Starting phenix.real_space_refine on Mon Feb 19 04:29:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvf_27737/02_2024/8dvf_27737_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvf_27737/02_2024/8dvf_27737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvf_27737/02_2024/8dvf_27737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvf_27737/02_2024/8dvf_27737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvf_27737/02_2024/8dvf_27737_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvf_27737/02_2024/8dvf_27737_updated.pdb" } resolution = 3.3 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 "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: 12.10, per 1000 atoms: 0.51 Number of scatterers: 23693 At special positions: 0 Unit cell: (131.652, 130.824, 141.588, 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: 10.44 Conformation dependent library (CDL) restraints added in 4.6 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 46.0% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.19 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: 3.708A 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: 3.728A 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: 3.608A 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 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: 3.593A 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: 3.989A 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: 3.843A 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: 3.854A 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: 3.661A pdb=" N ARG H 14 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.644A 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 96 removed outlier: 3.858A pdb=" N GLU H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG H 94 " --> pdb=" O ILE H 90 " (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: 3.607A 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: 3.853A 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 removed outlier: 3.513A pdb=" N ARG H 335 " --> pdb=" O MET H 331 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 416 through 419 removed outlier: 6.512A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.656A 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: 3.526A 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: 6.080A pdb=" N ARG C 274 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 7.301A 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: 7.533A pdb=" N SER C 225 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 6.457A 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: 6.346A pdb=" N ASN D 193 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA D 354 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU D 195 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 6.702A 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: 3.600A 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: 5.635A pdb=" N GLN D 403 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE D 388 " --> pdb=" O ILE D 401 " (cutoff:3.500A) removed outlier: 5.384A 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: 6.498A 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: 3.554A pdb=" N VAL E 194 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 3.522A 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: 7.477A 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: 7.246A pdb=" N SER E 225 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 6.276A 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: 7.838A 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: 6.438A 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: 3.509A 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: 8.23 Time building geometry restraints manager: 10.95 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: 7550 1.35 - 1.50: 6427 1.50 - 1.65: 9991 1.65 - 1.80: 110 1.80 - 1.95: 119 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 1.47e+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 1.25e+01 bond pdb=" N ILE A 321 " pdb=" CA ILE A 321 " ideal model delta sigma weight residual 1.452 1.494 -0.042 1.18e-02 7.18e+03 1.25e+01 bond pdb=" N VAL E 19 " pdb=" CA VAL E 19 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.18e-02 7.18e+03 1.14e+01 bond pdb=" N VAL A 323 " pdb=" CA VAL A 323 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.08e-02 8.57e+03 1.11e+01 ... (remaining 24192 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.12: 599 106.12 - 113.17: 13265 113.17 - 120.21: 8760 120.21 - 127.26: 9905 127.26 - 134.31: 278 Bond angle restraints: 32807 Sorted by residual: angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" C ILE A 321 " ideal model delta sigma weight residual 112.96 108.30 4.66 1.00e+00 1.00e+00 2.17e+01 angle pdb=" PB AGS C 501 " pdb=" O3B AGS C 501 " pdb=" PG AGS C 501 " ideal model delta sigma weight residual 120.12 132.65 -12.53 3.00e+00 1.11e-01 1.75e+01 angle pdb=" N ASP A 82 " pdb=" CA ASP A 82 " pdb=" C ASP A 82 " ideal model delta sigma weight residual 112.57 108.09 4.48 1.13e+00 7.83e-01 1.57e+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 122.30 117.08 5.22 1.35e+00 5.49e-01 1.49e+01 ... (remaining 32802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 14414 35.65 - 71.31: 203 71.31 - 106.96: 9 106.96 - 142.61: 1 142.61 - 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 -67.73 106.44 -174.17 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 - 0.047: 2726 0.047 - 0.093: 622 0.093 - 0.140: 242 0.140 - 0.186: 46 0.186 - 0.233: 11 Chirality restraints: 3647 Sorted by residual: chirality pdb=" CA ILE B 111 " pdb=" N ILE B 111 " pdb=" C ILE B 111 " pdb=" CB ILE B 111 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+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 1.21e+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 1.20e+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 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 266 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 266 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP H 266 " -0.005 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 3.33e-02 1.11e+01 pdb=" C GLU A 373 " 0.058 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 2.29e-02 5.23e+00 pdb=" C SER B 145 " 0.040 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: 115 2.47 - 3.08: 16582 3.08 - 3.68: 36591 3.68 - 4.29: 55762 4.29 - 4.90: 90536 Nonbonded interactions: 199586 Sorted by model distance: nonbonded pdb=" O1B AGS C 501 " pdb="MG MG C 502 " model vdw 1.862 2.170 nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.973 2.170 nonbonded pdb=" OE2 GLU B 227 " pdb="MG MG B 502 " model vdw 1.980 2.170 nonbonded pdb=" O2G AGS E 501 " pdb="MG MG E 502 " model vdw 1.984 2.170 nonbonded pdb=" O2B AGS F 501 " pdb="MG MG F 502 " model vdw 1.993 2.170 ... (remaining 199581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 432) selection = (chain 'C' and resid 1 through 432) selection = (chain 'D' and resid 1 through 432) selection = (chain 'E' and resid 1 through 432) selection = (chain 'F' and resid 1 through 432) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.490 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 64.940 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.150 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 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= 0.284 Angle : 0.682 12.535 32807 Z= 0.443 Chirality : 0.049 0.233 3647 Planarity : 0.004 0.075 4071 Dihedral : 12.507 178.268 9101 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.78 % Allowed : 7.13 % Favored : 91.08 % 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: 0.22 (0.16), residues: 2898 helix: 1.28 (0.14), residues: 1436 sheet: -0.35 (0.27), residues: 407 loop : -1.21 (0.18), residues: 1055 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 809 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 764 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.7889 (m-80) cc_final: 0.7364 (m-80) REVERT: A 47 TYR cc_start: 0.6915 (m-10) cc_final: 0.6704 (m-10) REVERT: A 104 PHE cc_start: 0.7783 (t80) cc_final: 0.7430 (t80) REVERT: A 150 VAL cc_start: 0.8809 (t) cc_final: 0.8597 (m) REVERT: A 164 SER cc_start: 0.8518 (m) cc_final: 0.8224 (t) REVERT: A 228 MET cc_start: 0.6399 (mtp) cc_final: 0.5939 (mtp) REVERT: A 292 SER cc_start: 0.7262 (p) cc_final: 0.7025 (t) REVERT: A 333 LYS cc_start: 0.5793 (OUTLIER) cc_final: 0.5550 (tttp) REVERT: B 66 THR cc_start: 0.6091 (p) cc_final: 0.5695 (m) REVERT: B 150 VAL cc_start: 0.8593 (t) cc_final: 0.8333 (p) REVERT: B 299 LEU cc_start: 0.8502 (mt) cc_final: 0.8068 (mt) REVERT: B 312 TYR cc_start: 0.5027 (t80) cc_final: 0.4788 (t80) REVERT: C 85 GLU cc_start: 0.5980 (mm-30) cc_final: 0.5748 (mm-30) REVERT: C 150 VAL cc_start: 0.7503 (p) cc_final: 0.7095 (p) REVERT: C 157 ASP cc_start: 0.7634 (m-30) cc_final: 0.7303 (m-30) REVERT: C 263 MET cc_start: 0.8289 (mmm) cc_final: 0.8037 (mmp) REVERT: C 312 TYR cc_start: 0.4659 (t80) cc_final: 0.4421 (t80) REVERT: C 324 TYR cc_start: 0.7816 (m-80) cc_final: 0.7608 (m-80) REVERT: D 103 MET cc_start: 0.7495 (mmm) cc_final: 0.7255 (mtp) REVERT: D 293 LEU cc_start: 0.8466 (tp) cc_final: 0.8196 (tt) REVERT: D 384 MET cc_start: 0.8386 (mtm) cc_final: 0.8126 (mtm) REVERT: E 344 VAL cc_start: 0.7064 (p) cc_final: 0.6842 (m) REVERT: E 392 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6214 (mm-30) REVERT: E 414 TRP cc_start: 0.7134 (m-90) cc_final: 0.6528 (m-90) REVERT: F 233 CYS cc_start: 0.7658 (m) cc_final: 0.7428 (m) REVERT: F 279 GLN cc_start: 0.7377 (tt0) cc_final: 0.7074 (tt0) REVERT: F 303 PHE cc_start: 0.8055 (t80) cc_final: 0.7852 (t80) REVERT: F 311 ASP cc_start: 0.7476 (t0) cc_final: 0.6692 (p0) REVERT: F 399 GLN cc_start: 0.6490 (OUTLIER) cc_final: 0.5592 (mt0) REVERT: F 418 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5881 (tt) REVERT: F 430 GLU cc_start: 0.5715 (mt-10) cc_final: 0.5410 (tt0) REVERT: H 35 PHE cc_start: 0.4147 (p90) cc_final: 0.3926 (p90) REVERT: H 51 ARG cc_start: 0.4962 (mtt180) cc_final: 0.4574 (mtp85) REVERT: H 80 GLU cc_start: 0.5633 (mm-30) cc_final: 0.4520 (pt0) REVERT: H 88 GLU cc_start: 0.6975 (pt0) cc_final: 0.6515 (pt0) REVERT: H 89 TYR cc_start: 0.6084 (t80) cc_final: 0.5859 (t80) REVERT: H 213 TYR cc_start: 0.4202 (p90) cc_final: 0.3856 (p90) REVERT: H 225 VAL cc_start: 0.5885 (t) cc_final: 0.5642 (t) REVERT: H 234 GLU cc_start: 0.5461 (mt-10) cc_final: 0.4972 (mt-10) REVERT: H 244 ASN cc_start: 0.5804 (m-40) cc_final: 0.5277 (t0) REVERT: H 254 ASP cc_start: 0.4001 (t0) cc_final: 0.3721 (t70) REVERT: H 264 ARG cc_start: 0.5244 (ptt180) cc_final: 0.4732 (ptt180) REVERT: H 270 ASN cc_start: 0.6320 (t0) cc_final: 0.6114 (t0) REVERT: H 276 ASP cc_start: 0.6781 (m-30) cc_final: 0.6504 (m-30) REVERT: H 278 ILE cc_start: 0.6903 (pp) cc_final: 0.6483 (mm) REVERT: H 281 MET cc_start: 0.6844 (mmt) cc_final: 0.6400 (mmm) REVERT: H 289 GLU cc_start: 0.6628 (mm-30) cc_final: 0.5600 (mm-30) REVERT: H 293 PHE cc_start: 0.6403 (m-80) cc_final: 0.5797 (m-80) REVERT: H 322 MET cc_start: 0.6755 (mtm) cc_final: 0.6541 (mtm) outliers start: 45 outliers final: 7 residues processed: 794 average time/residue: 0.4035 time to fit residues: 475.9813 Evaluate side-chains 394 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 384 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 334 MET 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: 0.3980 chunk 122 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 chunk 264 optimal weight: 0.0010 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 114 GLN A 116 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 ASN A 403 GLN B 355 GLN B 399 GLN D 167 ASN D 403 GLN E 57 ASN E 114 GLN F 398 GLN H 195 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2284 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= 0.177 Angle : 0.523 6.495 32807 Z= 0.279 Chirality : 0.041 0.188 3647 Planarity : 0.003 0.041 4071 Dihedral : 10.740 172.432 3418 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.46 % Allowed : 12.56 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2898 helix: 1.38 (0.14), residues: 1438 sheet: -0.22 (0.27), residues: 410 loop : -1.14 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 266 HIS 0.010 0.001 HIS C 43 PHE 0.019 0.002 PHE H 22 TYR 0.019 0.001 TYR F 15 ARG 0.004 0.000 ARG C 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 454 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 392 time to evaluate : 2.676 Fit side-chains revert: symmetry clash REVERT: A 22 TYR cc_start: 0.7942 (m-80) cc_final: 0.7420 (m-80) REVERT: A 243 ASP cc_start: 0.6849 (t0) cc_final: 0.6618 (t0) REVERT: C 85 GLU cc_start: 0.6165 (mm-30) cc_final: 0.5892 (mm-30) REVERT: C 157 ASP cc_start: 0.7720 (m-30) cc_final: 0.7374 (m-30) REVERT: C 263 MET cc_start: 0.8354 (mmm) cc_final: 0.8144 (mmp) REVERT: D 103 MET cc_start: 0.7499 (mmm) cc_final: 0.7253 (mtp) REVERT: D 264 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6744 (mm-30) REVERT: E 392 GLU cc_start: 0.6466 (mt-10) cc_final: 0.6005 (mm-30) REVERT: E 414 TRP cc_start: 0.7228 (m-90) cc_final: 0.6157 (m-90) REVERT: F 1 MET cc_start: 0.7867 (ptm) cc_final: 0.7598 (ptt) REVERT: F 303 PHE cc_start: 0.8110 (t80) cc_final: 0.7896 (t80) REVERT: F 418 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5785 (tt) REVERT: H 51 ARG cc_start: 0.5087 (mtt180) cc_final: 0.4747 (mtp85) REVERT: H 80 GLU cc_start: 0.5574 (mm-30) cc_final: 0.4574 (pt0) REVERT: H 151 LYS cc_start: 0.6200 (pttm) cc_final: 0.5922 (mtmt) REVERT: H 225 VAL cc_start: 0.5977 (t) cc_final: 0.5648 (t) REVERT: H 234 GLU cc_start: 0.5142 (mt-10) cc_final: 0.4896 (mt-10) REVERT: H 244 ASN cc_start: 0.5849 (m-40) cc_final: 0.5354 (t0) REVERT: H 274 HIS cc_start: 0.5130 (t-170) cc_final: 0.4864 (t-170) REVERT: H 278 ILE cc_start: 0.6765 (pp) cc_final: 0.6400 (mm) REVERT: H 281 MET cc_start: 0.6867 (mmt) cc_final: 0.6427 (mmm) outliers start: 62 outliers final: 41 residues processed: 439 average time/residue: 0.3961 time to fit residues: 274.6963 Evaluate side-chains 359 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 317 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 264 optimal weight: 30.0000 chunk 285 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 262 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 212 optimal weight: 0.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN B 355 GLN C 422 GLN D 167 ASN E 403 GLN F 57 ASN F 279 GLN F 355 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24197 Z= 0.196 Angle : 0.518 6.234 32807 Z= 0.276 Chirality : 0.042 0.218 3647 Planarity : 0.003 0.040 4071 Dihedral : 10.648 165.476 3411 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.93 % Allowed : 13.40 % Favored : 83.67 % 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: 0.36 (0.16), residues: 2898 helix: 1.38 (0.14), residues: 1429 sheet: -0.13 (0.27), residues: 409 loop : -1.17 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 266 HIS 0.005 0.001 HIS E 219 PHE 0.013 0.002 PHE D 65 TYR 0.023 0.001 TYR F 15 ARG 0.005 0.000 ARG H 126 *********************** 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 434 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 360 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7056 (t0) cc_final: 0.6840 (t0) REVERT: A 380 THR cc_start: 0.7602 (OUTLIER) cc_final: 0.7347 (m) REVERT: C 85 GLU cc_start: 0.6609 (mm-30) cc_final: 0.6175 (mm-30) REVERT: C 157 ASP cc_start: 0.7889 (m-30) cc_final: 0.7564 (m-30) REVERT: C 263 MET cc_start: 0.8467 (mmm) cc_final: 0.8224 (mmp) REVERT: D 103 MET cc_start: 0.7537 (mmm) cc_final: 0.7284 (mtp) REVERT: D 134 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7632 (mt) REVERT: E 228 MET cc_start: 0.7522 (mtm) cc_final: 0.7267 (ptm) REVERT: E 389 GLU cc_start: 0.6658 (tt0) cc_final: 0.6335 (tp30) REVERT: E 392 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6217 (mm-30) REVERT: E 414 TRP cc_start: 0.7173 (m-90) cc_final: 0.6041 (m-90) REVERT: F 1 MET cc_start: 0.8093 (ptm) cc_final: 0.7883 (ptt) REVERT: F 399 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6469 (tp40) REVERT: F 418 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5665 (tt) REVERT: H 51 ARG cc_start: 0.5244 (mtt180) cc_final: 0.4864 (mtp85) REVERT: H 80 GLU cc_start: 0.5771 (mm-30) cc_final: 0.5333 (mp0) REVERT: H 213 TYR cc_start: 0.4364 (p90) cc_final: 0.4116 (p90) REVERT: H 225 VAL cc_start: 0.5760 (t) cc_final: 0.5452 (t) REVERT: H 244 ASN cc_start: 0.5843 (m-40) cc_final: 0.5152 (t0) REVERT: H 274 HIS cc_start: 0.5046 (t-170) cc_final: 0.4700 (t-170) REVERT: H 278 ILE cc_start: 0.6702 (pp) cc_final: 0.6419 (mm) REVERT: H 281 MET cc_start: 0.6955 (mmt) cc_final: 0.6487 (mmm) REVERT: H 319 MET cc_start: 0.7249 (mmm) cc_final: 0.7021 (tmm) outliers start: 74 outliers final: 51 residues processed: 412 average time/residue: 0.3536 time to fit residues: 227.8419 Evaluate side-chains 366 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 311 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 419 MET Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 399 GLN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 285 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 281 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 251 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 180 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN D 403 GLN E 100 GLN E 200 ASN E 403 GLN F 216 GLN H 67 ASN H 188 ASN H 328 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 24197 Z= 0.454 Angle : 0.734 9.284 32807 Z= 0.385 Chirality : 0.049 0.222 3647 Planarity : 0.005 0.054 4071 Dihedral : 11.430 160.481 3409 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.16 % Allowed : 14.78 % 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: -0.53 (0.15), residues: 2898 helix: 0.52 (0.14), residues: 1415 sheet: -0.49 (0.26), residues: 412 loop : -1.41 (0.17), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 162 HIS 0.007 0.002 HIS B 87 PHE 0.029 0.003 PHE A 417 TYR 0.025 0.002 TYR E 15 ARG 0.006 0.001 ARG D 320 *********************** 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 458 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 353 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7855 (mttm) cc_final: 0.7439 (ttmm) REVERT: A 243 ASP cc_start: 0.7298 (t0) cc_final: 0.7074 (t0) REVERT: A 251 ASP cc_start: 0.7284 (t0) cc_final: 0.7059 (m-30) REVERT: A 345 GLU cc_start: 0.7887 (tp30) cc_final: 0.7627 (tp30) REVERT: A 355 GLN cc_start: 0.7497 (tp40) cc_final: 0.7282 (tp40) REVERT: A 417 PHE cc_start: 0.5134 (t80) cc_final: 0.4755 (t80) REVERT: B 306 THR cc_start: 0.8778 (p) cc_final: 0.8551 (m) REVERT: C 47 TYR cc_start: 0.5825 (OUTLIER) cc_final: 0.5119 (m-10) REVERT: C 113 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8516 (mp) REVERT: D 112 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6749 (tm-30) REVERT: D 227 GLU cc_start: 0.7820 (tt0) cc_final: 0.7514 (pm20) REVERT: D 231 GLU cc_start: 0.7689 (mp0) cc_final: 0.7169 (tm-30) REVERT: D 406 SER cc_start: 0.8260 (t) cc_final: 0.7785 (p) REVERT: E 98 VAL cc_start: 0.9022 (t) cc_final: 0.8788 (m) REVERT: E 253 HIS cc_start: 0.8233 (m90) cc_final: 0.7879 (m90) REVERT: E 389 GLU cc_start: 0.6960 (tt0) cc_final: 0.6490 (tp30) REVERT: E 392 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6710 (mm-30) REVERT: E 413 LYS cc_start: 0.7478 (tppt) cc_final: 0.7048 (tptp) REVERT: E 414 TRP cc_start: 0.7288 (m-90) cc_final: 0.6623 (m-90) REVERT: F 118 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6307 (mp0) REVERT: F 243 ASP cc_start: 0.7458 (m-30) cc_final: 0.6982 (t0) REVERT: H 158 GLU cc_start: 0.2792 (OUTLIER) cc_final: 0.2589 (pm20) REVERT: H 244 ASN cc_start: 0.5613 (m-40) cc_final: 0.5192 (t0) REVERT: H 278 ILE cc_start: 0.6776 (pp) cc_final: 0.6517 (mm) REVERT: H 281 MET cc_start: 0.7006 (mmt) cc_final: 0.6742 (mmm) outliers start: 105 outliers final: 70 residues processed: 438 average time/residue: 0.3569 time to fit residues: 242.8500 Evaluate side-chains 376 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 301 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 328 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 240 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN E 403 GLN E 425 ASN F 398 GLN H 67 ASN H 252 GLN H 325 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24197 Z= 0.165 Angle : 0.520 8.454 32807 Z= 0.277 Chirality : 0.041 0.189 3647 Planarity : 0.003 0.037 4071 Dihedral : 10.689 158.568 3404 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.46 % Allowed : 16.81 % Favored : 80.74 % 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: -0.04 (0.16), residues: 2898 helix: 1.05 (0.14), residues: 1410 sheet: -0.22 (0.27), residues: 395 loop : -1.34 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 150 HIS 0.007 0.001 HIS D 152 PHE 0.024 0.002 PHE C 104 TYR 0.020 0.001 TYR D 329 ARG 0.004 0.000 ARG H 309 *********************** 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 398 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 336 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7700 (mttm) cc_final: 0.7435 (ttmm) REVERT: A 74 LYS cc_start: 0.6866 (tptp) cc_final: 0.6379 (ttmm) REVERT: A 178 ILE cc_start: 0.7895 (tp) cc_final: 0.7685 (tt) REVERT: A 243 ASP cc_start: 0.7144 (t0) cc_final: 0.6855 (t0) REVERT: A 251 ASP cc_start: 0.7243 (t0) cc_final: 0.6950 (m-30) REVERT: B 306 THR cc_start: 0.8735 (p) cc_final: 0.8523 (m) REVERT: B 385 LEU cc_start: 0.7903 (mt) cc_final: 0.7698 (mt) REVERT: C 35 ASN cc_start: 0.7040 (m-40) cc_final: 0.6688 (m110) REVERT: D 406 SER cc_start: 0.8158 (t) cc_final: 0.7839 (p) REVERT: E 389 GLU cc_start: 0.6824 (tt0) cc_final: 0.6555 (tp30) REVERT: E 392 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6645 (mm-30) REVERT: E 414 TRP cc_start: 0.7273 (m-90) cc_final: 0.6607 (m-90) REVERT: F 118 GLU cc_start: 0.6880 (mp0) cc_final: 0.6204 (mp0) REVERT: F 243 ASP cc_start: 0.7407 (m-30) cc_final: 0.7025 (t0) REVERT: F 279 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: F 418 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5570 (tp) REVERT: H 158 GLU cc_start: 0.2946 (OUTLIER) cc_final: 0.2734 (pm20) REVERT: H 244 ASN cc_start: 0.5753 (m-40) cc_final: 0.5121 (t0) REVERT: H 278 ILE cc_start: 0.6656 (pp) cc_final: 0.6446 (mm) REVERT: H 281 MET cc_start: 0.6959 (mmt) cc_final: 0.6699 (mmm) outliers start: 62 outliers final: 39 residues processed: 381 average time/residue: 0.3718 time to fit residues: 220.7871 Evaluate side-chains 354 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 312 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 7.9990 chunk 253 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 281 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 93 optimal weight: 0.0770 chunk 147 optimal weight: 6.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 24197 Z= 0.342 Angle : 0.627 9.436 32807 Z= 0.328 Chirality : 0.044 0.203 3647 Planarity : 0.004 0.039 4071 Dihedral : 10.986 159.421 3404 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.57 % Allowed : 16.96 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 2898 helix: 0.76 (0.14), residues: 1408 sheet: -0.57 (0.26), residues: 406 loop : -1.43 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 162 HIS 0.005 0.001 HIS E 8 PHE 0.026 0.003 PHE H 81 TYR 0.027 0.002 TYR F 15 ARG 0.004 0.001 ARG A 320 *********************** 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 411 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 321 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7907 (mttm) cc_final: 0.7615 (ttmm) REVERT: A 74 LYS cc_start: 0.6971 (tptp) cc_final: 0.6429 (ttmm) REVERT: A 243 ASP cc_start: 0.7247 (t0) cc_final: 0.6993 (t0) REVERT: A 251 ASP cc_start: 0.7238 (t0) cc_final: 0.6957 (m-30) REVERT: B 306 THR cc_start: 0.8769 (p) cc_final: 0.8517 (m) REVERT: B 370 ASP cc_start: 0.6999 (m-30) cc_final: 0.6789 (m-30) REVERT: B 382 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8189 (m-30) REVERT: B 431 ILE cc_start: 0.7095 (mm) cc_final: 0.6857 (mt) REVERT: C 47 TYR cc_start: 0.5944 (OUTLIER) cc_final: 0.5132 (m-10) REVERT: C 74 LYS cc_start: 0.7380 (mmmm) cc_final: 0.7093 (mmmt) REVERT: C 196 MET cc_start: 0.8049 (ptm) cc_final: 0.7774 (ptt) REVERT: D 95 GLU cc_start: 0.8290 (tp30) cc_final: 0.7985 (mm-30) REVERT: D 112 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6728 (tm-30) REVERT: D 231 GLU cc_start: 0.7706 (mp0) cc_final: 0.7212 (tm-30) REVERT: D 406 SER cc_start: 0.8378 (t) cc_final: 0.7863 (p) REVERT: E 392 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6709 (mm-30) REVERT: E 414 TRP cc_start: 0.7312 (m-90) cc_final: 0.6585 (m-90) REVERT: F 118 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6354 (mp0) REVERT: F 247 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.6565 (m-30) REVERT: F 418 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5708 (tp) REVERT: H 158 GLU cc_start: 0.3165 (OUTLIER) cc_final: 0.2863 (pm20) REVERT: H 194 PHE cc_start: 0.4032 (p90) cc_final: 0.3688 (p90) REVERT: H 244 ASN cc_start: 0.5671 (m-40) cc_final: 0.5075 (t0) REVERT: H 278 ILE cc_start: 0.6712 (pp) cc_final: 0.6493 (mm) REVERT: H 281 MET cc_start: 0.6992 (mmt) cc_final: 0.6789 (mmm) outliers start: 90 outliers final: 61 residues processed: 387 average time/residue: 0.3515 time to fit residues: 213.4962 Evaluate side-chains 370 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 302 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 324 ASN Chi-restraints excluded: chain H residue 331 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 160 optimal weight: 7.9990 chunk 205 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 280 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24197 Z= 0.168 Angle : 0.531 9.152 32807 Z= 0.278 Chirality : 0.041 0.197 3647 Planarity : 0.003 0.033 4071 Dihedral : 10.670 160.041 3404 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.66 % Allowed : 17.92 % Favored : 79.43 % 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: 1.08 (0.14), residues: 1419 sheet: -0.42 (0.26), residues: 402 loop : -1.43 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 159 HIS 0.004 0.001 HIS B 8 PHE 0.018 0.001 PHE C 104 TYR 0.018 0.001 TYR F 15 ARG 0.003 0.000 ARG H 87 *********************** 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 385 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 318 time to evaluate : 4.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7773 (mttm) cc_final: 0.7506 (ttmm) REVERT: A 74 LYS cc_start: 0.6952 (tptp) cc_final: 0.6406 (ttmm) REVERT: A 251 ASP cc_start: 0.7184 (t0) cc_final: 0.6883 (m-30) REVERT: A 288 ASN cc_start: 0.6998 (OUTLIER) cc_final: 0.6733 (m110) REVERT: A 355 GLN cc_start: 0.7201 (tp40) cc_final: 0.6953 (mm-40) REVERT: B 306 THR cc_start: 0.8750 (p) cc_final: 0.8518 (m) REVERT: D 95 GLU cc_start: 0.8251 (tp30) cc_final: 0.7976 (mm-30) REVERT: D 112 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6796 (tm-30) REVERT: D 406 SER cc_start: 0.8264 (t) cc_final: 0.7860 (p) REVERT: E 23 MET cc_start: 0.8173 (mmp) cc_final: 0.7927 (mmt) REVERT: E 392 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6649 (mm-30) REVERT: E 413 LYS cc_start: 0.7516 (tppt) cc_final: 0.6809 (tptp) REVERT: E 414 TRP cc_start: 0.7248 (m-90) cc_final: 0.6018 (m-90) REVERT: F 118 GLU cc_start: 0.6984 (mp0) cc_final: 0.6275 (mp0) REVERT: F 247 ASP cc_start: 0.6804 (OUTLIER) cc_final: 0.6460 (m-30) REVERT: F 327 ASN cc_start: 0.6521 (OUTLIER) cc_final: 0.5881 (p0) REVERT: F 418 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.5833 (tp) REVERT: H 130 LEU cc_start: 0.2594 (OUTLIER) cc_final: 0.2357 (tp) REVERT: H 158 GLU cc_start: 0.3425 (OUTLIER) cc_final: 0.3129 (pm20) REVERT: H 244 ASN cc_start: 0.5708 (m-40) cc_final: 0.5082 (t0) REVERT: H 281 MET cc_start: 0.7012 (mmt) cc_final: 0.6799 (mmm) outliers start: 67 outliers final: 47 residues processed: 368 average time/residue: 0.3646 time to fit residues: 210.2856 Evaluate side-chains 356 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 302 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 324 ASN Chi-restraints excluded: chain H residue 331 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 0.3980 chunk 112 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 178 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 220 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24197 Z= 0.182 Angle : 0.529 11.667 32807 Z= 0.276 Chirality : 0.041 0.178 3647 Planarity : 0.003 0.033 4071 Dihedral : 10.601 160.081 3404 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.70 % Allowed : 18.23 % Favored : 79.07 % 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: 0.02 (0.16), residues: 2898 helix: 1.18 (0.14), residues: 1415 sheet: -0.33 (0.26), residues: 404 loop : -1.41 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 162 HIS 0.004 0.001 HIS H 274 PHE 0.015 0.002 PHE C 104 TYR 0.016 0.001 TYR F 15 ARG 0.003 0.000 ARG H 309 *********************** 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 378 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 310 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8047 (mp0) cc_final: 0.7796 (mp0) REVERT: A 38 LYS cc_start: 0.7758 (mttm) cc_final: 0.7473 (ttmm) REVERT: A 74 LYS cc_start: 0.6890 (tptp) cc_final: 0.6342 (ttmm) REVERT: A 251 ASP cc_start: 0.7176 (t0) cc_final: 0.6876 (m-30) REVERT: A 291 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7282 (ttm-80) REVERT: A 355 GLN cc_start: 0.7212 (tp40) cc_final: 0.6989 (mm-40) REVERT: B 306 THR cc_start: 0.8735 (p) cc_final: 0.8520 (m) REVERT: D 95 GLU cc_start: 0.8191 (tp30) cc_final: 0.7984 (mm-30) REVERT: D 112 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6824 (tm-30) REVERT: D 406 SER cc_start: 0.8271 (t) cc_final: 0.7834 (p) REVERT: E 23 MET cc_start: 0.8194 (mmp) cc_final: 0.7952 (mmt) REVERT: E 392 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6607 (mm-30) REVERT: E 414 TRP cc_start: 0.7263 (m-90) cc_final: 0.6030 (m-90) REVERT: F 118 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6288 (mp0) REVERT: F 247 ASP cc_start: 0.6761 (OUTLIER) cc_final: 0.6443 (m-30) REVERT: F 327 ASN cc_start: 0.6506 (OUTLIER) cc_final: 0.5839 (p0) REVERT: F 418 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.5830 (tp) REVERT: H 130 LEU cc_start: 0.2581 (OUTLIER) cc_final: 0.2330 (tp) REVERT: H 158 GLU cc_start: 0.3236 (OUTLIER) cc_final: 0.2973 (pm20) REVERT: H 211 GLU cc_start: 0.4436 (OUTLIER) cc_final: 0.4032 (mp0) REVERT: H 244 ASN cc_start: 0.5739 (m-40) cc_final: 0.5097 (t0) REVERT: H 274 HIS cc_start: 0.6008 (t-170) cc_final: 0.5529 (t-170) outliers start: 68 outliers final: 50 residues processed: 363 average time/residue: 0.3651 time to fit residues: 207.9284 Evaluate side-chains 356 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 297 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 211 GLU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 324 ASN Chi-restraints excluded: chain H residue 331 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 9.9990 chunk 268 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 260 optimal weight: 6.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- 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 200 ASN C 35 ASN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 24197 Z= 0.311 Angle : 0.616 10.300 32807 Z= 0.322 Chirality : 0.044 0.180 3647 Planarity : 0.004 0.040 4071 Dihedral : 10.901 161.574 3404 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.81 % Allowed : 18.27 % Favored : 78.91 % 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: -0.30 (0.15), residues: 2898 helix: 0.88 (0.14), residues: 1415 sheet: -0.55 (0.26), residues: 399 loop : -1.47 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 162 HIS 0.005 0.001 HIS E 8 PHE 0.022 0.002 PHE H 81 TYR 0.015 0.002 TYR E 15 ARG 0.004 0.000 ARG D 320 *********************** 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 373 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 302 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7935 (mttm) cc_final: 0.7678 (ttmm) REVERT: A 69 GLU cc_start: 0.5936 (mp0) cc_final: 0.5500 (mp0) REVERT: A 74 LYS cc_start: 0.6966 (tptp) cc_final: 0.6476 (ttmm) REVERT: A 251 ASP cc_start: 0.7155 (t0) cc_final: 0.6878 (m-30) REVERT: A 291 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7303 (ttm-80) REVERT: B 306 THR cc_start: 0.8795 (p) cc_final: 0.8559 (m) REVERT: B 382 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8241 (m-30) REVERT: C 47 TYR cc_start: 0.5936 (OUTLIER) cc_final: 0.5193 (m-10) REVERT: C 74 LYS cc_start: 0.7446 (mmmm) cc_final: 0.7114 (mmmt) REVERT: E 414 TRP cc_start: 0.7365 (m-90) cc_final: 0.6099 (m-90) REVERT: F 118 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6320 (mp0) REVERT: F 247 ASP cc_start: 0.6896 (OUTLIER) cc_final: 0.6575 (m-30) REVERT: F 327 ASN cc_start: 0.6532 (OUTLIER) cc_final: 0.5969 (p0) REVERT: F 418 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5751 (tp) REVERT: H 80 GLU cc_start: 0.6218 (mm-30) cc_final: 0.5514 (mp0) REVERT: H 130 LEU cc_start: 0.2700 (OUTLIER) cc_final: 0.2477 (tp) REVERT: H 158 GLU cc_start: 0.3364 (OUTLIER) cc_final: 0.3086 (pm20) REVERT: H 211 GLU cc_start: 0.4286 (OUTLIER) cc_final: 0.3853 (mp0) REVERT: H 244 ASN cc_start: 0.5503 (m-40) cc_final: 0.4936 (t0) outliers start: 71 outliers final: 57 residues processed: 358 average time/residue: 0.3703 time to fit residues: 209.3448 Evaluate side-chains 356 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 289 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 211 GLU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 324 ASN Chi-restraints excluded: chain H residue 331 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 10.0000 chunk 276 optimal weight: 30.0000 chunk 168 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 289 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 178 optimal weight: 8.9990 chunk 141 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 200 ASN C 35 ASN ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 24197 Z= 0.287 Angle : 0.735 59.200 32807 Z= 0.410 Chirality : 0.043 0.192 3647 Planarity : 0.004 0.077 4071 Dihedral : 10.896 161.505 3404 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.81 % Allowed : 18.79 % Favored : 78.40 % 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 (0.15), residues: 2898 helix: 0.87 (0.14), residues: 1415 sheet: -0.61 (0.26), residues: 402 loop : -1.48 (0.18), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 162 HIS 0.005 0.001 HIS E 8 PHE 0.041 0.002 PHE D 146 TYR 0.015 0.002 TYR E 22 ARG 0.003 0.000 ARG D 320 ********************** 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 364 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 293 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7934 (mttm) cc_final: 0.7677 (ttmm) REVERT: A 69 GLU cc_start: 0.5933 (mp0) cc_final: 0.5495 (mp0) REVERT: A 74 LYS cc_start: 0.6981 (tptp) cc_final: 0.6346 (ttmm) REVERT: A 251 ASP cc_start: 0.7148 (t0) cc_final: 0.6876 (m-30) REVERT: A 291 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7302 (ttm-80) REVERT: B 200 ASN cc_start: 0.8015 (t0) cc_final: 0.7682 (t0) REVERT: B 306 THR cc_start: 0.8793 (p) cc_final: 0.8559 (m) REVERT: B 382 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8239 (m-30) REVERT: C 47 TYR cc_start: 0.5932 (OUTLIER) cc_final: 0.5192 (m-10) REVERT: C 74 LYS cc_start: 0.7422 (mmmm) cc_final: 0.7106 (mmmt) REVERT: D 95 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7806 (mm-30) REVERT: F 118 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6317 (mp0) REVERT: F 247 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6554 (m-30) REVERT: F 327 ASN cc_start: 0.6548 (OUTLIER) cc_final: 0.5982 (p0) REVERT: F 418 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.5746 (tp) REVERT: H 80 GLU cc_start: 0.6220 (mm-30) cc_final: 0.5531 (mp0) REVERT: H 130 LEU cc_start: 0.2692 (OUTLIER) cc_final: 0.2484 (tp) REVERT: H 158 GLU cc_start: 0.3372 (OUTLIER) cc_final: 0.3086 (pm20) REVERT: H 211 GLU cc_start: 0.4286 (OUTLIER) cc_final: 0.3851 (mp0) REVERT: H 244 ASN cc_start: 0.5508 (m-40) cc_final: 0.4941 (t0) outliers start: 71 outliers final: 61 residues processed: 348 average time/residue: 0.3548 time to fit residues: 194.0182 Evaluate side-chains 364 residues out of total 2523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 293 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 211 GLU Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 262 ASP Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 324 ASN Chi-restraints excluded: chain H residue 331 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 212 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 237 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.142891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117865 restraints weight = 39638.756| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.11 r_work: 0.3342 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 24197 Z= 0.287 Angle : 0.735 59.200 32807 Z= 0.410 Chirality : 0.043 0.192 3647 Planarity : 0.004 0.077 4071 Dihedral : 10.896 161.505 3404 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.81 % Allowed : 18.75 % Favored : 78.44 % 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 (0.15), residues: 2898 helix: 0.87 (0.14), residues: 1415 sheet: -0.61 (0.26), residues: 402 loop : -1.48 (0.18), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 162 HIS 0.005 0.001 HIS E 8 PHE 0.041 0.002 PHE D 146 TYR 0.015 0.002 TYR E 22 ARG 0.003 0.000 ARG D 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5566.46 seconds wall clock time: 102 minutes 15.71 seconds (6135.71 seconds total)