Starting phenix.real_space_refine on Mon Feb 19 04:29:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/02_2024/8dvi_27739_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/02_2024/8dvi_27739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/02_2024/8dvi_27739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/02_2024/8dvi_27739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/02_2024/8dvi_27739_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvi_27739/02_2024/8dvi_27739_updated.pdb" } resolution = 3.2 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= 0.004 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 32 5.49 5 Mg 5 5.21 5 S 132 5.16 5 C 14995 2.51 5 N 3943 2.21 5 O 4586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "E PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H ARG 94": "NH1" <-> "NH2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H GLU 158": "OE1" <-> "OE2" Residue "H GLU 174": "OE1" <-> "OE2" Residue "H GLU 177": "OE1" <-> "OE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H GLU 211": "OE1" <-> "OE2" Residue "H GLU 223": "OE1" <-> "OE2" Residue "H GLU 234": "OE1" <-> "OE2" Residue "H GLU 243": "OE1" <-> "OE2" Residue "H GLU 256": "OE1" <-> "OE2" Residue "H GLU 271": "OE1" <-> "OE2" Residue "H GLU 289": "OE1" <-> "OE2" Residue "H GLU 311": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23693 Number of models: 1 Model: "" Number of chains: 14 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: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "H" Number of atoms: 2644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2644 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain breaks: 1 Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} 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: 13.15, per 1000 atoms: 0.56 Number of scatterers: 23693 At special positions: 0 Unit cell: (134.136, 130.824, 142.416, 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 132 16.00 P 32 15.00 Mg 5 11.99 O 4586 8.00 N 3943 7.00 C 14995 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: 10.07 Conformation dependent library (CDL) restraints added in 4.3 seconds 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5530 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 129 helices and 16 sheets defined 45.9% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.70 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 14 through 22 Proline residue: A 21 - end of helix 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 Processing helix chain 'A' and resid 87 through 117 Processing helix chain 'A' and resid 131 through 142 Proline residue: A 135 - end of helix removed outlier: 3.786A pdb=" N MET A 138 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.709A pdb=" N LEU A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 246 through 251 removed outlier: 3.727A pdb=" N ASP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 329 through 346 Processing helix chain 'A' and resid 358 through 362 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 10 Processing helix chain 'B' and resid 13 through 22 Proline residue: B 21 - end of helix 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 79 Processing helix chain 'B' and resid 89 through 118 Processing helix chain 'B' and resid 131 through 142 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 removed outlier: 3.512A pdb=" N ILE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 230 through 242 Processing helix chain 'B' and resid 248 through 251 No H-bonds generated for 'chain 'B' and resid 248 through 251' 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 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' 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 392 through 395 No H-bonds generated for 'chain 'B' and resid 392 through 395' Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 14 through 19 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 76 removed outlier: 4.001A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 118 Processing helix chain 'C' and resid 131 through 142 Proline residue: C 135 - end of helix Processing helix chain 'C' and resid 163 through 166 No H-bonds generated for 'chain 'C' and resid 163 through 166' Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 204 through 216 Processing helix chain 'C' and resid 230 through 241 Processing helix chain 'C' and resid 246 through 251 Processing helix chain 'C' and resid 256 through 268 Processing helix chain 'C' and resid 287 through 300 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 368 through 370 No H-bonds generated for 'chain 'C' and resid 368 through 370' Processing helix chain 'C' and resid 376 through 380 Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.550A pdb=" N ALA C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 13 through 22 removed outlier: 3.607A pdb=" N LYS D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) Proline residue: D 21 - end of helix 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 removed outlier: 3.671A pdb=" N PHE D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) 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 117 Processing helix chain 'D' and resid 131 through 142 Proline residue: D 135 - end of helix removed outlier: 3.523A pdb=" N LEU D 142 " --> pdb=" O ARG D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 164 removed outlier: 3.848A pdb=" N SER D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 230 through 242 Processing helix chain 'D' and resid 246 through 251 Processing helix chain 'D' and resid 256 through 267 Processing helix chain 'D' and resid 287 through 300 Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 328 through 346 Processing helix chain 'D' and resid 358 through 360 No H-bonds generated for 'chain 'D' and resid 358 through 360' 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 379 No H-bonds generated for 'chain 'D' and resid 376 through 379' Processing helix chain 'D' and resid 391 through 395 Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 13 through 19 removed outlier: 3.594A pdb=" N LYS E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 27 No H-bonds generated for 'chain 'E' and resid 25 through 27' 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 78 Processing helix chain 'E' and resid 87 through 118 Processing helix chain 'E' and resid 131 through 142 Proline residue: E 135 - end of helix removed outlier: 3.687A pdb=" N GLN E 140 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA E 141 " --> pdb=" O MET E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 166 Processing helix chain 'E' and resid 177 through 183 Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 230 through 241 Processing helix chain 'E' and resid 247 through 250 No H-bonds generated for 'chain 'E' and resid 247 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: 3.842A pdb=" N LYS E 333 " --> pdb=" O TYR E 329 " (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 2 through 11 Processing helix chain 'F' and resid 14 through 22 Proline residue: F 21 - end of helix Processing helix chain 'F' and resid 25 through 27 No H-bonds generated for 'chain 'F' and resid 25 through 27' Processing helix chain 'F' and resid 32 through 47 Processing helix chain 'F' and resid 53 through 61 Processing helix chain 'F' and resid 67 through 79 Processing helix chain 'F' and resid 89 through 117 Processing helix chain 'F' and resid 131 through 143 Proline residue: F 135 - end of helix removed outlier: 3.870A pdb=" N ALA F 141 " --> pdb=" O MET F 138 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU F 142 " --> pdb=" O ARG F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 166 Processing helix chain 'F' and resid 177 through 183 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 251 Processing helix chain 'F' and resid 256 through 268 Processing helix chain 'F' and resid 287 through 301 Processing helix chain 'F' and resid 328 through 346 Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'H' and resid 5 through 18 removed outlier: 3.660A pdb=" N ARG H 14 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS H 18 " --> pdb=" O ARG H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 81 Processing helix chain 'H' and resid 83 through 95 removed outlier: 3.858A pdb=" N GLU H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 142 Processing helix chain 'H' and resid 147 through 152 removed outlier: 4.001A pdb=" N LYS H 151 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 166 Processing helix chain 'H' and resid 222 through 224 No H-bonds generated for 'chain 'H' and resid 222 through 224' Processing helix chain 'H' and resid 238 through 241 removed outlier: 3.606A pdb=" N PHE H 241 " --> pdb=" O ASP H 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 238 through 241' Processing helix chain 'H' and resid 275 through 286 Processing helix chain 'H' and resid 304 through 311 Processing helix chain 'H' and resid 315 through 324 removed outlier: 3.852A pdb=" N LYS H 323 " --> pdb=" O MET H 319 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN H 324 " --> pdb=" O GLU H 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 339 Processing sheet with id= A, first strand: chain 'A' and resid 416 through 419 removed outlier: 6.511A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 383 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 353 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 420 through 422 Processing sheet with id= C, first strand: chain 'B' and resid 383 through 386 removed outlier: 3.627A pdb=" N PHE B 383 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 353 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 420 through 422 Processing sheet with id= E, first strand: chain 'C' and resid 402 through 406 removed outlier: 6.431A pdb=" N MET C 384 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 383 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA C 353 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ARG C 274 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR C 223 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE C 276 " --> pdb=" O TYR C 223 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N SER C 225 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS C 278 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 419 through 422 Processing sheet with id= G, first strand: chain 'D' and resid 349 through 354 removed outlier: 6.037A pdb=" N THR D 191 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR D 352 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN D 193 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA D 354 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU D 195 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE D 383 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N MET D 196 " --> pdb=" O PHE D 383 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU D 385 " --> pdb=" O MET D 196 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS D 405 " --> pdb=" O MET D 384 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA D 386 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLN D 403 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE D 388 " --> pdb=" O ILE D 401 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE D 401 " --> pdb=" O ILE D 388 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 220 through 225 removed outlier: 6.316A pdb=" N ARG D 274 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N TYR D 223 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE D 276 " --> pdb=" O TYR D 223 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER D 225 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS D 278 " --> pdb=" O SER D 225 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'E' and resid 416 through 418 removed outlier: 6.502A pdb=" N MET E 384 " --> pdb=" O ILE E 404 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE E 383 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL E 194 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA E 354 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA E 353 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG E 274 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TYR E 223 " --> pdb=" O ARG E 274 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE E 276 " --> pdb=" O TYR E 223 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SER E 225 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS E 278 " --> pdb=" O SER E 225 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 349 through 352 removed outlier: 6.196A pdb=" N THR F 191 " --> pdb=" O LEU F 350 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N THR F 352 " --> pdb=" O THR F 191 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN F 193 " --> pdb=" O THR F 352 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE F 383 " --> pdb=" O VAL F 194 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'F' and resid 221 through 225 Processing sheet with id= L, first strand: chain 'F' and resid 419 through 422 Processing sheet with id= M, first strand: chain 'H' and resid 23 through 25 Processing sheet with id= N, first strand: chain 'H' and resid 124 through 126 removed outlier: 3.753A pdb=" N SER H 193 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 264 through 266 removed outlier: 6.437A pdb=" N VAL H 230 " --> pdb=" O VAL H 265 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 290 through 292 removed outlier: 3.508A pdb=" N ALA H 327 " --> pdb=" O VAL H 291 " (cutoff:3.500A) 943 hydrogen bonds defined for protein. 2676 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: 7.16 Time building geometry restraints manager: 10.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7549 1.35 - 1.50: 6411 1.50 - 1.65: 10008 1.65 - 1.80: 105 1.80 - 1.95: 124 Bond restraints: 24197 Sorted by residual: bond pdb=" CE1 HIS D 87 " pdb=" NE2 HIS D 87 " ideal model delta sigma weight residual 1.321 1.359 -0.038 1.00e-02 1.00e+04 1.48e+01 bond pdb=" CE1 HIS B 152 " pdb=" NE2 HIS B 152 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.24e+01 bond pdb=" N VAL E 19 " pdb=" CA VAL E 19 " ideal model delta sigma weight residual 1.452 1.492 -0.039 1.18e-02 7.18e+03 1.12e+01 bond pdb=" N TRP D 20 " pdb=" CA TRP D 20 " ideal model delta sigma weight residual 1.462 1.492 -0.030 9.50e-03 1.11e+04 9.92e+00 bond pdb=" N TRP E 20 " pdb=" CA TRP E 20 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.04e-02 9.25e+03 9.69e+00 ... (remaining 24192 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.13: 614 106.13 - 113.17: 13252 113.17 - 120.21: 8750 120.21 - 127.25: 9906 127.25 - 134.29: 285 Bond angle restraints: 32807 Sorted by residual: angle pdb=" PB AGS C 501 " pdb=" O3B AGS C 501 " pdb=" PG AGS C 501 " ideal model delta sigma weight residual 120.12 132.58 -12.46 3.00e+00 1.11e-01 1.73e+01 angle pdb=" N ASP A 82 " pdb=" CA ASP A 82 " pdb=" C ASP A 82 " ideal model delta sigma weight residual 112.57 108.05 4.52 1.13e+00 7.83e-01 1.60e+01 angle pdb=" N GLU H 92 " pdb=" CA GLU H 92 " pdb=" C GLU H 92 " ideal model delta sigma weight residual 111.71 107.18 4.53 1.15e+00 7.56e-01 1.55e+01 angle pdb=" CA PHE D 383 " pdb=" CB PHE D 383 " pdb=" CG PHE D 383 " ideal model delta sigma weight residual 113.80 117.73 -3.93 1.00e+00 1.00e+00 1.55e+01 angle pdb=" C GLY F 151 " pdb=" N HIS F 152 " pdb=" CA HIS F 152 " ideal model delta sigma weight residual 122.30 117.07 5.23 1.35e+00 5.49e-01 1.50e+01 ... (remaining 32802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 14414 35.65 - 71.31: 202 71.31 - 106.96: 10 106.96 - 142.62: 1 142.62 - 178.27: 4 Dihedral angle restraints: 14631 sinusoidal: 6069 harmonic: 8562 Sorted by residual: dihedral pdb=" O1B AGS E 501 " pdb=" O3B AGS E 501 " pdb=" PB AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sinusoidal sigma weight residual 68.91 -112.82 -178.27 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS F 501 " pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sinusoidal sigma weight residual -67.73 106.43 -174.16 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS B 501 " pdb=" O3B AGS B 501 " pdb=" PB AGS B 501 " pdb=" PG AGS B 501 " ideal model delta sinusoidal sigma weight residual 68.91 -88.62 157.53 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 14628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2650 0.044 - 0.088: 645 0.088 - 0.132: 288 0.132 - 0.176: 48 0.176 - 0.220: 16 Chirality restraints: 3647 Sorted by residual: chirality pdb=" CA ILE H 93 " pdb=" N ILE H 93 " pdb=" C ILE H 93 " pdb=" CB ILE H 93 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL A 150 " pdb=" N VAL A 150 " pdb=" C VAL A 150 " pdb=" CB VAL A 150 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ARG A 124 " pdb=" N ARG A 124 " pdb=" C ARG A 124 " pdb=" CB ARG A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3644 not shown) Planarity restraints: 4071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 266 " 0.018 2.00e-02 2.50e+03 2.32e-02 1.35e+01 pdb=" CG TRP H 266 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP H 266 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP H 266 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 266 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP H 266 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP H 266 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 266 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 266 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP H 266 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 373 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLU A 373 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU A 373 " -0.021 2.00e-02 2.50e+03 pdb=" N SER A 374 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 145 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C SER B 145 " 0.039 2.00e-02 2.50e+03 pdb=" O SER B 145 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE B 146 " -0.013 2.00e-02 2.50e+03 ... (remaining 4068 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 114 2.47 - 3.07: 16454 3.07 - 3.68: 36605 3.68 - 4.29: 55796 4.29 - 4.90: 90692 Nonbonded interactions: 199661 Sorted by model distance: nonbonded pdb=" O1B AGS C 501 " pdb="MG MG C 502 " model vdw 1.856 2.170 nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.972 2.170 nonbonded pdb=" OE2 GLU B 227 " pdb="MG MG B 502 " model vdw 1.979 2.170 nonbonded pdb=" O2G AGS E 501 " pdb="MG MG E 502 " model vdw 1.985 2.170 nonbonded pdb=" O2B AGS F 501 " pdb="MG MG F 502 " model vdw 1.993 2.170 ... (remaining 199656 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: 0.010 Normalize map: mean=0, sd=1: 2.470 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: 0.000 Extract box with map and model: 11.130 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 63.350 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.004 0.051 24197 Z= 0.292 Angle : 0.682 12.461 32807 Z= 0.446 Chirality : 0.049 0.220 3647 Planarity : 0.004 0.075 4071 Dihedral : 12.486 178.275 9101 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.78 % Allowed : 7.25 % Favored : 90.96 % 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: 0.23 (0.16), residues: 2898 helix: 1.29 (0.14), residues: 1435 sheet: -0.35 (0.27), residues: 407 loop : -1.20 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP H 266 HIS 0.008 0.001 HIS B 152 PHE 0.022 0.002 PHE D 383 TYR 0.014 0.001 TYR E 329 ARG 0.004 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 722 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7054 (m) cc_final: 0.6730 (t) REVERT: A 327 ASN cc_start: 0.3766 (OUTLIER) cc_final: 0.3367 (p0) REVERT: A 347 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7665 (mm-30) REVERT: A 368 MET cc_start: 0.6148 (OUTLIER) cc_final: 0.5816 (ttm) REVERT: A 369 SER cc_start: 0.5907 (m) cc_final: 0.5494 (p) REVERT: B 48 HIS cc_start: 0.7610 (m90) cc_final: 0.7105 (m90) REVERT: B 96 LYS cc_start: 0.8324 (mtpp) cc_final: 0.8100 (mtpp) REVERT: B 267 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7587 (ttp-170) REVERT: B 422 GLN cc_start: 0.6749 (mt0) cc_final: 0.6413 (mm-40) REVERT: C 128 MET cc_start: 0.5747 (tpp) cc_final: 0.5430 (mmt) REVERT: C 323 VAL cc_start: 0.7577 (t) cc_final: 0.7043 (t) REVERT: D 26 GLU cc_start: 0.7746 (mp0) cc_final: 0.7447 (mm-30) REVERT: D 265 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7465 (tmmt) REVERT: E 109 LYS cc_start: 0.7506 (tptt) cc_final: 0.7221 (ttmt) REVERT: E 338 GLU cc_start: 0.6474 (mt-10) cc_final: 0.6216 (mp0) REVERT: E 380 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.7935 (p) REVERT: F 128 MET cc_start: 0.6055 (ttt) cc_final: 0.5835 (ttm) REVERT: F 156 ASP cc_start: 0.7667 (t0) cc_final: 0.7429 (t0) REVERT: F 167 ASN cc_start: 0.6020 (OUTLIER) cc_final: 0.4854 (m-40) REVERT: F 213 ASP cc_start: 0.7586 (m-30) cc_final: 0.7311 (m-30) REVERT: F 276 ILE cc_start: 0.8836 (mt) cc_final: 0.8628 (tt) REVERT: F 345 GLU cc_start: 0.7727 (tt0) cc_final: 0.7486 (tt0) REVERT: F 355 GLN cc_start: 0.6770 (tt0) cc_final: 0.6483 (pm20) REVERT: F 399 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6921 (tp40) REVERT: F 423 LYS cc_start: 0.8029 (mttm) cc_final: 0.7779 (mttp) REVERT: H 161 LYS cc_start: 0.4172 (tmmt) cc_final: 0.3865 (mttt) REVERT: H 283 LYS cc_start: 0.7693 (tttt) cc_final: 0.7449 (mtmt) REVERT: H 294 TRP cc_start: 0.7286 (m100) cc_final: 0.7085 (m100) REVERT: H 305 ASN cc_start: 0.6222 (t0) cc_final: 0.5935 (t0) REVERT: H 307 MET cc_start: 0.6672 (mtt) cc_final: 0.6405 (mtt) outliers start: 45 outliers final: 4 residues processed: 750 average time/residue: 0.4269 time to fit residues: 467.5168 Evaluate side-chains 381 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 372 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 10.0000 chunk 220 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 117 optimal weight: 0.0670 chunk 228 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 264 optimal weight: 20.0000 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 140 GLN A 167 ASN A 288 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN B 253 HIS ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS C 114 GLN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 288 ASN C 295 ASN D 48 HIS D 200 ASN E 114 GLN E 403 GLN F 8 HIS F 62 ASN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN H 195 GLN H 317 GLN ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24197 Z= 0.178 Angle : 0.518 8.006 32807 Z= 0.277 Chirality : 0.041 0.240 3647 Planarity : 0.004 0.051 4071 Dihedral : 10.828 174.711 3415 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.02 % Allowed : 11.69 % Favored : 86.29 % 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: 0.37 (0.16), residues: 2898 helix: 1.38 (0.14), residues: 1438 sheet: -0.17 (0.27), residues: 407 loop : -1.13 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 266 HIS 0.012 0.001 HIS B 87 PHE 0.014 0.001 PHE D 65 TYR 0.017 0.001 TYR H 213 ARG 0.006 0.000 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 397 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6364 (pp20) cc_final: 0.6157 (pp20) REVERT: A 263 MET cc_start: 0.7067 (mmm) cc_final: 0.6775 (mmm) REVERT: A 369 SER cc_start: 0.6105 (m) cc_final: 0.5712 (p) REVERT: B 48 HIS cc_start: 0.7554 (m90) cc_final: 0.7074 (m90) REVERT: B 177 ARG cc_start: 0.7731 (mtm-85) cc_final: 0.7528 (mtm-85) REVERT: B 253 HIS cc_start: 0.6627 (m-70) cc_final: 0.6392 (m90) REVERT: B 317 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7409 (pttm) REVERT: B 333 LYS cc_start: 0.7720 (ttpp) cc_final: 0.7359 (ttmt) REVERT: B 422 GLN cc_start: 0.6845 (mt0) cc_final: 0.6408 (mm-40) REVERT: C 13 GLN cc_start: 0.7765 (tp40) cc_final: 0.7286 (tp-100) REVERT: C 69 GLU cc_start: 0.7068 (pt0) cc_final: 0.6496 (mm-30) REVERT: C 128 MET cc_start: 0.5621 (tpp) cc_final: 0.5368 (mmt) REVERT: D 26 GLU cc_start: 0.7876 (mp0) cc_final: 0.7664 (mm-30) REVERT: D 29 GLU cc_start: 0.5902 (OUTLIER) cc_final: 0.5610 (tm-30) REVERT: D 315 ILE cc_start: 0.7980 (mt) cc_final: 0.7773 (mm) REVERT: E 118 GLU cc_start: 0.7321 (pp20) cc_final: 0.7062 (mp0) REVERT: E 306 THR cc_start: 0.8345 (m) cc_final: 0.7902 (t) REVERT: E 338 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6194 (mp0) REVERT: E 419 MET cc_start: 0.8571 (tpt) cc_final: 0.8318 (tpt) REVERT: F 156 ASP cc_start: 0.7915 (t0) cc_final: 0.7657 (t0) REVERT: F 167 ASN cc_start: 0.6182 (OUTLIER) cc_final: 0.5214 (m110) REVERT: F 228 MET cc_start: 0.6564 (mtm) cc_final: 0.6348 (mtm) REVERT: F 276 ILE cc_start: 0.8827 (mt) cc_final: 0.8621 (tt) REVERT: F 355 GLN cc_start: 0.6968 (tt0) cc_final: 0.6560 (pm20) REVERT: F 399 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7087 (tp40) REVERT: H 161 LYS cc_start: 0.3919 (tmmt) cc_final: 0.3606 (mmtt) REVERT: H 260 PHE cc_start: 0.6759 (m-80) cc_final: 0.5756 (m-10) REVERT: H 292 MET cc_start: 0.5747 (tpp) cc_final: 0.5028 (tpt) outliers start: 51 outliers final: 22 residues processed: 434 average time/residue: 0.3979 time to fit residues: 265.2157 Evaluate side-chains 351 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 325 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 219 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 264 optimal weight: 10.0000 chunk 285 optimal weight: 9.9990 chunk 235 optimal weight: 0.9990 chunk 262 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN D 48 HIS ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN E 403 GLN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24197 Z= 0.351 Angle : 0.630 9.814 32807 Z= 0.333 Chirality : 0.046 0.277 3647 Planarity : 0.005 0.058 4071 Dihedral : 11.216 176.885 3409 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.49 % Allowed : 12.88 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2898 helix: 1.04 (0.14), residues: 1445 sheet: -0.24 (0.27), residues: 403 loop : -1.14 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 162 HIS 0.006 0.002 HIS B 8 PHE 0.019 0.003 PHE H 81 TYR 0.016 0.002 TYR H 213 ARG 0.007 0.001 ARG C 291 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 350 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7009 (m) cc_final: 0.6736 (t) REVERT: A 118 GLU cc_start: 0.6429 (pp20) cc_final: 0.6062 (pp20) REVERT: A 263 MET cc_start: 0.7277 (mmm) cc_final: 0.6932 (mmm) REVERT: A 368 MET cc_start: 0.5998 (OUTLIER) cc_final: 0.5726 (ttp) REVERT: B 48 HIS cc_start: 0.7700 (m90) cc_final: 0.7187 (m90) REVERT: B 248 ASP cc_start: 0.7684 (m-30) cc_final: 0.7283 (m-30) REVERT: B 338 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7434 (mt-10) REVERT: B 422 GLN cc_start: 0.7185 (mt0) cc_final: 0.6728 (mm-40) REVERT: C 69 GLU cc_start: 0.7187 (pt0) cc_final: 0.6510 (mm-30) REVERT: C 128 MET cc_start: 0.5740 (tpp) cc_final: 0.5412 (mmt) REVERT: C 138 MET cc_start: 0.7226 (tpt) cc_final: 0.6963 (tpt) REVERT: C 188 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7854 (mt-10) REVERT: C 243 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7776 (t0) REVERT: D 247 ASP cc_start: 0.7533 (m-30) cc_final: 0.6900 (t70) REVERT: E 48 HIS cc_start: 0.5622 (m90) cc_final: 0.5074 (m170) REVERT: E 77 ILE cc_start: 0.7811 (pt) cc_final: 0.7199 (mt) REVERT: E 100 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7926 (tm-30) REVERT: E 118 GLU cc_start: 0.7527 (pp20) cc_final: 0.7327 (tm-30) REVERT: E 296 GLU cc_start: 0.6356 (mt-10) cc_final: 0.6125 (mt-10) REVERT: E 338 GLU cc_start: 0.6592 (mt-10) cc_final: 0.5986 (mp0) REVERT: F 61 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7840 (mm-30) REVERT: F 156 ASP cc_start: 0.8149 (t0) cc_final: 0.7898 (m-30) REVERT: F 243 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7375 (t0) REVERT: F 367 ASN cc_start: 0.5978 (p0) cc_final: 0.5636 (m-40) REVERT: H 88 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.6072 (mm-30) REVERT: H 141 LYS cc_start: 0.5056 (pttp) cc_final: 0.4796 (ttmt) REVERT: H 161 LYS cc_start: 0.3872 (tmmt) cc_final: 0.3568 (mmtt) REVERT: H 271 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7153 (mt-10) REVERT: H 292 MET cc_start: 0.6918 (tpp) cc_final: 0.6372 (tpt) outliers start: 88 outliers final: 57 residues processed: 417 average time/residue: 0.3647 time to fit residues: 236.5364 Evaluate side-chains 375 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 314 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 8.9990 chunk 199 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 177 optimal weight: 0.0060 chunk 265 optimal weight: 0.3980 chunk 281 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 overall best weight: 2.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN D 48 HIS D 200 ASN E 114 GLN E 200 ASN F 13 GLN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 HIS H 317 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24197 Z= 0.233 Angle : 0.538 9.457 32807 Z= 0.287 Chirality : 0.042 0.273 3647 Planarity : 0.004 0.034 4071 Dihedral : 11.013 177.999 3409 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.93 % Allowed : 14.19 % Favored : 82.88 % 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: 0.24 (0.16), residues: 2898 helix: 1.22 (0.14), residues: 1436 sheet: -0.22 (0.27), residues: 391 loop : -1.12 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 162 HIS 0.010 0.001 HIS B 253 PHE 0.020 0.002 PHE C 104 TYR 0.017 0.001 TYR H 86 ARG 0.004 0.000 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 332 time to evaluate : 2.846 Fit side-chains revert: symmetry clash REVERT: A 64 SER cc_start: 0.6998 (m) cc_final: 0.6769 (t) REVERT: A 263 MET cc_start: 0.7387 (mmm) cc_final: 0.6990 (mmm) REVERT: A 368 MET cc_start: 0.5952 (OUTLIER) cc_final: 0.5706 (ttp) REVERT: A 430 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6707 (mm-30) REVERT: B 48 HIS cc_start: 0.7675 (m90) cc_final: 0.7200 (m90) REVERT: B 248 ASP cc_start: 0.7862 (m-30) cc_final: 0.7555 (m-30) REVERT: B 333 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7309 (ttpt) REVERT: B 422 GLN cc_start: 0.7070 (mt0) cc_final: 0.6813 (mm-40) REVERT: C 69 GLU cc_start: 0.7112 (pt0) cc_final: 0.6515 (mm-30) REVERT: C 128 MET cc_start: 0.5569 (tpp) cc_final: 0.5291 (mmt) REVERT: C 138 MET cc_start: 0.7209 (tpt) cc_final: 0.6995 (tpt) REVERT: C 188 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7891 (mt-10) REVERT: D 155 MET cc_start: 0.7393 (tpt) cc_final: 0.7183 (tpt) REVERT: D 196 MET cc_start: 0.8892 (ptp) cc_final: 0.8682 (ptt) REVERT: D 247 ASP cc_start: 0.7485 (m-30) cc_final: 0.6878 (t70) REVERT: E 48 HIS cc_start: 0.5663 (m90) cc_final: 0.5162 (m170) REVERT: E 296 GLU cc_start: 0.6344 (mt-10) cc_final: 0.6100 (mt-10) REVERT: E 306 THR cc_start: 0.8421 (m) cc_final: 0.7971 (t) REVERT: E 338 GLU cc_start: 0.6542 (mt-10) cc_final: 0.5840 (mp0) REVERT: F 131 VAL cc_start: 0.8458 (t) cc_final: 0.8239 (p) REVERT: F 156 ASP cc_start: 0.8150 (t0) cc_final: 0.7850 (m-30) REVERT: F 367 ASN cc_start: 0.6043 (p0) cc_final: 0.5703 (m-40) REVERT: F 384 MET cc_start: 0.8296 (ttp) cc_final: 0.7940 (ttt) REVERT: H 88 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.6145 (mm-30) REVERT: H 141 LYS cc_start: 0.5009 (pttp) cc_final: 0.4773 (ttmt) REVERT: H 292 MET cc_start: 0.6899 (tpp) cc_final: 0.6525 (tpt) outliers start: 74 outliers final: 55 residues processed: 387 average time/residue: 0.3642 time to fit residues: 220.5188 Evaluate side-chains 362 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 304 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 368 MET 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 50 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 337 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 8.9990 chunk 159 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 209 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 240 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 252 optimal weight: 0.0010 chunk 70 optimal weight: 4.9990 overall best weight: 5.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN D 48 HIS ** D 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 24197 Z= 0.410 Angle : 0.668 10.619 32807 Z= 0.351 Chirality : 0.046 0.275 3647 Planarity : 0.005 0.039 4071 Dihedral : 11.356 179.187 3407 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.96 % Allowed : 14.31 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2898 helix: 0.82 (0.14), residues: 1434 sheet: -0.44 (0.27), residues: 392 loop : -1.23 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 162 HIS 0.006 0.002 HIS B 8 PHE 0.026 0.003 PHE A 417 TYR 0.025 0.002 TYR D 312 ARG 0.005 0.001 ARG C 291 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 314 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7124 (m) cc_final: 0.6813 (t) REVERT: A 259 TYR cc_start: 0.7557 (t80) cc_final: 0.7297 (t80) REVERT: A 263 MET cc_start: 0.7457 (mmm) cc_final: 0.7255 (mmm) REVERT: A 279 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: A 368 MET cc_start: 0.6102 (OUTLIER) cc_final: 0.5729 (ttp) REVERT: A 430 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6702 (mm-30) REVERT: B 248 ASP cc_start: 0.7888 (m-30) cc_final: 0.7571 (m-30) REVERT: C 69 GLU cc_start: 0.7086 (pt0) cc_final: 0.6486 (mm-30) REVERT: C 128 MET cc_start: 0.5632 (tpp) cc_final: 0.5305 (mmt) REVERT: C 138 MET cc_start: 0.7483 (tpt) cc_final: 0.7274 (tpt) REVERT: C 243 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7774 (t0) REVERT: D 247 ASP cc_start: 0.7491 (m-30) cc_final: 0.6791 (t70) REVERT: E 48 HIS cc_start: 0.5812 (m90) cc_final: 0.5362 (m170) REVERT: E 77 ILE cc_start: 0.7875 (pt) cc_final: 0.7107 (mt) REVERT: E 338 GLU cc_start: 0.6651 (mt-10) cc_final: 0.5867 (mp0) REVERT: F 228 MET cc_start: 0.6778 (mtm) cc_final: 0.6564 (mtm) REVERT: H 49 LYS cc_start: 0.0979 (mttt) cc_final: 0.0716 (ptpt) REVERT: H 88 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6147 (mm-30) outliers start: 100 outliers final: 70 residues processed: 390 average time/residue: 0.3722 time to fit residues: 226.7624 Evaluate side-chains 369 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 294 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 0.8980 chunk 253 optimal weight: 7.9990 chunk 55 optimal weight: 0.0010 chunk 165 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 281 optimal weight: 7.9990 chunk 233 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 overall best weight: 2.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN D 200 ASN E 200 ASN F 62 ASN F 114 GLN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24197 Z= 0.240 Angle : 0.551 12.179 32807 Z= 0.293 Chirality : 0.042 0.250 3647 Planarity : 0.004 0.040 4071 Dihedral : 11.111 176.980 3407 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.21 % Allowed : 15.26 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2898 helix: 1.07 (0.14), residues: 1429 sheet: -0.35 (0.28), residues: 368 loop : -1.20 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 162 HIS 0.004 0.001 HIS A 8 PHE 0.024 0.002 PHE C 104 TYR 0.024 0.001 TYR D 329 ARG 0.003 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 313 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.7117 (m) cc_final: 0.6855 (t) REVERT: A 259 TYR cc_start: 0.7542 (t80) cc_final: 0.7212 (t80) REVERT: A 263 MET cc_start: 0.7511 (mmm) cc_final: 0.7280 (mmm) REVERT: A 368 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.5709 (ttp) REVERT: A 430 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6827 (mm-30) REVERT: B 248 ASP cc_start: 0.7930 (m-30) cc_final: 0.7620 (m-30) REVERT: B 312 TYR cc_start: 0.7083 (t80) cc_final: 0.6772 (t80) REVERT: B 333 LYS cc_start: 0.7859 (ttpp) cc_final: 0.7245 (ttpt) REVERT: C 38 LYS cc_start: 0.7637 (mtmt) cc_final: 0.7246 (ptpt) REVERT: C 69 GLU cc_start: 0.7062 (pt0) cc_final: 0.6505 (mm-30) REVERT: C 128 MET cc_start: 0.5588 (tpp) cc_final: 0.5211 (mmt) REVERT: D 196 MET cc_start: 0.8920 (ptp) cc_final: 0.8720 (ptt) REVERT: D 247 ASP cc_start: 0.7515 (m-30) cc_final: 0.6860 (t70) REVERT: E 48 HIS cc_start: 0.5878 (m90) cc_final: 0.5486 (m170) REVERT: E 77 ILE cc_start: 0.7859 (pt) cc_final: 0.7164 (mt) REVERT: E 338 GLU cc_start: 0.6579 (mt-10) cc_final: 0.5785 (mp0) REVERT: F 228 MET cc_start: 0.6760 (mtm) cc_final: 0.6547 (mtm) REVERT: H 49 LYS cc_start: 0.1176 (mttt) cc_final: 0.0910 (ptpt) REVERT: H 88 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6148 (mm-30) outliers start: 81 outliers final: 59 residues processed: 376 average time/residue: 0.3464 time to fit residues: 204.8715 Evaluate side-chains 354 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 292 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 237 optimal weight: 10.0000 chunk 157 optimal weight: 0.6980 chunk 280 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN C 295 ASN F 114 GLN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24197 Z= 0.186 Angle : 0.522 13.491 32807 Z= 0.277 Chirality : 0.041 0.245 3647 Planarity : 0.003 0.039 4071 Dihedral : 10.910 174.000 3407 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.05 % Allowed : 15.50 % Favored : 81.45 % 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: 0.18 (0.16), residues: 2898 helix: 1.22 (0.14), residues: 1432 sheet: -0.26 (0.28), residues: 367 loop : -1.18 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 89 HIS 0.005 0.001 HIS D 87 PHE 0.027 0.001 PHE C 104 TYR 0.025 0.001 TYR D 329 ARG 0.003 0.000 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 307 time to evaluate : 3.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 TYR cc_start: 0.7514 (t80) cc_final: 0.7148 (t80) REVERT: A 263 MET cc_start: 0.7577 (mmm) cc_final: 0.7098 (mmm) REVERT: A 279 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: A 368 MET cc_start: 0.5964 (OUTLIER) cc_final: 0.5713 (ttp) REVERT: A 430 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6826 (mm-30) REVERT: B 158 TYR cc_start: 0.8041 (p90) cc_final: 0.7592 (p90) REVERT: B 248 ASP cc_start: 0.7883 (m-30) cc_final: 0.7576 (m-30) REVERT: B 333 LYS cc_start: 0.7872 (ttpp) cc_final: 0.7338 (ttmt) REVERT: C 69 GLU cc_start: 0.7080 (pt0) cc_final: 0.6521 (mm-30) REVERT: C 128 MET cc_start: 0.5386 (tpp) cc_final: 0.5023 (mmt) REVERT: D 196 MET cc_start: 0.8872 (ptp) cc_final: 0.8618 (ptt) REVERT: D 247 ASP cc_start: 0.7478 (m-30) cc_final: 0.6837 (t70) REVERT: E 48 HIS cc_start: 0.5865 (m90) cc_final: 0.5493 (m170) REVERT: E 77 ILE cc_start: 0.7861 (pt) cc_final: 0.7154 (mt) REVERT: E 138 MET cc_start: 0.8376 (mmm) cc_final: 0.8159 (mmm) REVERT: E 306 THR cc_start: 0.8402 (m) cc_final: 0.7910 (t) REVERT: E 338 GLU cc_start: 0.6536 (mt-10) cc_final: 0.5726 (mp0) REVERT: F 228 MET cc_start: 0.6773 (mtm) cc_final: 0.6564 (mtm) REVERT: F 302 ASN cc_start: 0.6886 (t0) cc_final: 0.6661 (t0) REVERT: H 49 LYS cc_start: 0.1441 (mttt) cc_final: 0.1112 (ptpt) REVERT: H 88 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6146 (mm-30) outliers start: 77 outliers final: 61 residues processed: 371 average time/residue: 0.3563 time to fit residues: 206.1929 Evaluate side-chains 361 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 296 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN D 200 ASN E 114 GLN F 114 GLN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 305 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 24197 Z= 0.295 Angle : 0.592 13.698 32807 Z= 0.313 Chirality : 0.043 0.195 3647 Planarity : 0.004 0.040 4071 Dihedral : 11.085 174.290 3407 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.37 % Allowed : 15.30 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2898 helix: 1.07 (0.14), residues: 1428 sheet: -0.50 (0.28), residues: 379 loop : -1.22 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 162 HIS 0.005 0.001 HIS H 18 PHE 0.026 0.002 PHE C 104 TYR 0.025 0.002 TYR D 329 ARG 0.005 0.001 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 303 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 TYR cc_start: 0.7544 (t80) cc_final: 0.7182 (t80) REVERT: A 279 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: A 368 MET cc_start: 0.5929 (OUTLIER) cc_final: 0.5674 (ttp) REVERT: A 430 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6819 (mm-30) REVERT: B 158 TYR cc_start: 0.8090 (p90) cc_final: 0.7526 (p90) REVERT: B 248 ASP cc_start: 0.7900 (m-30) cc_final: 0.7584 (m-30) REVERT: C 69 GLU cc_start: 0.7071 (pt0) cc_final: 0.6497 (mm-30) REVERT: C 128 MET cc_start: 0.5531 (tpp) cc_final: 0.5112 (mmt) REVERT: D 65 PHE cc_start: 0.5792 (OUTLIER) cc_final: 0.5036 (p90) REVERT: D 196 MET cc_start: 0.8926 (ptp) cc_final: 0.8683 (ptt) REVERT: D 247 ASP cc_start: 0.7455 (m-30) cc_final: 0.6809 (t70) REVERT: E 77 ILE cc_start: 0.7850 (pt) cc_final: 0.7134 (mt) REVERT: E 138 MET cc_start: 0.8315 (mmm) cc_final: 0.8071 (mmm) REVERT: F 228 MET cc_start: 0.6897 (mtm) cc_final: 0.6675 (mtm) REVERT: F 302 ASN cc_start: 0.6934 (t0) cc_final: 0.6706 (t0) REVERT: H 49 LYS cc_start: 0.1574 (mttt) cc_final: 0.1298 (ptpt) REVERT: H 88 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6117 (mm-30) REVERT: H 141 LYS cc_start: 0.6374 (ttpt) cc_final: 0.6112 (pttt) outliers start: 85 outliers final: 70 residues processed: 374 average time/residue: 0.3638 time to fit residues: 213.3539 Evaluate side-chains 367 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 292 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 359 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 4.9990 chunk 268 optimal weight: 10.0000 chunk 245 optimal weight: 0.5980 chunk 261 optimal weight: 0.1980 chunk 157 optimal weight: 0.1980 chunk 113 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 80 optimal weight: 0.4980 chunk 236 optimal weight: 5.9990 chunk 247 optimal weight: 0.5980 chunk 260 optimal weight: 8.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN D 412 ASN F 114 GLN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 24197 Z= 0.137 Angle : 0.510 12.178 32807 Z= 0.271 Chirality : 0.040 0.174 3647 Planarity : 0.003 0.048 4071 Dihedral : 10.675 169.192 3407 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.90 % Allowed : 17.00 % Favored : 81.09 % 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: 0.29 (0.16), residues: 2898 helix: 1.37 (0.14), residues: 1426 sheet: -0.31 (0.27), residues: 378 loop : -1.18 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 162 HIS 0.004 0.001 HIS B 87 PHE 0.029 0.001 PHE C 104 TYR 0.028 0.001 TYR D 329 ARG 0.013 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 315 time to evaluate : 3.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 TYR cc_start: 0.7429 (t80) cc_final: 0.7026 (t80) REVERT: A 368 MET cc_start: 0.5885 (OUTLIER) cc_final: 0.5682 (ttp) REVERT: A 430 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6758 (mm-30) REVERT: B 158 TYR cc_start: 0.7939 (p90) cc_final: 0.7500 (p90) REVERT: B 248 ASP cc_start: 0.7892 (m-30) cc_final: 0.7604 (m-30) REVERT: B 333 LYS cc_start: 0.7836 (ttpp) cc_final: 0.7276 (ttmt) REVERT: C 69 GLU cc_start: 0.7075 (pt0) cc_final: 0.6550 (mm-30) REVERT: C 128 MET cc_start: 0.5370 (tpp) cc_final: 0.5064 (mmt) REVERT: C 188 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7834 (mt-10) REVERT: C 422 GLN cc_start: 0.7795 (mt0) cc_final: 0.7407 (mm-40) REVERT: D 196 MET cc_start: 0.8836 (ptp) cc_final: 0.8596 (ptt) REVERT: D 247 ASP cc_start: 0.7509 (m-30) cc_final: 0.6910 (t70) REVERT: E 306 THR cc_start: 0.8377 (m) cc_final: 0.7898 (t) REVERT: E 338 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6174 (mp0) REVERT: F 114 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7899 (mt0) REVERT: F 228 MET cc_start: 0.6863 (mtm) cc_final: 0.6650 (mtm) REVERT: F 302 ASN cc_start: 0.6954 (t0) cc_final: 0.6724 (t0) REVERT: F 399 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.7111 (tp40) REVERT: H 49 LYS cc_start: 0.1725 (mttt) cc_final: 0.1409 (ptpt) REVERT: H 88 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6079 (mm-30) REVERT: H 141 LYS cc_start: 0.6227 (ttpt) cc_final: 0.5982 (pttt) outliers start: 48 outliers final: 34 residues processed: 350 average time/residue: 0.3614 time to fit residues: 195.7819 Evaluate side-chains 336 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 297 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 0.0670 chunk 276 optimal weight: 10.0000 chunk 168 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 289 optimal weight: 7.9990 chunk 266 optimal weight: 0.6980 chunk 230 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN F 114 GLN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24197 Z= 0.153 Angle : 0.516 11.658 32807 Z= 0.271 Chirality : 0.040 0.173 3647 Planarity : 0.003 0.042 4071 Dihedral : 10.605 168.359 3407 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.55 % Allowed : 17.40 % Favored : 81.05 % 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: 0.35 (0.16), residues: 2898 helix: 1.43 (0.14), residues: 1426 sheet: -0.30 (0.27), residues: 380 loop : -1.17 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 162 HIS 0.004 0.001 HIS A 8 PHE 0.028 0.001 PHE C 104 TYR 0.025 0.001 TYR D 329 ARG 0.010 0.000 ARG A 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 295 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7628 (mp0) REVERT: A 259 TYR cc_start: 0.7413 (t80) cc_final: 0.7018 (t80) REVERT: A 368 MET cc_start: 0.5847 (OUTLIER) cc_final: 0.5639 (ttp) REVERT: A 430 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6677 (mm-30) REVERT: B 48 HIS cc_start: 0.7663 (m90) cc_final: 0.7212 (m170) REVERT: B 158 TYR cc_start: 0.7941 (p90) cc_final: 0.7561 (p90) REVERT: B 248 ASP cc_start: 0.7888 (m-30) cc_final: 0.7599 (m-30) REVERT: B 333 LYS cc_start: 0.7856 (ttpp) cc_final: 0.7304 (ttmt) REVERT: C 69 GLU cc_start: 0.7079 (pt0) cc_final: 0.6533 (mm-30) REVERT: C 128 MET cc_start: 0.5323 (tpp) cc_final: 0.5036 (mmt) REVERT: C 422 GLN cc_start: 0.7795 (mt0) cc_final: 0.7415 (mm-40) REVERT: D 92 LYS cc_start: 0.8469 (mmmt) cc_final: 0.8246 (mmmm) REVERT: D 196 MET cc_start: 0.8849 (ptp) cc_final: 0.8589 (ptt) REVERT: D 247 ASP cc_start: 0.7512 (m-30) cc_final: 0.6905 (t70) REVERT: E 306 THR cc_start: 0.8392 (m) cc_final: 0.7895 (t) REVERT: E 338 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6240 (mp0) REVERT: F 228 MET cc_start: 0.6864 (mtm) cc_final: 0.6651 (mtm) REVERT: F 302 ASN cc_start: 0.6998 (t0) cc_final: 0.6771 (t0) REVERT: H 34 ARG cc_start: 0.3386 (ttt180) cc_final: 0.2948 (mtm-85) REVERT: H 49 LYS cc_start: 0.1888 (mttt) cc_final: 0.1553 (ptpt) REVERT: H 88 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.6092 (mm-30) REVERT: H 141 LYS cc_start: 0.6209 (ttpt) cc_final: 0.5937 (pttp) outliers start: 39 outliers final: 32 residues processed: 321 average time/residue: 0.3831 time to fit residues: 190.4968 Evaluate side-chains 323 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 288 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN F 114 GLN ** F 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.138669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110356 restraints weight = 38526.720| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.19 r_work: 0.3208 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.230 24197 Z= 0.261 Angle : 0.669 59.155 32807 Z= 0.388 Chirality : 0.045 1.157 3647 Planarity : 0.003 0.039 4071 Dihedral : 10.559 168.432 3404 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.66 % Allowed : 17.08 % Favored : 81.25 % Cbeta Deviations : 0.04 % 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: 0.33 (0.16), residues: 2898 helix: 1.42 (0.14), residues: 1427 sheet: -0.29 (0.27), residues: 380 loop : -1.18 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 89 HIS 0.004 0.001 HIS A 8 PHE 0.027 0.001 PHE C 104 TYR 0.023 0.001 TYR D 329 ARG 0.005 0.000 ARG A 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5627.56 seconds wall clock time: 103 minutes 17.55 seconds (6197.55 seconds total)