REVERT: A 19 VAL cc_start: 0.2530 (OUTLIER) cc_final: 0.2184 (m) REVERT: A 23 MET cc_start: 0.3312 (mtp) cc_final: 0.3014 (mmm) REVERT: A 26 GLU cc_start: 0.4102 (pm20) cc_final: 0.3265 (pt0) REVERT: A 138 MET cc_start: 0.5102 (mpp) cc_final: 0.4633 (mpt) REVERT: A 150 VAL cc_start: 0.6955 (OUTLIER) cc_final: 0.6402 (t) REVERT: A 155 MET cc_start: 0.6799 (tmm) cc_final: 0.6550 (tmm) REVERT: A 228 MET cc_start: 0.1513 (tpp) cc_final: 0.0591 (mtm) REVERT: A 298 LYS cc_start: 0.4130 (tptp) cc_final: 0.3731 (mtpm) REVERT: A 325 SER cc_start: 0.4483 (t) cc_final: 0.4221 (p) REVERT: A 347 GLU cc_start: 0.6214 (mt-10) cc_final: 0.5195 (mt-10) REVERT: A 431 ILE cc_start: 0.4398 (tp) cc_final: 0.4036 (pt) REVERT: B 8 HIS cc_start: 0.6267 (m-70) cc_final: 0.5920 (m90) REVERT: B 70 TYR cc_start: 0.6004 (t80) cc_final: 0.5598 (t80) REVERT: B 76 LEU cc_start: 0.5841 (mp) cc_final: 0.5562 (tt) REVERT: B 177 ARG cc_start: 0.4550 (mtm110) cc_final: 0.3912 (mmp-170) REVERT: B 241 MET cc_start: 0.4005 (ptp) cc_final: 0.2538 (mtp) REVERT: B 249 ILE cc_start: 0.6022 (mm) cc_final: 0.5721 (mt) REVERT: B 267 ARG cc_start: 0.6574 (ttp-110) cc_final: 0.5485 (mmt-90) REVERT: B 304 VAL cc_start: 0.7136 (OUTLIER) cc_final: 0.6906 (p) REVERT: B 348 THR cc_start: 0.8162 (p) cc_final: 0.7720 (t) REVERT: C 1 MET cc_start: 0.7252 (ptm) cc_final: 0.6908 (ptm) REVERT: C 3 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6444 (mt-10) REVERT: C 23 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7270 (mmp) REVERT: C 50 VAL cc_start: 0.6460 (t) cc_final: 0.6153 (p) REVERT: C 103 MET cc_start: 0.7058 (tpp) cc_final: 0.6038 (tpp) REVERT: C 235 LYS cc_start: 0.6365 (tttt) cc_final: 0.5781 (ttmt) REVERT: C 243 ASP cc_start: 0.6132 (t0) cc_final: 0.5930 (t0) REVERT: C 247 ASP cc_start: 0.4251 (OUTLIER) cc_final: 0.3951 (m-30) REVERT: C 274 ARG cc_start: 0.3660 (mpp-170) cc_final: 0.3270 (ttm170) REVERT: C 293 LEU cc_start: 0.4450 (OUTLIER) cc_final: 0.3398 (tt) REVERT: C 294 LEU cc_start: 0.5307 (OUTLIER) cc_final: 0.5037 (tt) REVERT: C 326 GLU cc_start: 0.4988 (tp30) cc_final: 0.4725 (mp0) REVERT: C 365 ASP cc_start: 0.6559 (p0) cc_final: 0.5376 (t70) REVERT: D 4 ILE cc_start: 0.6910 (mp) cc_final: 0.6705 (mm) REVERT: D 36 THR cc_start: 0.7486 (t) cc_final: 0.7243 (m) REVERT: D 79 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.7045 (mmtm) REVERT: D 93 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6507 (tp30) REVERT: D 95 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6630 (mt-10) REVERT: D 100 GLN cc_start: 0.6427 (tm-30) cc_final: 0.6194 (mt0) REVERT: D 140 GLN cc_start: 0.6510 (mt0) cc_final: 0.5847 (mm-40) REVERT: D 146 PHE cc_start: 0.7054 (m-10) cc_final: 0.6803 (m-80) REVERT: D 177 ARG cc_start: 0.7286 (mtm110) cc_final: 0.6017 (mmm160) REVERT: D 184 LYS cc_start: 0.7652 (mmtp) cc_final: 0.7009 (mtpt) REVERT: D 231 GLU cc_start: 0.6348 (mp0) cc_final: 0.6142 (mp0) REVERT: D 288 ASN cc_start: 0.6156 (m-40) cc_final: 0.5873 (m-40) REVERT: D 347 GLU cc_start: 0.6578 (mm-30) cc_final: 0.6244 (mm-30) REVERT: D 364 SER cc_start: 0.6391 (p) cc_final: 0.5876 (t) REVERT: D 368 MET cc_start: 0.6555 (ttp) cc_final: 0.6225 (ttm) REVERT: D 384 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7361 (mtt) REVERT: D 387 VAL cc_start: 0.6720 (OUTLIER) cc_final: 0.6495 (t) REVERT: E 86 ASP cc_start: 0.7223 (t0) cc_final: 0.6803 (t70) REVERT: E 92 LYS cc_start: 0.6427 (ttmt) cc_final: 0.5655 (mptp) REVERT: E 95 GLU cc_start: 0.6496 (tt0) cc_final: 0.6233 (tt0) REVERT: E 166 MET cc_start: 0.6765 (ptp) cc_final: 0.6416 (ptt) REVERT: E 254 ILE cc_start: 0.6710 (mm) cc_final: 0.6479 (tp) REVERT: E 292 SER cc_start: 0.7645 (t) cc_final: 0.7100 (p) REVERT: E 323 VAL cc_start: 0.3379 (OUTLIER) cc_final: 0.2992 (t) REVERT: E 384 MET cc_start: 0.7816 (mtm) cc_final: 0.7589 (mtm) REVERT: E 389 GLU cc_start: 0.5688 (tt0) cc_final: 0.5345 (tp30) REVERT: F 1 MET cc_start: 0.2342 (tmm) cc_final: 0.1366 (mmt) REVERT: F 184 LYS cc_start: 0.6975 (mmtp) cc_final: 0.6371 (mtmm) REVERT: F 226 MET cc_start: 0.6365 (mmt) cc_final: 0.5775 (mmt) REVERT: F 248 ASP cc_start: 0.6058 (OUTLIER) cc_final: 0.5494 (m-30) REVERT: F 263 MET cc_start: 0.5852 (mmp) cc_final: 0.5574 (mmm) REVERT: F 265 LYS cc_start: 0.6718 (ttmm) cc_final: 0.6517 (ttmt) REVERT: F 338 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6832 (tp30) REVERT: F 368 MET cc_start: 0.5627 (OUTLIER) cc_final: 0.5076 (tmm) REVERT: F 407 ARG cc_start: 0.7006 (tmm-80) cc_final: 0.6745 (ttt180) REVERT: F 427 LYS cc_start: 0.6357 (ttpt) cc_final: 0.6153 (ttmt) outliers start: 118 outliers final: 38 residues processed: 369 average time/residue: 1.2006 time to fit residues: 510.2855 Evaluate side-chains 291 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 240 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 368 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 195 optimal weight: 0.9990 chunk 160 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 254 optimal weight: 20.0000 chunk 209 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 152 HIS B 422 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN C 279 GLN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS E 279 GLN E 425 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21324 Z= 0.243 Angle : 0.578 10.120 28898 Z= 0.305 Chirality : 0.042 0.203 3238 Planarity : 0.004 0.037 3597 Dihedral : 10.724 172.728 2994 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 6.03 % Allowed : 15.55 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.17), residues: 2580 helix: 1.08 (0.15), residues: 1268 sheet: -0.54 (0.30), residues: 331 loop : -1.45 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 20 HIS 0.013 0.001 HIS B 152 PHE 0.020 0.002 PHE F 417 TYR 0.021 0.002 TYR D 22 ARG 0.005 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 254 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TRP cc_start: 0.4178 (t60) cc_final: 0.3893 (t60) REVERT: A 155 MET cc_start: 0.6754 (tmm) cc_final: 0.6489 (tmm) REVERT: A 228 MET cc_start: 0.1232 (tpp) cc_final: 0.0467 (mtm) REVERT: A 298 LYS cc_start: 0.3865 (tptp) cc_final: 0.3589 (mtpm) REVERT: B 8 HIS cc_start: 0.6022 (m-70) cc_final: 0.5576 (m-70) REVERT: B 23 MET cc_start: 0.6488 (OUTLIER) cc_final: 0.6072 (tpp) REVERT: B 26 GLU cc_start: 0.5186 (pm20) cc_final: 0.4908 (pm20) REVERT: B 70 TYR cc_start: 0.5981 (t80) cc_final: 0.5651 (t80) REVERT: B 76 LEU cc_start: 0.5893 (mp) cc_final: 0.5538 (tt) REVERT: B 138 MET cc_start: 0.3488 (mtt) cc_final: 0.3229 (mtt) REVERT: B 144 ILE cc_start: 0.5525 (OUTLIER) cc_final: 0.5188 (mm) REVERT: B 155 MET cc_start: 0.6613 (tpp) cc_final: 0.4140 (mpp) REVERT: B 177 ARG cc_start: 0.4501 (mtm110) cc_final: 0.3878 (mmp-170) REVERT: B 241 MET cc_start: 0.3947 (OUTLIER) cc_final: 0.3109 (mtp) REVERT: B 249 ILE cc_start: 0.6135 (mm) cc_final: 0.5837 (mt) REVERT: B 267 ARG cc_start: 0.6489 (ttp-110) cc_final: 0.5430 (mmt-90) REVERT: B 304 VAL cc_start: 0.7191 (OUTLIER) cc_final: 0.6946 (p) REVERT: B 384 MET cc_start: 0.7610 (mtp) cc_final: 0.7405 (mtm) REVERT: C 1 MET cc_start: 0.7364 (ptm) cc_final: 0.7036 (ptm) REVERT: C 3 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6388 (mt-10) REVERT: C 23 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7300 (mmp) REVERT: C 29 GLU cc_start: 0.6449 (tm-30) cc_final: 0.6230 (tm-30) REVERT: C 103 MET cc_start: 0.7117 (tpp) cc_final: 0.6096 (tpp) REVERT: C 205 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.5810 (tp) REVERT: C 235 LYS cc_start: 0.6230 (tttt) cc_final: 0.5671 (ttmt) REVERT: C 247 ASP cc_start: 0.4298 (OUTLIER) cc_final: 0.4001 (m-30) REVERT: C 274 ARG cc_start: 0.3579 (mpp-170) cc_final: 0.3217 (ttm170) REVERT: C 293 LEU cc_start: 0.4697 (OUTLIER) cc_final: 0.3772 (tm) REVERT: C 308 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7119 (mt) REVERT: C 312 TYR cc_start: 0.4549 (OUTLIER) cc_final: 0.3149 (m-80) REVERT: C 326 GLU cc_start: 0.5048 (tp30) cc_final: 0.4761 (mp0) REVERT: C 365 ASP cc_start: 0.6540 (p0) cc_final: 0.5373 (t70) REVERT: D 12 ASP cc_start: 0.7596 (t0) cc_final: 0.7251 (t0) REVERT: D 26 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7041 (mt-10) REVERT: D 79 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.7081 (mmtm) REVERT: D 93 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6499 (tp30) REVERT: D 95 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6748 (mt-10) REVERT: D 140 GLN cc_start: 0.6558 (mt0) cc_final: 0.6011 (tt0) REVERT: D 146 PHE cc_start: 0.7083 (m-10) cc_final: 0.6841 (m-80) REVERT: D 177 ARG cc_start: 0.7248 (mtm110) cc_final: 0.5972 (mmm160) REVERT: D 184 LYS cc_start: 0.7634 (mmtp) cc_final: 0.7035 (mtpt) REVERT: D 241 MET cc_start: 0.7220 (mmm) cc_final: 0.6916 (mmt) REVERT: D 288 ASN cc_start: 0.6191 (m-40) cc_final: 0.5882 (m-40) REVERT: D 347 GLU cc_start: 0.6607 (mm-30) cc_final: 0.6254 (mm-30) REVERT: D 350 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7218 (tp) REVERT: D 364 SER cc_start: 0.6525 (p) cc_final: 0.6057 (t) REVERT: D 368 MET cc_start: 0.6599 (ttp) cc_final: 0.6313 (ttm) REVERT: D 387 VAL cc_start: 0.6776 (OUTLIER) cc_final: 0.6569 (t) REVERT: E 86 ASP cc_start: 0.7261 (t0) cc_final: 0.6797 (t70) REVERT: E 92 LYS cc_start: 0.6430 (ttmt) cc_final: 0.5631 (mptp) REVERT: E 95 GLU cc_start: 0.6487 (tt0) cc_final: 0.6185 (tt0) REVERT: E 138 MET cc_start: 0.4668 (mtm) cc_final: 0.4445 (mtm) REVERT: E 254 ILE cc_start: 0.6836 (mm) cc_final: 0.6570 (tp) REVERT: E 292 SER cc_start: 0.7602 (t) cc_final: 0.7096 (p) REVERT: E 296 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.5786 (tt0) REVERT: E 323 VAL cc_start: 0.3427 (OUTLIER) cc_final: 0.3043 (t) REVERT: E 389 GLU cc_start: 0.5681 (tt0) cc_final: 0.5318 (tp30) REVERT: F 1 MET cc_start: 0.2208 (tmm) cc_final: 0.1511 (mmm) REVERT: F 158 TYR cc_start: 0.6294 (p90) cc_final: 0.6033 (p90) REVERT: F 166 MET cc_start: 0.6652 (mtt) cc_final: 0.6260 (mtm) REVERT: F 184 LYS cc_start: 0.6989 (mmtp) cc_final: 0.6469 (mtmm) REVERT: F 226 MET cc_start: 0.6102 (mmt) cc_final: 0.5748 (mmt) REVERT: F 248 ASP cc_start: 0.6130 (OUTLIER) cc_final: 0.5598 (m-30) REVERT: F 298 LYS cc_start: 0.6987 (tppp) cc_final: 0.6779 (tppt) REVERT: F 338 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6734 (tp30) REVERT: F 384 MET cc_start: 0.6771 (OUTLIER) cc_final: 0.5983 (ttm) REVERT: F 407 ARG cc_start: 0.7022 (tmm-80) cc_final: 0.6704 (ttt180) outliers start: 135 outliers final: 48 residues processed: 356 average time/residue: 1.1466 time to fit residues: 472.9356 Evaluate side-chains 296 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 230 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 296 GLU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 384 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 158 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 250 optimal weight: 0.0970 chunk 123 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN B 13 GLN B 152 HIS ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21324 Z= 0.226 Angle : 0.567 12.351 28898 Z= 0.300 Chirality : 0.042 0.169 3238 Planarity : 0.003 0.037 3597 Dihedral : 10.620 176.910 2994 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 5.27 % Allowed : 17.25 % Favored : 77.48 % 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: -0.20 (0.17), residues: 2580 helix: 1.05 (0.15), residues: 1262 sheet: -0.59 (0.31), residues: 328 loop : -1.52 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 154 HIS 0.013 0.001 HIS B 152 PHE 0.020 0.002 PHE F 417 TYR 0.020 0.002 TYR B 15 ARG 0.004 0.000 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 239 time to evaluate : 2.276 Fit side-chains revert: symmetry clash REVERT: A 89 TRP cc_start: 0.4376 (t60) cc_final: 0.4061 (t60) REVERT: A 138 MET cc_start: 0.5045 (mpp) cc_final: 0.4700 (mpt) REVERT: A 155 MET cc_start: 0.6795 (tmm) cc_final: 0.6480 (tmm) REVERT: A 228 MET cc_start: 0.1093 (tpp) cc_final: 0.0533 (mtm) REVERT: A 298 LYS cc_start: 0.3805 (tptp) cc_final: 0.3488 (mtpm) REVERT: A 430 GLU cc_start: 0.3634 (OUTLIER) cc_final: 0.2630 (mm-30) REVERT: A 431 ILE cc_start: 0.4493 (OUTLIER) cc_final: 0.4078 (pt) REVERT: B 1 MET cc_start: 0.5027 (ptm) cc_final: 0.4799 (ptm) REVERT: B 8 HIS cc_start: 0.5982 (m-70) cc_final: 0.5510 (m-70) REVERT: B 15 TYR cc_start: 0.5742 (t80) cc_final: 0.5173 (t80) REVERT: B 23 MET cc_start: 0.6324 (OUTLIER) cc_final: 0.5922 (tpp) REVERT: B 26 GLU cc_start: 0.5082 (pm20) cc_final: 0.4857 (pm20) REVERT: B 70 TYR cc_start: 0.5999 (t80) cc_final: 0.5693 (t80) REVERT: B 76 LEU cc_start: 0.5944 (mp) cc_final: 0.5521 (tt) REVERT: B 138 MET cc_start: 0.3385 (mtt) cc_final: 0.3144 (mtt) REVERT: B 144 ILE cc_start: 0.5320 (OUTLIER) cc_final: 0.4999 (mm) REVERT: B 155 MET cc_start: 0.6686 (tpp) cc_final: 0.4215 (mpp) REVERT: B 177 ARG cc_start: 0.4484 (mtm110) cc_final: 0.3809 (mmt180) REVERT: B 249 ILE cc_start: 0.6250 (mm) cc_final: 0.5949 (mt) REVERT: B 253 HIS cc_start: 0.6303 (OUTLIER) cc_final: 0.6058 (t-90) REVERT: B 264 GLU cc_start: 0.5319 (mt-10) cc_final: 0.4872 (mt-10) REVERT: B 267 ARG cc_start: 0.6436 (ttp-110) cc_final: 0.5312 (mpt90) REVERT: B 304 VAL cc_start: 0.7191 (OUTLIER) cc_final: 0.6927 (p) REVERT: C 1 MET cc_start: 0.7336 (ptm) cc_final: 0.6986 (ptm) REVERT: C 3 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6443 (mt-10) REVERT: C 23 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7317 (mmp) REVERT: C 48 HIS cc_start: 0.5000 (m90) cc_final: 0.4617 (m170) REVERT: C 103 MET cc_start: 0.7068 (tpp) cc_final: 0.6050 (tpp) REVERT: C 205 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5731 (tp) REVERT: C 235 LYS cc_start: 0.6235 (tttt) cc_final: 0.5692 (ttmt) REVERT: C 247 ASP cc_start: 0.4293 (OUTLIER) cc_final: 0.3975 (m-30) REVERT: C 274 ARG cc_start: 0.3564 (mpp-170) cc_final: 0.3172 (ttm170) REVERT: C 308 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7126 (mt) REVERT: C 365 ASP cc_start: 0.6602 (p0) cc_final: 0.5426 (t70) REVERT: D 26 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: D 93 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6520 (tp30) REVERT: D 95 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6719 (mt-10) REVERT: D 140 GLN cc_start: 0.6538 (mt0) cc_final: 0.6081 (mp10) REVERT: D 146 PHE cc_start: 0.7137 (m-10) cc_final: 0.6919 (m-80) REVERT: D 177 ARG cc_start: 0.7276 (mtm110) cc_final: 0.5993 (mmm160) REVERT: D 184 LYS cc_start: 0.7536 (mmtp) cc_final: 0.6990 (mtpt) REVERT: D 288 ASN cc_start: 0.6260 (m-40) cc_final: 0.5899 (m-40) REVERT: D 320 ARG cc_start: 0.4202 (mtt90) cc_final: 0.3916 (mtt180) REVERT: D 347 GLU cc_start: 0.6570 (mm-30) cc_final: 0.6293 (mm-30) REVERT: D 350 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7231 (tp) REVERT: D 368 MET cc_start: 0.6678 (ttp) cc_final: 0.6386 (ttm) REVERT: D 387 VAL cc_start: 0.6781 (OUTLIER) cc_final: 0.6554 (t) REVERT: E 86 ASP cc_start: 0.7314 (t0) cc_final: 0.6794 (t70) REVERT: E 92 LYS cc_start: 0.6472 (ttmt) cc_final: 0.5671 (mptp) REVERT: E 95 GLU cc_start: 0.6514 (tt0) cc_final: 0.6243 (tt0) REVERT: E 226 MET cc_start: 0.6554 (mmm) cc_final: 0.6024 (mtp) REVERT: E 254 ILE cc_start: 0.6853 (mm) cc_final: 0.6605 (tp) REVERT: E 292 SER cc_start: 0.7610 (t) cc_final: 0.7147 (p) REVERT: E 296 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.5750 (tp30) REVERT: E 323 VAL cc_start: 0.3604 (OUTLIER) cc_final: 0.3242 (t) REVERT: E 389 GLU cc_start: 0.5803 (tt0) cc_final: 0.5441 (tp30) REVERT: F 1 MET cc_start: 0.2352 (tmm) cc_final: 0.1597 (mmm) REVERT: F 158 TYR cc_start: 0.6320 (p90) cc_final: 0.6055 (p90) REVERT: F 166 MET cc_start: 0.6717 (mtt) cc_final: 0.6350 (mtm) REVERT: F 184 LYS cc_start: 0.6991 (mmtp) cc_final: 0.6497 (mtmm) REVERT: F 226 MET cc_start: 0.6046 (mmt) cc_final: 0.5733 (mmt) REVERT: F 227 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6837 (pt0) REVERT: F 248 ASP cc_start: 0.6025 (OUTLIER) cc_final: 0.5506 (m-30) REVERT: F 298 LYS cc_start: 0.6959 (tppp) cc_final: 0.6751 (tppt) REVERT: F 338 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6734 (tp30) REVERT: F 368 MET cc_start: 0.5890 (tpp) cc_final: 0.5455 (tmm) REVERT: F 407 ARG cc_start: 0.6998 (tmm-80) cc_final: 0.6785 (ttt180) outliers start: 118 outliers final: 57 residues processed: 331 average time/residue: 1.1725 time to fit residues: 446.3584 Evaluate side-chains 299 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 225 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 296 GLU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 7.9990 chunk 142 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 186 optimal weight: 0.0020 chunk 103 optimal weight: 6.9990 chunk 213 optimal weight: 8.9990 chunk 173 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 127 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 overall best weight: 2.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 152 HIS ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21324 Z= 0.281 Angle : 0.616 14.200 28898 Z= 0.324 Chirality : 0.043 0.208 3238 Planarity : 0.004 0.036 3597 Dihedral : 10.734 169.787 2994 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 6.03 % Allowed : 16.98 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2580 helix: 0.82 (0.15), residues: 1267 sheet: -0.52 (0.32), residues: 307 loop : -1.67 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 89 HIS 0.013 0.001 HIS B 152 PHE 0.022 0.002 PHE F 417 TYR 0.021 0.002 TYR D 22 ARG 0.004 0.001 ARG D 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 227 time to evaluate : 2.221 Fit side-chains revert: symmetry clash REVERT: A 89 TRP cc_start: 0.4515 (t60) cc_final: 0.4080 (t60) REVERT: A 97 TYR cc_start: 0.4230 (t80) cc_final: 0.3950 (t80) REVERT: A 155 MET cc_start: 0.6551 (tmm) cc_final: 0.6346 (tmm) REVERT: A 228 MET cc_start: 0.0807 (tpp) cc_final: 0.0219 (mtm) REVERT: A 298 LYS cc_start: 0.3901 (tptp) cc_final: 0.3496 (mtpm) REVERT: A 430 GLU cc_start: 0.3513 (OUTLIER) cc_final: 0.2547 (mm-30) REVERT: B 1 MET cc_start: 0.5181 (ptm) cc_final: 0.4930 (ptm) REVERT: B 8 HIS cc_start: 0.6042 (m-70) cc_final: 0.5580 (m-70) REVERT: B 23 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.6196 (tpp) REVERT: B 26 GLU cc_start: 0.5074 (pm20) cc_final: 0.4802 (pm20) REVERT: B 76 LEU cc_start: 0.5984 (mp) cc_final: 0.5437 (tt) REVERT: B 138 MET cc_start: 0.3331 (OUTLIER) cc_final: 0.3085 (mtt) REVERT: B 144 ILE cc_start: 0.5214 (OUTLIER) cc_final: 0.4885 (mm) REVERT: B 177 ARG cc_start: 0.4335 (mtm110) cc_final: 0.3724 (mmt180) REVERT: B 249 ILE cc_start: 0.6190 (mm) cc_final: 0.5879 (mt) REVERT: B 253 HIS cc_start: 0.6246 (OUTLIER) cc_final: 0.5934 (t-90) REVERT: B 264 GLU cc_start: 0.5486 (mt-10) cc_final: 0.5076 (mt-10) REVERT: B 267 ARG cc_start: 0.6407 (ttp-110) cc_final: 0.5344 (mpt90) REVERT: B 279 GLN cc_start: 0.6473 (OUTLIER) cc_final: 0.5692 (tp40) REVERT: B 304 VAL cc_start: 0.7194 (OUTLIER) cc_final: 0.6920 (p) REVERT: C 3 GLU cc_start: 0.7238 (mm-30) cc_final: 0.7000 (mm-30) REVERT: C 23 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7286 (mmp) REVERT: C 48 HIS cc_start: 0.4974 (m90) cc_final: 0.4571 (m170) REVERT: C 49 SER cc_start: 0.4956 (p) cc_final: 0.4652 (t) REVERT: C 103 MET cc_start: 0.7069 (tpp) cc_final: 0.6094 (tpp) REVERT: C 136 ASP cc_start: 0.6680 (p0) cc_final: 0.6180 (m-30) REVERT: C 205 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5672 (tp) REVERT: C 235 LYS cc_start: 0.6201 (tttt) cc_final: 0.5663 (ttmt) REVERT: C 247 ASP cc_start: 0.4360 (OUTLIER) cc_final: 0.4055 (m-30) REVERT: C 274 ARG cc_start: 0.3511 (mpp-170) cc_final: 0.3059 (ttm170) REVERT: C 308 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7142 (mt) REVERT: C 312 TYR cc_start: 0.4597 (OUTLIER) cc_final: 0.3204 (m-80) REVERT: C 365 ASP cc_start: 0.6528 (p0) cc_final: 0.5430 (t70) REVERT: D 26 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7022 (mt-10) REVERT: D 93 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6562 (tp30) REVERT: D 95 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6693 (mt-10) REVERT: D 100 GLN cc_start: 0.6341 (OUTLIER) cc_final: 0.6093 (tm-30) REVERT: D 140 GLN cc_start: 0.6665 (mt0) cc_final: 0.6166 (mp10) REVERT: D 146 PHE cc_start: 0.7178 (m-10) cc_final: 0.6963 (m-80) REVERT: D 177 ARG cc_start: 0.7117 (mtm110) cc_final: 0.5973 (mmm160) REVERT: D 184 LYS cc_start: 0.7510 (mmtp) cc_final: 0.6846 (mttt) REVERT: D 288 ASN cc_start: 0.6251 (m-40) cc_final: 0.5859 (t0) REVERT: D 327 ASN cc_start: 0.5287 (OUTLIER) cc_final: 0.4693 (p0) REVERT: D 347 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6427 (mm-30) REVERT: D 350 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7244 (tp) REVERT: D 368 MET cc_start: 0.6564 (ttp) cc_final: 0.6281 (ttm) REVERT: E 70 TYR cc_start: 0.3556 (OUTLIER) cc_final: 0.3330 (t80) REVERT: E 86 ASP cc_start: 0.7278 (t0) cc_final: 0.6756 (t70) REVERT: E 92 LYS cc_start: 0.6478 (ttmt) cc_final: 0.5685 (mptp) REVERT: E 95 GLU cc_start: 0.6541 (tt0) cc_final: 0.6234 (tt0) REVERT: E 254 ILE cc_start: 0.6910 (mm) cc_final: 0.6625 (tp) REVERT: E 292 SER cc_start: 0.7607 (t) cc_final: 0.7112 (p) REVERT: E 296 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.5718 (tp30) REVERT: E 317 LYS cc_start: 0.4990 (OUTLIER) cc_final: 0.4617 (ptmm) REVERT: E 389 GLU cc_start: 0.5884 (tt0) cc_final: 0.5491 (tp30) REVERT: F 1 MET cc_start: 0.2391 (tmm) cc_final: 0.1784 (tpp) REVERT: F 140 GLN cc_start: 0.5877 (tt0) cc_final: 0.5578 (mt0) REVERT: F 158 TYR cc_start: 0.6161 (p90) cc_final: 0.5809 (p90) REVERT: F 166 MET cc_start: 0.6744 (mtt) cc_final: 0.6361 (mtm) REVERT: F 184 LYS cc_start: 0.7029 (mmtp) cc_final: 0.6328 (ttpp) REVERT: F 200 ASN cc_start: 0.7106 (OUTLIER) cc_final: 0.6746 (m110) REVERT: F 298 LYS cc_start: 0.6946 (tppp) cc_final: 0.6725 (tppt) REVERT: F 338 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6636 (tp30) REVERT: F 368 MET cc_start: 0.6115 (tpp) cc_final: 0.5580 (tmm) REVERT: F 407 ARG cc_start: 0.7004 (tmm-80) cc_final: 0.6745 (ttt180) outliers start: 135 outliers final: 68 residues processed: 333 average time/residue: 1.1389 time to fit residues: 437.7649 Evaluate side-chains 306 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 218 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 296 GLU Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 384 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 250 optimal weight: 6.9990 chunk 208 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN A 415 ASN B 152 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21324 Z= 0.293 Angle : 0.639 15.509 28898 Z= 0.335 Chirality : 0.044 0.213 3238 Planarity : 0.004 0.037 3597 Dihedral : 10.750 158.284 2994 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 5.90 % Allowed : 17.87 % Favored : 76.23 % 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: -0.61 (0.17), residues: 2580 helix: 0.71 (0.15), residues: 1262 sheet: -0.64 (0.32), residues: 305 loop : -1.75 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 89 HIS 0.015 0.002 HIS B 152 PHE 0.023 0.002 PHE F 417 TYR 0.021 0.002 TYR D 22 ARG 0.009 0.001 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 231 time to evaluate : 2.331 Fit side-chains REVERT: A 89 TRP cc_start: 0.4584 (t60) cc_final: 0.4168 (t60) REVERT: A 97 TYR cc_start: 0.4276 (t80) cc_final: 0.4002 (t80) REVERT: A 138 MET cc_start: 0.4957 (mpp) cc_final: 0.4541 (mpt) REVERT: A 228 MET cc_start: 0.0950 (tpp) cc_final: 0.0252 (mtm) REVERT: A 430 GLU cc_start: 0.3480 (OUTLIER) cc_final: 0.2514 (mm-30) REVERT: A 431 ILE cc_start: 0.4563 (OUTLIER) cc_final: 0.3849 (pt) REVERT: B 1 MET cc_start: 0.5199 (ptm) cc_final: 0.4969 (ptm) REVERT: B 8 HIS cc_start: 0.6121 (m-70) cc_final: 0.5741 (m-70) REVERT: B 15 TYR cc_start: 0.6023 (t80) cc_final: 0.5527 (t80) REVERT: B 23 MET cc_start: 0.6458 (tpp) cc_final: 0.6142 (tpp) REVERT: B 76 LEU cc_start: 0.5962 (mp) cc_final: 0.5369 (tt) REVERT: B 79 LYS cc_start: 0.5986 (pttt) cc_final: 0.5774 (pttm) REVERT: B 138 MET cc_start: 0.3351 (OUTLIER) cc_final: 0.3045 (mtt) REVERT: B 144 ILE cc_start: 0.5174 (OUTLIER) cc_final: 0.4828 (mm) REVERT: B 155 MET cc_start: 0.6846 (tpp) cc_final: 0.4418 (mpp) REVERT: B 226 MET cc_start: 0.6131 (OUTLIER) cc_final: 0.5073 (mtt) REVERT: B 249 ILE cc_start: 0.6317 (mm) cc_final: 0.6079 (mm) REVERT: B 264 GLU cc_start: 0.5360 (mt-10) cc_final: 0.5037 (mt-10) REVERT: B 267 ARG cc_start: 0.6377 (ttp-110) cc_final: 0.5264 (mpt90) REVERT: B 279 GLN cc_start: 0.6558 (OUTLIER) cc_final: 0.5769 (tp40) REVERT: B 304 VAL cc_start: 0.7211 (OUTLIER) cc_final: 0.6936 (p) REVERT: C 23 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7241 (mmp) REVERT: C 48 HIS cc_start: 0.4899 (m90) cc_final: 0.4537 (m170) REVERT: C 49 SER cc_start: 0.4994 (p) cc_final: 0.4670 (t) REVERT: C 103 MET cc_start: 0.7070 (tpp) cc_final: 0.6075 (tpp) REVERT: C 136 ASP cc_start: 0.6647 (p0) cc_final: 0.6364 (m-30) REVERT: C 205 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5642 (tp) REVERT: C 235 LYS cc_start: 0.6134 (tttt) cc_final: 0.5597 (ttmt) REVERT: C 247 ASP cc_start: 0.4403 (OUTLIER) cc_final: 0.4093 (m-30) REVERT: C 274 ARG cc_start: 0.3600 (mpp-170) cc_final: 0.3025 (ttm170) REVERT: C 365 ASP cc_start: 0.6542 (p0) cc_final: 0.5478 (t70) REVERT: D 26 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6991 (mt-10) REVERT: D 93 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6584 (tp30) REVERT: D 95 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6613 (mt-10) REVERT: D 140 GLN cc_start: 0.6651 (mt0) cc_final: 0.6180 (mp10) REVERT: D 146 PHE cc_start: 0.7189 (m-10) cc_final: 0.6973 (m-80) REVERT: D 177 ARG cc_start: 0.6975 (mtm110) cc_final: 0.5938 (mmm160) REVERT: D 184 LYS cc_start: 0.7455 (mmtp) cc_final: 0.6875 (mtpt) REVERT: D 241 MET cc_start: 0.7218 (mmm) cc_final: 0.6898 (mmt) REVERT: D 288 ASN cc_start: 0.6150 (m-40) cc_final: 0.5794 (t0) REVERT: D 327 ASN cc_start: 0.5271 (OUTLIER) cc_final: 0.4589 (p0) REVERT: D 347 GLU cc_start: 0.6692 (mm-30) cc_final: 0.6480 (mm-30) REVERT: D 368 MET cc_start: 0.6495 (ttp) cc_final: 0.6202 (ttm) REVERT: E 70 TYR cc_start: 0.3602 (OUTLIER) cc_final: 0.3348 (t80) REVERT: E 86 ASP cc_start: 0.7290 (t0) cc_final: 0.6769 (t70) REVERT: E 92 LYS cc_start: 0.6565 (ttmt) cc_final: 0.5701 (mptp) REVERT: E 95 GLU cc_start: 0.6498 (tt0) cc_final: 0.6162 (tt0) REVERT: E 104 PHE cc_start: 0.6690 (t80) cc_final: 0.6298 (t80) REVERT: E 226 MET cc_start: 0.6746 (mmm) cc_final: 0.6316 (mtp) REVERT: E 254 ILE cc_start: 0.6711 (mm) cc_final: 0.6464 (tp) REVERT: E 292 SER cc_start: 0.7592 (t) cc_final: 0.7105 (p) REVERT: E 296 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.5707 (tp30) REVERT: E 317 LYS cc_start: 0.5037 (OUTLIER) cc_final: 0.4665 (ptmm) REVERT: E 389 GLU cc_start: 0.6088 (tt0) cc_final: 0.5645 (tp30) REVERT: F 1 MET cc_start: 0.2051 (tmm) cc_final: 0.1575 (ptm) REVERT: F 166 MET cc_start: 0.6742 (mtt) cc_final: 0.6370 (mtm) REVERT: F 184 LYS cc_start: 0.7000 (mmtp) cc_final: 0.6357 (ttpp) REVERT: F 338 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6444 (tp30) REVERT: F 368 MET cc_start: 0.6215 (tpp) cc_final: 0.5605 (tmm) REVERT: F 407 ARG cc_start: 0.7023 (tmm-80) cc_final: 0.6763 (ttt180) outliers start: 132 outliers final: 70 residues processed: 333 average time/residue: 1.0922 time to fit residues: 422.4606 Evaluate side-chains 306 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 221 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 296 GLU Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 382 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 142 optimal weight: 0.0970 chunk 182 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 152 HIS B 288 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21324 Z= 0.173 Angle : 0.556 15.713 28898 Z= 0.293 Chirality : 0.041 0.155 3238 Planarity : 0.003 0.034 3597 Dihedral : 10.353 159.170 2992 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.51 % Allowed : 19.84 % Favored : 75.65 % 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: -0.34 (0.17), residues: 2580 helix: 0.98 (0.15), residues: 1263 sheet: -0.70 (0.32), residues: 312 loop : -1.63 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 20 HIS 0.012 0.001 HIS B 152 PHE 0.013 0.001 PHE F 417 TYR 0.017 0.001 TYR D 22 ARG 0.006 0.000 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 236 time to evaluate : 2.325 Fit side-chains revert: symmetry clash REVERT: A 89 TRP cc_start: 0.4516 (t60) cc_final: 0.4097 (t60) REVERT: A 97 TYR cc_start: 0.4331 (t80) cc_final: 0.4040 (t80) REVERT: A 138 MET cc_start: 0.4977 (mpp) cc_final: 0.4570 (mpt) REVERT: A 228 MET cc_start: 0.0734 (tpp) cc_final: 0.0083 (mtm) REVERT: A 430 GLU cc_start: 0.3483 (OUTLIER) cc_final: 0.2548 (mm-30) REVERT: B 1 MET cc_start: 0.5199 (ptm) cc_final: 0.4995 (ptm) REVERT: B 15 TYR cc_start: 0.6087 (t80) cc_final: 0.5669 (t80) REVERT: B 23 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.6059 (tpp) REVERT: B 76 LEU cc_start: 0.5907 (mp) cc_final: 0.5339 (tt) REVERT: B 79 LYS cc_start: 0.6040 (pttt) cc_final: 0.5669 (pttm) REVERT: B 138 MET cc_start: 0.3317 (mtt) cc_final: 0.3019 (mtt) REVERT: B 144 ILE cc_start: 0.5113 (OUTLIER) cc_final: 0.4768 (mm) REVERT: B 155 MET cc_start: 0.6918 (tpp) cc_final: 0.4398 (mpp) REVERT: B 177 ARG cc_start: 0.4216 (mtm110) cc_final: 0.3611 (mmt180) REVERT: B 226 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.4993 (mtt) REVERT: B 249 ILE cc_start: 0.6291 (mm) cc_final: 0.6049 (mm) REVERT: B 264 GLU cc_start: 0.5289 (mt-10) cc_final: 0.4904 (mt-10) REVERT: B 267 ARG cc_start: 0.6363 (ttp-110) cc_final: 0.5239 (mpt90) REVERT: B 304 VAL cc_start: 0.7204 (OUTLIER) cc_final: 0.6941 (p) REVERT: B 384 MET cc_start: 0.7423 (mtp) cc_final: 0.7210 (mtm) REVERT: C 1 MET cc_start: 0.7309 (ptm) cc_final: 0.6943 (ptm) REVERT: C 3 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6716 (pm20) REVERT: C 23 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7264 (mmp) REVERT: C 48 HIS cc_start: 0.4794 (m90) cc_final: 0.4473 (m170) REVERT: C 49 SER cc_start: 0.4991 (p) cc_final: 0.4621 (t) REVERT: C 103 MET cc_start: 0.7000 (tpp) cc_final: 0.6014 (tpp) REVERT: C 136 ASP cc_start: 0.6589 (p0) cc_final: 0.6310 (m-30) REVERT: C 205 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5389 (tp) REVERT: C 235 LYS cc_start: 0.6131 (tttt) cc_final: 0.5598 (ttmt) REVERT: C 247 ASP cc_start: 0.4355 (OUTLIER) cc_final: 0.3998 (m-30) REVERT: C 274 ARG cc_start: 0.3559 (mpp-170) cc_final: 0.3031 (ttm170) REVERT: C 308 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7118 (mt) REVERT: C 365 ASP cc_start: 0.6633 (p0) cc_final: 0.5475 (t70) REVERT: D 26 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7034 (mt-10) REVERT: D 93 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6601 (tp30) REVERT: D 95 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6447 (mm-30) REVERT: D 100 GLN cc_start: 0.6258 (tt0) cc_final: 0.5915 (mt0) REVERT: D 140 GLN cc_start: 0.6575 (mt0) cc_final: 0.6142 (mp10) REVERT: D 177 ARG cc_start: 0.7057 (mtm110) cc_final: 0.5987 (mmm160) REVERT: D 184 LYS cc_start: 0.7496 (mmtp) cc_final: 0.6855 (mttt) REVERT: D 268 GLU cc_start: 0.6009 (mm-30) cc_final: 0.5557 (pp20) REVERT: D 327 ASN cc_start: 0.5114 (OUTLIER) cc_final: 0.4605 (p0) REVERT: D 347 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6573 (mm-30) REVERT: D 368 MET cc_start: 0.6515 (ttp) cc_final: 0.6261 (ttm) REVERT: E 70 TYR cc_start: 0.3614 (OUTLIER) cc_final: 0.3376 (t80) REVERT: E 86 ASP cc_start: 0.7303 (t0) cc_final: 0.6791 (t70) REVERT: E 92 LYS cc_start: 0.6552 (ttmt) cc_final: 0.5730 (mptp) REVERT: E 95 GLU cc_start: 0.6505 (tt0) cc_final: 0.6138 (tt0) REVERT: E 104 PHE cc_start: 0.6644 (t80) cc_final: 0.6219 (t80) REVERT: E 226 MET cc_start: 0.6652 (mmm) cc_final: 0.6033 (mtp) REVERT: E 292 SER cc_start: 0.7722 (t) cc_final: 0.7295 (p) REVERT: E 296 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.5740 (tp30) REVERT: E 317 LYS cc_start: 0.5105 (OUTLIER) cc_final: 0.4724 (ptmm) REVERT: E 389 GLU cc_start: 0.6079 (tt0) cc_final: 0.5642 (tp30) REVERT: F 1 MET cc_start: 0.2090 (tmm) cc_final: 0.1618 (ptm) REVERT: F 158 TYR cc_start: 0.6160 (p90) cc_final: 0.5907 (p90) REVERT: F 166 MET cc_start: 0.6700 (mtt) cc_final: 0.6314 (mtm) REVERT: F 184 LYS cc_start: 0.6996 (mmtp) cc_final: 0.6354 (ttpp) REVERT: F 227 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6934 (pt0) REVERT: F 368 MET cc_start: 0.6126 (tpp) cc_final: 0.5405 (tmm) REVERT: F 407 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6732 (ttt180) outliers start: 101 outliers final: 51 residues processed: 314 average time/residue: 1.1781 time to fit residues: 426.0157 Evaluate side-chains 291 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 224 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 125 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 296 GLU Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 407 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS B 152 HIS ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21324 Z= 0.216 Angle : 0.586 15.792 28898 Z= 0.307 Chirality : 0.042 0.159 3238 Planarity : 0.003 0.037 3597 Dihedral : 10.289 152.664 2992 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 5.00 % Allowed : 19.97 % Favored : 75.02 % 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: -0.42 (0.17), residues: 2580 helix: 0.91 (0.15), residues: 1276 sheet: -0.71 (0.32), residues: 312 loop : -1.70 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 89 HIS 0.013 0.001 HIS B 152 PHE 0.018 0.002 PHE F 417 TYR 0.018 0.001 TYR D 22 ARG 0.006 0.000 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 230 time to evaluate : 2.176 Fit side-chains revert: symmetry clash REVERT: A 89 TRP cc_start: 0.4564 (t60) cc_final: 0.4205 (t60) REVERT: A 97 TYR cc_start: 0.4249 (t80) cc_final: 0.3956 (t80) REVERT: A 138 MET cc_start: 0.4931 (mpp) cc_final: 0.4564 (mpt) REVERT: A 228 MET cc_start: 0.0683 (tpp) cc_final: -0.0004 (mtm) REVERT: A 347 GLU cc_start: 0.6294 (mt-10) cc_final: 0.5276 (mt-10) REVERT: A 430 GLU cc_start: 0.3457 (OUTLIER) cc_final: 0.2535 (mm-30) REVERT: B 1 MET cc_start: 0.5356 (ptm) cc_final: 0.5128 (ptm) REVERT: B 15 TYR cc_start: 0.6042 (t80) cc_final: 0.5635 (t80) REVERT: B 23 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.5950 (tpp) REVERT: B 76 LEU cc_start: 0.5922 (mp) cc_final: 0.5336 (tt) REVERT: B 79 LYS cc_start: 0.6020 (pttt) cc_final: 0.5744 (pttm) REVERT: B 138 MET cc_start: 0.3237 (mtt) cc_final: 0.2943 (mtt) REVERT: B 144 ILE cc_start: 0.5161 (OUTLIER) cc_final: 0.4771 (mm) REVERT: B 155 MET cc_start: 0.6934 (tpp) cc_final: 0.4421 (mpp) REVERT: B 177 ARG cc_start: 0.4230 (mtm110) cc_final: 0.3598 (mmt180) REVERT: B 226 MET cc_start: 0.6042 (OUTLIER) cc_final: 0.5002 (mtt) REVERT: B 249 ILE cc_start: 0.6339 (mm) cc_final: 0.6117 (mm) REVERT: B 253 HIS cc_start: 0.6104 (OUTLIER) cc_final: 0.5757 (t-90) REVERT: B 264 GLU cc_start: 0.5325 (mt-10) cc_final: 0.4972 (mt-10) REVERT: B 267 ARG cc_start: 0.6403 (ttp-110) cc_final: 0.5287 (mpt90) REVERT: B 304 VAL cc_start: 0.7191 (OUTLIER) cc_final: 0.6925 (p) REVERT: B 384 MET cc_start: 0.7442 (mtp) cc_final: 0.7235 (mtm) REVERT: C 1 MET cc_start: 0.7339 (ptm) cc_final: 0.6979 (ptm) REVERT: C 3 GLU cc_start: 0.7584 (mm-30) cc_final: 0.6735 (pm20) REVERT: C 23 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7423 (mmp) REVERT: C 48 HIS cc_start: 0.4741 (m90) cc_final: 0.4447 (m170) REVERT: C 49 SER cc_start: 0.4923 (p) cc_final: 0.4566 (t) REVERT: C 103 MET cc_start: 0.7002 (tpp) cc_final: 0.5990 (tpp) REVERT: C 136 ASP cc_start: 0.6674 (p0) cc_final: 0.6352 (m-30) REVERT: C 205 LEU cc_start: 0.6004 (OUTLIER) cc_final: 0.5397 (tp) REVERT: C 235 LYS cc_start: 0.6098 (tttt) cc_final: 0.5559 (ttmt) REVERT: C 247 ASP cc_start: 0.4458 (OUTLIER) cc_final: 0.4111 (m-30) REVERT: C 274 ARG cc_start: 0.3494 (mpp-170) cc_final: 0.2999 (ttm170) REVERT: C 365 ASP cc_start: 0.6640 (p0) cc_final: 0.5489 (t70) REVERT: D 1 MET cc_start: 0.5510 (ppp) cc_final: 0.5215 (ppp) REVERT: D 26 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7022 (mt-10) REVERT: D 46 GLU cc_start: 0.7313 (tt0) cc_final: 0.6842 (mm-30) REVERT: D 93 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6583 (tp30) REVERT: D 95 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6164 (mm-30) REVERT: D 100 GLN cc_start: 0.6282 (tt0) cc_final: 0.5926 (mt0) REVERT: D 140 GLN cc_start: 0.6593 (mt0) cc_final: 0.6136 (mp10) REVERT: D 146 PHE cc_start: 0.7044 (m-10) cc_final: 0.6839 (m-10) REVERT: D 177 ARG cc_start: 0.7043 (mtm110) cc_final: 0.5984 (mmm160) REVERT: D 184 LYS cc_start: 0.7497 (mmtp) cc_final: 0.6955 (mtpt) REVERT: D 327 ASN cc_start: 0.5273 (OUTLIER) cc_final: 0.4720 (p0) REVERT: D 347 GLU cc_start: 0.6753 (mm-30) cc_final: 0.6528 (mm-30) REVERT: E 70 TYR cc_start: 0.3608 (OUTLIER) cc_final: 0.3332 (t80) REVERT: E 86 ASP cc_start: 0.7310 (t0) cc_final: 0.6768 (t70) REVERT: E 92 LYS cc_start: 0.6540 (ttmt) cc_final: 0.5728 (mptp) REVERT: E 95 GLU cc_start: 0.6528 (tt0) cc_final: 0.6165 (tt0) REVERT: E 104 PHE cc_start: 0.6677 (t80) cc_final: 0.6218 (t80) REVERT: E 177 ARG cc_start: 0.6734 (mtm110) cc_final: 0.6495 (mtm110) REVERT: E 226 MET cc_start: 0.6576 (mmm) cc_final: 0.5880 (mtp) REVERT: E 292 SER cc_start: 0.7668 (t) cc_final: 0.7200 (p) REVERT: E 296 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.5731 (tp30) REVERT: E 317 LYS cc_start: 0.5095 (OUTLIER) cc_final: 0.4711 (ptmm) REVERT: E 389 GLU cc_start: 0.6093 (tt0) cc_final: 0.5656 (tp30) REVERT: F 1 MET cc_start: 0.1895 (tmm) cc_final: 0.1532 (ptm) REVERT: F 158 TYR cc_start: 0.5955 (p90) cc_final: 0.5702 (p90) REVERT: F 166 MET cc_start: 0.6728 (mtt) cc_final: 0.6311 (mtm) REVERT: F 184 LYS cc_start: 0.6991 (mmtp) cc_final: 0.6373 (ttpp) REVERT: F 200 ASN cc_start: 0.7000 (OUTLIER) cc_final: 0.6522 (m110) REVERT: F 227 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6984 (pt0) REVERT: F 338 GLU cc_start: 0.6204 (tp30) cc_final: 0.5738 (mm-30) REVERT: F 368 MET cc_start: 0.6163 (tpp) cc_final: 0.5500 (tmm) REVERT: F 407 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6754 (ttt180) outliers start: 112 outliers final: 57 residues processed: 316 average time/residue: 1.1355 time to fit residues: 414.8809 Evaluate side-chains 294 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 220 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 296 GLU Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 407 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 0.9990 chunk 239 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 182 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN B 152 HIS ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21324 Z= 0.204 Angle : 0.576 16.062 28898 Z= 0.302 Chirality : 0.042 0.228 3238 Planarity : 0.003 0.033 3597 Dihedral : 10.150 146.383 2992 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.38 % Allowed : 20.69 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2580 helix: 0.93 (0.15), residues: 1275 sheet: -0.71 (0.32), residues: 312 loop : -1.69 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 89 HIS 0.012 0.001 HIS B 152 PHE 0.016 0.002 PHE F 417 TYR 0.017 0.001 TYR D 22 ARG 0.005 0.000 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 230 time to evaluate : 2.516 Fit side-chains revert: symmetry clash REVERT: A 89 TRP cc_start: 0.4605 (t60) cc_final: 0.4060 (m-10) REVERT: A 97 TYR cc_start: 0.4234 (t80) cc_final: 0.3956 (t80) REVERT: A 138 MET cc_start: 0.5014 (mpp) cc_final: 0.4636 (mpt) REVERT: A 228 MET cc_start: 0.0650 (tpp) cc_final: -0.0150 (mtm) REVERT: A 347 GLU cc_start: 0.6292 (mt-10) cc_final: 0.5278 (mt-10) REVERT: A 430 GLU cc_start: 0.3417 (OUTLIER) cc_final: 0.2532 (mm-30) REVERT: B 1 MET cc_start: 0.5352 (ptm) cc_final: 0.5132 (ptm) REVERT: B 15 TYR cc_start: 0.6030 (t80) cc_final: 0.5548 (t80) REVERT: B 23 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.5995 (tpp) REVERT: B 76 LEU cc_start: 0.5899 (mp) cc_final: 0.5321 (tt) REVERT: B 79 LYS cc_start: 0.6001 (pttt) cc_final: 0.5760 (pttm) REVERT: B 138 MET cc_start: 0.3176 (mtt) cc_final: 0.2915 (mtt) REVERT: B 144 ILE cc_start: 0.5204 (OUTLIER) cc_final: 0.4812 (mm) REVERT: B 155 MET cc_start: 0.6931 (tpp) cc_final: 0.4418 (mpp) REVERT: B 177 ARG cc_start: 0.4219 (mtm110) cc_final: 0.3577 (mmt180) REVERT: B 226 MET cc_start: 0.6029 (OUTLIER) cc_final: 0.4983 (mtt) REVERT: B 249 ILE cc_start: 0.6303 (mm) cc_final: 0.6093 (mm) REVERT: B 264 GLU cc_start: 0.5336 (mt-10) cc_final: 0.4963 (mt-10) REVERT: B 267 ARG cc_start: 0.6402 (ttp-110) cc_final: 0.5287 (mpt90) REVERT: B 304 VAL cc_start: 0.7214 (OUTLIER) cc_final: 0.6943 (p) REVERT: B 384 MET cc_start: 0.7445 (mtp) cc_final: 0.7236 (mtm) REVERT: C 1 MET cc_start: 0.7341 (ptm) cc_final: 0.6995 (ptm) REVERT: C 3 GLU cc_start: 0.7596 (mm-30) cc_final: 0.6749 (pm20) REVERT: C 23 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7417 (mmp) REVERT: C 48 HIS cc_start: 0.4713 (m90) cc_final: 0.4423 (m170) REVERT: C 49 SER cc_start: 0.4914 (p) cc_final: 0.4557 (t) REVERT: C 103 MET cc_start: 0.7006 (tpp) cc_final: 0.6075 (tpp) REVERT: C 136 ASP cc_start: 0.6691 (p0) cc_final: 0.6376 (m-30) REVERT: C 205 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5402 (tp) REVERT: C 235 LYS cc_start: 0.6082 (tttt) cc_final: 0.5547 (ttmt) REVERT: C 274 ARG cc_start: 0.3475 (mpp-170) cc_final: 0.2983 (ttm170) REVERT: C 365 ASP cc_start: 0.6668 (p0) cc_final: 0.5529 (t70) REVERT: D 26 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7037 (mt-10) REVERT: D 46 GLU cc_start: 0.7319 (tt0) cc_final: 0.6837 (mm-30) REVERT: D 93 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6574 (tp30) REVERT: D 95 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6078 (mm-30) REVERT: D 100 GLN cc_start: 0.6241 (tt0) cc_final: 0.5910 (mt0) REVERT: D 140 GLN cc_start: 0.6522 (mt0) cc_final: 0.6099 (mp10) REVERT: D 146 PHE cc_start: 0.6985 (m-10) cc_final: 0.6760 (m-10) REVERT: D 177 ARG cc_start: 0.7016 (mtm110) cc_final: 0.5965 (mmm160) REVERT: D 184 LYS cc_start: 0.7521 (mmtp) cc_final: 0.6972 (mtpt) REVERT: D 268 GLU cc_start: 0.6006 (mm-30) cc_final: 0.5473 (pp20) REVERT: D 327 ASN cc_start: 0.5250 (OUTLIER) cc_final: 0.4698 (p0) REVERT: D 347 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6542 (mm-30) REVERT: E 70 TYR cc_start: 0.3612 (OUTLIER) cc_final: 0.3336 (t80) REVERT: E 86 ASP cc_start: 0.7310 (t0) cc_final: 0.6760 (t70) REVERT: E 92 LYS cc_start: 0.6539 (ttmt) cc_final: 0.5725 (mptp) REVERT: E 95 GLU cc_start: 0.6550 (tt0) cc_final: 0.6166 (tt0) REVERT: E 104 PHE cc_start: 0.6666 (t80) cc_final: 0.6204 (t80) REVERT: E 145 SER cc_start: 0.6099 (t) cc_final: 0.5871 (m) REVERT: E 177 ARG cc_start: 0.6743 (mtm110) cc_final: 0.6498 (mtm110) REVERT: E 226 MET cc_start: 0.6543 (mmm) cc_final: 0.5910 (mtp) REVERT: E 292 SER cc_start: 0.7671 (t) cc_final: 0.7203 (p) REVERT: E 296 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.5747 (tp30) REVERT: E 317 LYS cc_start: 0.5108 (OUTLIER) cc_final: 0.4730 (ptmm) REVERT: E 389 GLU cc_start: 0.6220 (tt0) cc_final: 0.5634 (tp30) REVERT: F 1 MET cc_start: 0.1858 (tmm) cc_final: 0.1524 (ptm) REVERT: F 158 TYR cc_start: 0.5904 (p90) cc_final: 0.5627 (p90) REVERT: F 166 MET cc_start: 0.6742 (mtt) cc_final: 0.6338 (mtm) REVERT: F 184 LYS cc_start: 0.6969 (mmtp) cc_final: 0.6361 (ttpp) REVERT: F 227 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6957 (pt0) REVERT: F 338 GLU cc_start: 0.6135 (tp30) cc_final: 0.5728 (mm-30) REVERT: F 368 MET cc_start: 0.6102 (tpp) cc_final: 0.5431 (tmm) REVERT: F 407 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6754 (ttt180) outliers start: 98 outliers final: 64 residues processed: 305 average time/residue: 1.2122 time to fit residues: 426.1374 Evaluate side-chains 299 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 221 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 125 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 296 GLU Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 407 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 171 optimal weight: 0.1980 chunk 258 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 205 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 125 optimal weight: 0.2980 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 355 GLN B 152 HIS ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21324 Z= 0.172 Angle : 0.562 16.302 28898 Z= 0.293 Chirality : 0.041 0.162 3238 Planarity : 0.003 0.032 3597 Dihedral : 9.867 139.779 2992 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.75 % Allowed : 21.67 % Favored : 74.58 % 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: -0.28 (0.17), residues: 2580 helix: 1.06 (0.15), residues: 1275 sheet: -0.63 (0.32), residues: 312 loop : -1.69 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 20 HIS 0.012 0.001 HIS B 152 PHE 0.017 0.001 PHE B 16 TYR 0.017 0.001 TYR B 256 ARG 0.007 0.000 ARG F 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 233 time to evaluate : 2.485 Fit side-chains revert: symmetry clash REVERT: A 89 TRP cc_start: 0.4640 (t60) cc_final: 0.4085 (m-10) REVERT: A 138 MET cc_start: 0.5078 (mpp) cc_final: 0.4757 (mpt) REVERT: A 203 LYS cc_start: 0.3612 (mmtm) cc_final: 0.2711 (mppt) REVERT: A 228 MET cc_start: 0.0565 (tpp) cc_final: -0.0160 (mtm) REVERT: A 347 GLU cc_start: 0.6286 (mt-10) cc_final: 0.5276 (mt-10) REVERT: A 430 GLU cc_start: 0.3461 (OUTLIER) cc_final: 0.2536 (mm-30) REVERT: B 1 MET cc_start: 0.5296 (ptm) cc_final: 0.5066 (ptm) REVERT: B 15 TYR cc_start: 0.6055 (t80) cc_final: 0.5545 (t80) REVERT: B 23 MET cc_start: 0.6385 (OUTLIER) cc_final: 0.6109 (tpp) REVERT: B 76 LEU cc_start: 0.5886 (mp) cc_final: 0.5336 (tt) REVERT: B 138 MET cc_start: 0.3170 (mtt) cc_final: 0.2907 (mtt) REVERT: B 144 ILE cc_start: 0.5189 (OUTLIER) cc_final: 0.4781 (mm) REVERT: B 155 MET cc_start: 0.6965 (tpp) cc_final: 0.4386 (mpp) REVERT: B 177 ARG cc_start: 0.4091 (mtm110) cc_final: 0.3521 (mmt180) REVERT: B 226 MET cc_start: 0.6042 (OUTLIER) cc_final: 0.4983 (mtt) REVERT: B 249 ILE cc_start: 0.6302 (mm) cc_final: 0.6092 (mm) REVERT: B 264 GLU cc_start: 0.5315 (mt-10) cc_final: 0.4975 (mt-10) REVERT: B 267 ARG cc_start: 0.6389 (ttp-110) cc_final: 0.5311 (mpt90) REVERT: B 304 VAL cc_start: 0.7129 (OUTLIER) cc_final: 0.6846 (p) REVERT: B 384 MET cc_start: 0.7408 (mtp) cc_final: 0.6971 (mtt) REVERT: C 1 MET cc_start: 0.7311 (ptm) cc_final: 0.6968 (ptm) REVERT: C 3 GLU cc_start: 0.7616 (mm-30) cc_final: 0.6741 (pm20) REVERT: C 23 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7242 (mmp) REVERT: C 48 HIS cc_start: 0.4689 (m90) cc_final: 0.4425 (m170) REVERT: C 103 MET cc_start: 0.6912 (tpp) cc_final: 0.6006 (tpp) REVERT: C 136 ASP cc_start: 0.6683 (p0) cc_final: 0.6362 (m-30) REVERT: C 205 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5235 (tp) REVERT: C 235 LYS cc_start: 0.6062 (tttt) cc_final: 0.5530 (ttmt) REVERT: C 274 ARG cc_start: 0.3414 (mpp-170) cc_final: 0.3011 (ttm170) REVERT: C 297 LEU cc_start: 0.4232 (OUTLIER) cc_final: 0.3637 (tp) REVERT: C 338 GLU cc_start: 0.4715 (tt0) cc_final: 0.3315 (mt-10) REVERT: C 365 ASP cc_start: 0.6645 (p0) cc_final: 0.5463 (t70) REVERT: D 46 GLU cc_start: 0.7344 (tt0) cc_final: 0.6918 (mm-30) REVERT: D 93 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6600 (tp30) REVERT: D 95 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6031 (mm-30) REVERT: D 100 GLN cc_start: 0.6164 (tt0) cc_final: 0.5852 (mt0) REVERT: D 140 GLN cc_start: 0.6577 (mt0) cc_final: 0.6166 (mp10) REVERT: D 177 ARG cc_start: 0.6940 (mtm110) cc_final: 0.5884 (mmm160) REVERT: D 184 LYS cc_start: 0.7496 (mmtp) cc_final: 0.6835 (mttt) REVERT: D 241 MET cc_start: 0.7081 (mmm) cc_final: 0.6789 (mmt) REVERT: D 268 GLU cc_start: 0.6030 (mm-30) cc_final: 0.5469 (pp20) REVERT: E 70 TYR cc_start: 0.3569 (OUTLIER) cc_final: 0.3282 (t80) REVERT: E 86 ASP cc_start: 0.7280 (t0) cc_final: 0.7063 (t70) REVERT: E 92 LYS cc_start: 0.6609 (ttmt) cc_final: 0.5788 (mptp) REVERT: E 95 GLU cc_start: 0.6597 (tt0) cc_final: 0.6240 (tt0) REVERT: E 104 PHE cc_start: 0.6658 (t80) cc_final: 0.6197 (t80) REVERT: E 145 SER cc_start: 0.5794 (t) cc_final: 0.5470 (m) REVERT: E 177 ARG cc_start: 0.6640 (mtm110) cc_final: 0.6380 (mtm110) REVERT: E 227 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5555 (mt-10) REVERT: E 292 SER cc_start: 0.7746 (t) cc_final: 0.7306 (p) REVERT: E 296 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.5734 (tp30) REVERT: E 323 VAL cc_start: 0.3735 (OUTLIER) cc_final: 0.3343 (t) REVERT: E 373 GLU cc_start: 0.6451 (mt-10) cc_final: 0.6237 (mt-10) REVERT: E 389 GLU cc_start: 0.6203 (tt0) cc_final: 0.5646 (tp30) REVERT: F 1 MET cc_start: 0.1876 (tmm) cc_final: 0.1572 (ptm) REVERT: F 158 TYR cc_start: 0.5834 (p90) cc_final: 0.5542 (p90) REVERT: F 166 MET cc_start: 0.6675 (mtt) cc_final: 0.6306 (mtm) REVERT: F 184 LYS cc_start: 0.6983 (mmtp) cc_final: 0.6389 (ttpp) REVERT: F 200 ASN cc_start: 0.6909 (OUTLIER) cc_final: 0.6347 (m110) REVERT: F 263 MET cc_start: 0.6096 (mmm) cc_final: 0.5847 (mmm) REVERT: F 338 GLU cc_start: 0.6251 (tp30) cc_final: 0.5779 (mm-30) REVERT: F 368 MET cc_start: 0.6199 (tpp) cc_final: 0.5577 (tmm) REVERT: F 407 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6747 (ttt180) outliers start: 84 outliers final: 50 residues processed: 299 average time/residue: 1.1784 time to fit residues: 406.3766 Evaluate side-chains 296 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 232 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 125 ASN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 296 GLU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 407 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 0.9990 chunk 218 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 205 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 152 HIS ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.209335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.178055 restraints weight = 27250.071| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 2.64 r_work: 0.3930 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21324 Z= 0.237 Angle : 0.612 16.532 28898 Z= 0.319 Chirality : 0.043 0.252 3238 Planarity : 0.004 0.035 3597 Dihedral : 9.871 131.147 2992 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.75 % Allowed : 21.85 % Favored : 74.40 % 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: -0.38 (0.17), residues: 2580 helix: 0.91 (0.15), residues: 1276 sheet: -0.67 (0.31), residues: 326 loop : -1.66 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 89 HIS 0.012 0.001 HIS B 152 PHE 0.019 0.002 PHE F 417 TYR 0.027 0.002 TYR A 97 ARG 0.005 0.000 ARG E 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7419.76 seconds wall clock time: 133 minutes 40.54 seconds (8020.54 seconds total)