Starting phenix.real_space_refine on Sat Mar 7 02:57:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j0s_35909/03_2026/8j0s_35909.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j0s_35909/03_2026/8j0s_35909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j0s_35909/03_2026/8j0s_35909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j0s_35909/03_2026/8j0s_35909.map" model { file = "/net/cci-nas-00/data/ceres_data/8j0s_35909/03_2026/8j0s_35909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j0s_35909/03_2026/8j0s_35909.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.010 sd= 1.115 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: 7 Type Number sf(0) Gaussians Br 7 7.06 5 P 13 5.49 5 Mg 5 5.21 5 S 121 5.16 5 C 23825 2.51 5 N 6467 2.21 5 O 7148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 134 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37586 Number of models: 1 Model: "" Number of chains: 32 Chain: "a" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1839 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "A" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3916 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 494} Chain: "B" Number of atoms: 3747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3747 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 470} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 4040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4040 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 506} Chain breaks: 2 Chain: "D" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3614 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 445} Chain: "E" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3614 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 445} Chain: "F" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3614 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 445} Chain: "G" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2256 Classifications: {'peptide': 288} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 277} Chain breaks: 1 Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 901 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "1" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "2" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "3" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "4" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "5" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "6" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "7" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "8" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "9" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "b" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1107 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "d" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3424 Classifications: {'peptide': 445} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 433} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.61, per 1000 atoms: 0.23 Number of scatterers: 37586 At special positions: 0 Unit cell: (126.29, 137.97, 247.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 7 34.99 S 121 16.00 P 13 15.00 Mg 5 11.99 O 7148 8.00 N 6467 7.00 C 23825 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.7 seconds 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8894 Finding SS restraints... Secondary structure from input PDB file: 197 helices and 23 sheets defined 59.7% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'a' and resid 30 through 51 Processing helix chain 'a' and resid 59 through 79 Processing helix chain 'a' and resid 86 through 104 Processing helix chain 'a' and resid 105 through 107 No H-bonds generated for 'chain 'a' and resid 105 through 107' Processing helix chain 'a' and resid 124 through 127 Processing helix chain 'a' and resid 128 through 152 removed outlier: 3.503A pdb=" N VAL a 132 " --> pdb=" O ASP a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 154 through 163 removed outlier: 3.995A pdb=" N ILE a 158 " --> pdb=" O VAL a 154 " (cutoff:3.500A) Processing helix chain 'a' and resid 165 through 167 No H-bonds generated for 'chain 'a' and resid 165 through 167' Processing helix chain 'a' and resid 168 through 202 Proline residue: a 180 - end of helix removed outlier: 4.081A pdb=" N LEU a 187 " --> pdb=" O LEU a 183 " (cutoff:3.500A) Processing helix chain 'a' and resid 203 through 204 No H-bonds generated for 'chain 'a' and resid 203 through 204' Processing helix chain 'a' and resid 205 through 208 Processing helix chain 'a' and resid 209 through 243 removed outlier: 3.988A pdb=" N PHE a 222 " --> pdb=" O ALA a 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 21 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.678A pdb=" N PHE A 106 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 177 through 188 Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.861A pdb=" N GLY A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.567A pdb=" N GLY A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.827A pdb=" N GLN A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.753A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.624A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 393 through 404 Processing helix chain 'A' and resid 405 through 413 removed outlier: 5.055A pdb=" N ALA A 408 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N SER A 411 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 440 through 454 removed outlier: 3.914A pdb=" N GLY A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 478 Processing helix chain 'A' and resid 479 through 490 removed outlier: 4.355A pdb=" N LEU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 Processing helix chain 'B' and resid 9 through 22 removed outlier: 4.019A pdb=" N SER B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 22 " --> pdb=" O TYR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.999A pdb=" N ASN B 84 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.652A pdb=" N PHE B 106 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 removed outlier: 4.013A pdb=" N ARG B 142 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 189 through 195 removed outlier: 3.556A pdb=" N SER B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 Processing helix chain 'B' and resid 242 through 262 Proline residue: B 250 - end of helix removed outlier: 3.763A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.640A pdb=" N GLN B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 300 through 310 removed outlier: 3.722A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.806A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 431 Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 479 through 490 removed outlier: 4.234A pdb=" N LEU B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 508 Processing helix chain 'C' and resid 12 through 20 removed outlier: 3.619A pdb=" N GLU C 16 " --> pdb=" O GLN C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 4.201A pdb=" N ASN C 84 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.522A pdb=" N PHE C 106 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 107 " --> pdb=" O ASP C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 107' Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.661A pdb=" N ARG C 142 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.865A pdb=" N GLY C 196 " --> pdb=" O ASN C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 227 through 230 removed outlier: 4.001A pdb=" N ASP C 230 " --> pdb=" O GLY C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 242 through 262 Proline residue: C 250 - end of helix removed outlier: 3.774A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.702A pdb=" N GLN C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 removed outlier: 3.554A pdb=" N ALA C 296 " --> pdb=" O GLY C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.818A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 392 through 407 Processing helix chain 'C' and resid 414 through 431 Processing helix chain 'C' and resid 440 through 453 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 478 Processing helix chain 'C' and resid 479 through 490 removed outlier: 4.246A pdb=" N LEU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 510 removed outlier: 3.904A pdb=" N GLY C 510 " --> pdb=" O ASN C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 533 Processing helix chain 'D' and resid 53 through 57 removed outlier: 3.746A pdb=" N ALA D 57 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 176 through 189 Processing helix chain 'D' and resid 204 through 218 Processing helix chain 'D' and resid 220 through 222 No H-bonds generated for 'chain 'D' and resid 220 through 222' Processing helix chain 'D' and resid 234 through 255 removed outlier: 5.146A pdb=" N ALA D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU D 243 " --> pdb=" O MET D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 277 removed outlier: 4.184A pdb=" N PHE D 270 " --> pdb=" O ASN D 266 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 293 through 303 Processing helix chain 'D' and resid 322 through 325 Processing helix chain 'D' and resid 328 through 335 Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 345 through 351 removed outlier: 3.571A pdb=" N LYS D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 373 through 400 removed outlier: 4.646A pdb=" N ASP D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ILE D 396 " --> pdb=" O ASP D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 405 removed outlier: 3.769A pdb=" N LEU D 405 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 423 Processing helix chain 'D' and resid 427 through 429 No H-bonds generated for 'chain 'D' and resid 427 through 429' Processing helix chain 'D' and resid 430 through 435 Processing helix chain 'D' and resid 442 through 456 Processing helix chain 'D' and resid 471 through 481 Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.620A pdb=" N VAL E 105 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 152 through 159 Processing helix chain 'E' and resid 176 through 191 Processing helix chain 'E' and resid 204 through 218 Processing helix chain 'E' and resid 220 through 222 No H-bonds generated for 'chain 'E' and resid 220 through 222' Processing helix chain 'E' and resid 234 through 255 removed outlier: 3.684A pdb=" N ARG E 238 " --> pdb=" O PRO E 234 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALA E 242 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU E 243 " --> pdb=" O MET E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 281 removed outlier: 3.880A pdb=" N PHE E 270 " --> pdb=" O ASN E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 303 Processing helix chain 'E' and resid 321 through 325 Processing helix chain 'E' and resid 328 through 335 Processing helix chain 'E' and resid 345 through 351 removed outlier: 3.558A pdb=" N LYS E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 400 removed outlier: 4.395A pdb=" N ASP E 395 " --> pdb=" O LYS E 391 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE E 396 " --> pdb=" O ASP E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 405 Processing helix chain 'E' and resid 406 through 423 Processing helix chain 'E' and resid 427 through 431 removed outlier: 3.617A pdb=" N GLU E 431 " --> pdb=" O MET E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 456 Processing helix chain 'E' and resid 462 through 467 Processing helix chain 'E' and resid 471 through 480 Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.699A pdb=" N VAL F 105 " --> pdb=" O GLY F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'F' and resid 152 through 159 Processing helix chain 'F' and resid 176 through 189 Processing helix chain 'F' and resid 204 through 218 Processing helix chain 'F' and resid 220 through 222 No H-bonds generated for 'chain 'F' and resid 220 through 222' Processing helix chain 'F' and resid 234 through 255 removed outlier: 5.142A pdb=" N ALA F 242 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU F 243 " --> pdb=" O MET F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 281 removed outlier: 3.902A pdb=" N PHE F 270 " --> pdb=" O ASN F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 303 Processing helix chain 'F' and resid 322 through 325 Processing helix chain 'F' and resid 328 through 335 Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 345 through 351 removed outlier: 3.526A pdb=" N LYS F 351 " --> pdb=" O ALA F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 393 removed outlier: 3.521A pdb=" N LEU F 393 " --> pdb=" O ARG F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 400 Processing helix chain 'F' and resid 401 through 405 removed outlier: 4.082A pdb=" N GLU F 404 " --> pdb=" O GLY F 401 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 405 " --> pdb=" O ILE F 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 401 through 405' Processing helix chain 'F' and resid 406 through 423 Processing helix chain 'F' and resid 427 through 429 No H-bonds generated for 'chain 'F' and resid 427 through 429' Processing helix chain 'F' and resid 430 through 435 Processing helix chain 'F' and resid 442 through 456 Processing helix chain 'F' and resid 471 through 483 Processing helix chain 'G' and resid 3 through 59 Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 65 through 69 removed outlier: 3.551A pdb=" N VAL G 69 " --> pdb=" O PRO G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 108 Processing helix chain 'G' and resid 120 through 130 removed outlier: 3.539A pdb=" N GLN G 124 " --> pdb=" O GLY G 120 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG G 130 " --> pdb=" O TYR G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 163 Processing helix chain 'G' and resid 225 through 302 removed outlier: 3.545A pdb=" N LEU G 229 " --> pdb=" O ASP G 225 " (cutoff:3.500A) Proline residue: G 235 - end of helix Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.543A pdb=" N ILE H 90 " --> pdb=" O GLU H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 98 Processing helix chain 'H' and resid 103 through 118 Processing helix chain '1' and resid 2 through 42 Processing helix chain '1' and resid 43 through 46 Processing helix chain '1' and resid 47 through 48 No H-bonds generated for 'chain '1' and resid 47 through 48' Processing helix chain '1' and resid 49 through 76 removed outlier: 3.552A pdb=" N PHE 1 54 " --> pdb=" O PHE 1 50 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE 1 55 " --> pdb=" O THR 1 51 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 42 Processing helix chain '2' and resid 45 through 76 removed outlier: 4.040A pdb=" N THR 2 51 " --> pdb=" O GLY 2 47 " (cutoff:3.500A) Proline residue: 2 52 - end of helix Processing helix chain '3' and resid 2 through 42 Processing helix chain '3' and resid 45 through 77 removed outlier: 4.495A pdb=" N THR 3 51 " --> pdb=" O GLY 3 47 " (cutoff:3.500A) Proline residue: 3 52 - end of helix Processing helix chain '4' and resid 2 through 42 Processing helix chain '4' and resid 43 through 48 removed outlier: 3.859A pdb=" N GLN 4 46 " --> pdb=" O PRO 4 43 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLY 4 47 " --> pdb=" O GLU 4 44 " (cutoff:3.500A) Processing helix chain '4' and resid 49 through 76 Processing helix chain '5' and resid 2 through 42 Processing helix chain '5' and resid 43 through 47 removed outlier: 4.161A pdb=" N GLY 5 47 " --> pdb=" O GLU 5 44 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 76 Processing helix chain '6' and resid 2 through 42 Processing helix chain '6' and resid 45 through 76 removed outlier: 3.946A pdb=" N THR 6 51 " --> pdb=" O GLY 6 47 " (cutoff:3.500A) Proline residue: 6 52 - end of helix Processing helix chain '7' and resid 2 through 42 Processing helix chain '7' and resid 43 through 48 removed outlier: 4.428A pdb=" N GLY 7 47 " --> pdb=" O GLU 7 44 " (cutoff:3.500A) Processing helix chain '7' and resid 49 through 76 removed outlier: 3.517A pdb=" N ALA 7 62 " --> pdb=" O GLY 7 58 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 42 Processing helix chain '8' and resid 45 through 76 removed outlier: 3.518A pdb=" N PHE 8 50 " --> pdb=" O GLN 8 46 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR 8 51 " --> pdb=" O GLY 8 47 " (cutoff:3.500A) Proline residue: 8 52 - end of helix Processing helix chain '9' and resid 2 through 42 Processing helix chain '9' and resid 45 through 76 removed outlier: 4.754A pdb=" N THR 9 51 " --> pdb=" O GLY 9 47 " (cutoff:3.500A) Proline residue: 9 52 - end of helix Processing helix chain 'b' and resid 29 through 49 removed outlier: 3.605A pdb=" N VAL b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA b 43 " --> pdb=" O LEU b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 99 removed outlier: 3.793A pdb=" N GLN b 82 " --> pdb=" O PHE b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 101 through 145 removed outlier: 4.017A pdb=" N GLU b 131 " --> pdb=" O GLN b 127 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU b 142 " --> pdb=" O ASP b 138 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP b 143 " --> pdb=" O ALA b 139 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG b 145 " --> pdb=" O GLU b 141 " (cutoff:3.500A) Processing helix chain 'b' and resid 147 through 161 removed outlier: 3.646A pdb=" N MET b 151 " --> pdb=" O HIS b 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 135 removed outlier: 5.003A pdb=" N VAL d 23 " --> pdb=" O TRP d 19 " (cutoff:3.500A) Proline residue: d 24 - end of helix removed outlier: 3.521A pdb=" N GLU d 75 " --> pdb=" O ARG d 71 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP d 92 " --> pdb=" O GLU d 88 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL d 93 " --> pdb=" O ALA d 89 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE d 98 " --> pdb=" O GLU d 94 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN d 101 " --> pdb=" O ARG d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 155 Processing helix chain 'd' and resid 176 through 191 removed outlier: 3.955A pdb=" N THR d 189 " --> pdb=" O ASP d 185 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 216 removed outlier: 3.600A pdb=" N GLU d 216 " --> pdb=" O LEU d 212 " (cutoff:3.500A) Processing helix chain 'd' and resid 216 through 224 removed outlier: 4.232A pdb=" N THR d 220 " --> pdb=" O GLU d 216 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR d 222 " --> pdb=" O VAL d 218 " (cutoff:3.500A) Processing helix chain 'd' and resid 230 through 239 Processing helix chain 'd' and resid 246 through 258 Processing helix chain 'd' and resid 264 through 286 removed outlier: 4.111A pdb=" N ILE d 268 " --> pdb=" O ASN d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 290 through 306 removed outlier: 3.715A pdb=" N VAL d 305 " --> pdb=" O ARG d 301 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN d 306 " --> pdb=" O ILE d 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 313 Processing helix chain 'd' and resid 319 through 332 removed outlier: 4.468A pdb=" N LYS d 329 " --> pdb=" O ARG d 325 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL d 330 " --> pdb=" O LEU d 326 " (cutoff:3.500A) Processing helix chain 'd' and resid 334 through 338 Processing helix chain 'd' and resid 341 through 352 Processing helix chain 'd' and resid 357 through 373 removed outlier: 3.783A pdb=" N LEU d 363 " --> pdb=" O GLU d 359 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG d 373 " --> pdb=" O ALA d 369 " (cutoff:3.500A) Processing helix chain 'd' and resid 387 through 403 Processing helix chain 'd' and resid 413 through 417 removed outlier: 3.647A pdb=" N LEU d 417 " --> pdb=" O ALA d 414 " (cutoff:3.500A) Processing helix chain 'd' and resid 432 through 443 Processing sheet with id=AA1, first strand: chain 'a' and resid 17 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 38 removed outlier: 5.524A pdb=" N VAL A 34 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP A 36 " --> pdb=" O HIS A 43 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 41 through 46 current: chain 'A' and resid 62 through 69 removed outlier: 5.743A pdb=" N ALA A 66 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 77 " --> pdb=" O ALA A 66 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 74 through 78 current: chain 'E' and resid 30 through 34 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 30 through 34 current: chain 'E' and resid 58 through 69 removed outlier: 6.567A pdb=" N ARG E 74 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N HIS E 67 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU E 72 " --> pdb=" O HIS E 67 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 72 through 77 current: chain 'd' and resid 427 through 430 Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 102 removed outlier: 3.730A pdb=" N THR A 128 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.756A pdb=" N ILE A 209 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 69 removed outlier: 3.603A pdb=" N ILE B 62 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU B 54 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU B 55 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N HIS B 43 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA B 37 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 9.775A pdb=" N ILE F 91 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLU F 50 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR F 93 " --> pdb=" O HIS F 48 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N HIS F 48 " --> pdb=" O THR F 93 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ARG F 95 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASN F 45 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG F 74 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N HIS F 67 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU F 72 " --> pdb=" O HIS F 67 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP F 32 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 102 removed outlier: 4.452A pdb=" N THR B 128 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.129A pdb=" N VAL B 111 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ALA B 238 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 267 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N LEU B 327 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE B 269 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE B 329 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE B 271 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N GLU B 331 " --> pdb=" O PHE B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 62 through 69 removed outlier: 3.975A pdb=" N GLU C 54 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLU C 96 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N GLU C 57 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N THR C 94 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N HIS C 43 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA C 37 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU C 63 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU D 89 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU D 50 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG D 74 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N HIS D 67 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU D 72 " --> pdb=" O HIS D 67 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL D 30 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP D 32 " --> pdb=" O VAL D 24 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.032A pdb=" N VAL C 111 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C 209 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE C 171 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 534 through 540 removed outlier: 6.334A pdb=" N ALA G 203 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 12.115A pdb=" N VAL C 538 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N MET G 205 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 10.768A pdb=" N VAL C 540 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N VAL G 207 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU G 182 " --> pdb=" O ILE G 202 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N THR G 187 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N THR G 135 " --> pdb=" O PRO G 114 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU G 116 " --> pdb=" O THR G 135 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER G 137 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL G 118 " --> pdb=" O SER G 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 98 through 101 removed outlier: 4.170A pdb=" N GLU D 127 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 109 through 110 removed outlier: 6.851A pdb=" N SER D 196 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL D 227 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE D 198 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLY D 229 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLY D 200 " --> pdb=" O GLY D 229 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL D 260 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N MET D 316 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU D 262 " --> pdb=" O MET D 316 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA D 318 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE D 264 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N TYR D 320 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D 167 " --> pdb=" O GLN D 317 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL D 319 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU D 169 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS D 166 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N THR D 342 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA D 168 " --> pdb=" O THR D 342 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU D 344 " --> pdb=" O ALA D 168 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE D 170 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 147 through 148 removed outlier: 3.915A pdb=" N TYR D 161 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 98 through 101 removed outlier: 4.145A pdb=" N GLU E 127 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 109 through 110 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 109 through 110 current: chain 'E' and resid 224 through 230 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 224 through 230 current: chain 'E' and resid 311 through 318 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 311 through 318 current: chain 'E' and resid 363 through 364 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 147 through 148 removed outlier: 4.344A pdb=" N TYR E 161 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 98 through 101 removed outlier: 4.323A pdb=" N GLU F 127 " --> pdb=" O VAL F 101 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 109 through 110 removed outlier: 6.386A pdb=" N PHE F 110 " --> pdb=" O PHE F 228 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER F 196 " --> pdb=" O ALA F 225 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL F 227 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE F 198 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLY F 229 " --> pdb=" O PHE F 198 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY F 200 " --> pdb=" O GLY F 229 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL F 260 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N MET F 316 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU F 262 " --> pdb=" O MET F 316 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA F 318 " --> pdb=" O LEU F 262 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE F 264 " --> pdb=" O ALA F 318 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N TYR F 320 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE F 167 " --> pdb=" O GLN F 317 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL F 319 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU F 169 " --> pdb=" O VAL F 319 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS F 166 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR F 342 " --> pdb=" O LYS F 166 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA F 168 " --> pdb=" O THR F 342 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 147 through 148 removed outlier: 3.958A pdb=" N TYR F 161 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 221 through 223 removed outlier: 6.361A pdb=" N SER G 221 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N GLN H 44 " --> pdb=" O SER G 221 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLU G 223 " --> pdb=" O GLN H 44 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL H 9 " --> pdb=" O ALA H 81 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA H 10 " --> pdb=" O ASN H 14 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASN H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 30 through 34 removed outlier: 4.592A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA H 49 " --> pdb=" O VAL H 65 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'd' and resid 376 through 380 2311 hydrogen bonds defined for protein. 6681 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: 8.46 Time building geometry restraints manager: 4.39 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: 12717 1.35 - 1.50: 9487 1.50 - 1.64: 15801 1.64 - 1.79: 105 1.79 - 1.94: 123 Bond restraints: 38233 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.22e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.62e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.53e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.50e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.40e+01 ... (remaining 38228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 51586 3.41 - 6.82: 272 6.82 - 10.23: 25 10.23 - 13.65: 4 13.65 - 17.06: 4 Bond angle restraints: 51891 Sorted by residual: angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 122.81 17.06 1.00e+00 1.00e+00 2.91e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 122.95 16.92 1.00e+00 1.00e+00 2.86e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 123.68 16.19 1.00e+00 1.00e+00 2.62e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 121.98 14.85 1.00e+00 1.00e+00 2.20e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 123.79 13.04 1.00e+00 1.00e+00 1.70e+02 ... (remaining 51886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.08: 21815 25.08 - 50.16: 1077 50.16 - 75.23: 101 75.23 - 100.31: 30 100.31 - 125.39: 3 Dihedral angle restraints: 23026 sinusoidal: 9167 harmonic: 13859 Sorted by residual: dihedral pdb=" O1B ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PB ADP D 600 " pdb=" PA ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 65.39 -125.39 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 63.52 -123.52 1 2.00e+01 2.50e-03 3.73e+01 dihedral pdb=" O2A ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PA ADP D 600 " pdb=" PB ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 53.24 -113.24 1 2.00e+01 2.50e-03 3.35e+01 ... (remaining 23023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4488 0.048 - 0.097: 1187 0.097 - 0.145: 294 0.145 - 0.194: 30 0.194 - 0.242: 4 Chirality restraints: 6003 Sorted by residual: chirality pdb=" CA LEU a 200 " pdb=" N LEU a 200 " pdb=" C LEU a 200 " pdb=" CB LEU a 200 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB THR 6 51 " pdb=" CA THR 6 51 " pdb=" OG1 THR 6 51 " pdb=" CG2 THR 6 51 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA THR 6 51 " pdb=" N THR 6 51 " pdb=" C THR 6 51 " pdb=" CB THR 6 51 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 6000 not shown) Planarity restraints: 6746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY a 116 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C GLY a 116 " 0.063 2.00e-02 2.50e+03 pdb=" O GLY a 116 " -0.023 2.00e-02 2.50e+03 pdb=" N HIS a 117 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG a 186 " -0.278 9.50e-02 1.11e+02 1.25e-01 9.57e+00 pdb=" NE ARG a 186 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG a 186 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG a 186 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG a 186 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN a 110 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C GLN a 110 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN a 110 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR a 111 " 0.018 2.00e-02 2.50e+03 ... (remaining 6743 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 102 2.43 - 3.05: 24326 3.05 - 3.66: 56860 3.66 - 4.28: 91743 4.28 - 4.90: 149994 Nonbonded interactions: 323025 Sorted by model distance: nonbonded pdb=" O1B ADP D 600 " pdb="MG MG D 601 " model vdw 1.810 2.170 nonbonded pdb=" O2B ATP C 600 " pdb="MG MG C 601 " model vdw 1.888 2.170 nonbonded pdb=" O3G ATP B 600 " pdb="MG MG B 601 " model vdw 1.956 2.170 nonbonded pdb=" O1B ATP A 600 " pdb="MG MG A 601 " model vdw 1.964 2.170 nonbonded pdb=" OG1 THR C 179 " pdb="MG MG C 601 " model vdw 1.998 2.170 ... (remaining 323020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '1' and resid 1 through 81) selection = chain '2' selection = chain '3' selection = (chain '4' and resid 1 through 81) selection = (chain '5' and resid 1 through 81) selection = (chain '6' and resid 1 through 81) selection = (chain '7' and resid 1 through 81) selection = (chain '8' and resid 1 through 81) selection = (chain '9' and resid 1 through 81) } ncs_group { reference = (chain 'A' and (resid 5 through 22 or resid 29 through 404 or resid 417 or (resi \ d 418 through 419 and (name N or name CA or name C or name O or name CB )) or re \ sid 420 through 514 or resid 600 through 601)) selection = chain 'B' selection = (chain 'C' and (resid 5 through 404 or resid 417 or (resid 418 through 419 and ( \ name N or name CA or name C or name O or name CB )) or resid 420 through 514 or \ resid 600 through 601)) } ncs_group { reference = (chain 'D' and resid 18 through 486) selection = chain 'E' selection = (chain 'F' and resid 18 through 486) } 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: 12.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 34.980 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 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:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.006 0.109 38233 Z= 0.302 Angle : 0.725 17.057 51891 Z= 0.443 Chirality : 0.046 0.242 6003 Planarity : 0.005 0.125 6746 Dihedral : 14.313 125.391 14132 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.11), residues: 4858 helix: -0.90 (0.09), residues: 2574 sheet: -1.17 (0.19), residues: 561 loop : -1.94 (0.13), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 133 TYR 0.022 0.001 TYR a 143 PHE 0.025 0.002 PHE A 245 TRP 0.014 0.001 TRP E 129 HIS 0.008 0.001 HIS d 348 Details of bonding type rmsd covalent geometry : bond 0.00589 (38233) covalent geometry : angle 0.72510 (51891) hydrogen bonds : bond 0.12862 ( 2311) hydrogen bonds : angle 6.69363 ( 6681) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 666 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.7844 (p0) cc_final: 0.7499 (p0) REVERT: A 192 ASN cc_start: 0.7912 (m-40) cc_final: 0.7613 (m-40) REVERT: B 481 GLU cc_start: 0.7084 (mp0) cc_final: 0.6700 (mp0) REVERT: B 485 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7345 (tt0) REVERT: B 499 LYS cc_start: 0.7121 (tttt) cc_final: 0.6890 (tppp) REVERT: C 499 LYS cc_start: 0.7852 (ttmt) cc_final: 0.7615 (tptt) REVERT: C 531 ASP cc_start: 0.7272 (m-30) cc_final: 0.6876 (t0) REVERT: D 368 ASP cc_start: 0.7834 (t70) cc_final: 0.7561 (t70) REVERT: D 394 GLN cc_start: 0.8043 (mt0) cc_final: 0.7826 (mt0) REVERT: F 351 LYS cc_start: 0.8716 (mtmt) cc_final: 0.8430 (mttp) REVERT: d 359 GLU cc_start: 0.6731 (tt0) cc_final: 0.5887 (tt0) outliers start: 0 outliers final: 1 residues processed: 666 average time/residue: 0.8921 time to fit residues: 691.3343 Evaluate side-chains 484 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 483 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.8980 chunk 470 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 26 ASN A 84 ASN A 90 GLN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN B 435 GLN C 192 ASN C 211 GLN C 335 ASN C 369 ASN D 128 HIS D 186 ASN ** D 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS F 128 HIS F 209 ASN F 256 GLN ** F 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 GLN H 14 ASN 1 67 ASN ** 2 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 ASN ** b 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 58 HIS d 140 GLN d 273 HIS d 277 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112225 restraints weight = 46317.022| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.73 r_work: 0.3242 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 38233 Z= 0.139 Angle : 0.590 11.662 51891 Z= 0.301 Chirality : 0.043 0.195 6003 Planarity : 0.005 0.059 6746 Dihedral : 7.723 138.948 5575 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.39 % Favored : 97.59 % Rotamer: Outliers : 1.93 % Allowed : 10.52 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.12), residues: 4858 helix: 0.83 (0.10), residues: 2639 sheet: -0.82 (0.20), residues: 556 loop : -1.16 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 7 48 TYR 0.033 0.001 TYR a 143 PHE 0.031 0.001 PHE d 11 TRP 0.011 0.001 TRP a 216 HIS 0.006 0.001 HIS d 273 Details of bonding type rmsd covalent geometry : bond 0.00302 (38233) covalent geometry : angle 0.58988 (51891) hydrogen bonds : bond 0.04698 ( 2311) hydrogen bonds : angle 4.64312 ( 6681) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 556 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 111 TYR cc_start: 0.7309 (p90) cc_final: 0.7067 (p90) REVERT: A 36 ASP cc_start: 0.8108 (p0) cc_final: 0.7834 (p0) REVERT: A 192 ASN cc_start: 0.7971 (m-40) cc_final: 0.7384 (m-40) REVERT: A 356 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7167 (mt-10) REVERT: B 71 GLU cc_start: 0.7799 (pt0) cc_final: 0.7297 (pm20) REVERT: B 90 GLN cc_start: 0.8357 (mm110) cc_final: 0.8151 (mm110) REVERT: B 481 GLU cc_start: 0.6303 (mp0) cc_final: 0.5870 (mp0) REVERT: B 485 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6940 (tt0) REVERT: B 499 LYS cc_start: 0.6367 (tttt) cc_final: 0.5972 (tppp) REVERT: C 191 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.7026 (mp-120) REVERT: C 499 LYS cc_start: 0.7138 (ttmt) cc_final: 0.6497 (tptt) REVERT: D 37 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7623 (ttm-80) REVERT: D 214 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7417 (tm-30) REVERT: D 394 GLN cc_start: 0.6939 (mt0) cc_final: 0.6532 (mt0) REVERT: E 50 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: E 346 ARG cc_start: 0.7443 (ttm-80) cc_final: 0.7126 (ttp80) REVERT: E 408 GLU cc_start: 0.6678 (mp0) cc_final: 0.6144 (pm20) REVERT: E 436 GLN cc_start: 0.6481 (mp10) cc_final: 0.6155 (pt0) REVERT: F 214 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: F 345 SER cc_start: 0.8518 (t) cc_final: 0.8255 (p) REVERT: F 351 LYS cc_start: 0.8347 (mtmt) cc_final: 0.8078 (mtmp) REVERT: G 139 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7682 (mmm) REVERT: G 180 ASP cc_start: 0.8076 (m-30) cc_final: 0.7846 (m-30) REVERT: G 232 SER cc_start: 0.8608 (m) cc_final: 0.8173 (p) REVERT: H 14 ASN cc_start: 0.8587 (t0) cc_final: 0.8310 (t0) REVERT: H 89 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: H 98 ASP cc_start: 0.7689 (t0) cc_final: 0.7488 (t0) REVERT: d 17 LEU cc_start: 0.8991 (tt) cc_final: 0.8778 (tp) REVERT: d 75 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8166 (tm-30) REVERT: d 195 ASP cc_start: 0.8132 (p0) cc_final: 0.7794 (p0) REVERT: d 235 ARG cc_start: 0.8248 (mmm160) cc_final: 0.7910 (mmm160) REVERT: d 360 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7485 (tm-30) outliers start: 75 outliers final: 25 residues processed: 590 average time/residue: 0.8019 time to fit residues: 556.7675 Evaluate side-chains 510 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 479 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 240 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 214 GLU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 6 residue 51 THR Chi-restraints excluded: chain 8 residue 51 THR Chi-restraints excluded: chain b residue 119 GLU Chi-restraints excluded: chain d residue 206 LEU Chi-restraints excluded: chain d residue 273 HIS Chi-restraints excluded: chain d residue 275 SER Chi-restraints excluded: chain d residue 404 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 324 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 228 optimal weight: 4.9990 chunk 328 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 26 ASN A 84 ASN A 112 ASN A 305 HIS B 53 GLN B 192 ASN ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 GLN B 437 GLN C 12 GLN C 192 ASN C 335 ASN C 369 ASN C 437 GLN E 71 ASN F 256 GLN ** F 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 67 ASN b 71 ASN b 95 GLN ** b 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.108365 restraints weight = 46849.152| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.74 r_work: 0.3180 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 38233 Z= 0.287 Angle : 0.668 9.045 51891 Z= 0.342 Chirality : 0.048 0.349 6003 Planarity : 0.005 0.072 6746 Dihedral : 8.023 169.884 5573 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 2.81 % Allowed : 12.06 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.12), residues: 4858 helix: 1.18 (0.10), residues: 2621 sheet: -0.52 (0.21), residues: 549 loop : -0.95 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 1 48 TYR 0.029 0.002 TYR a 143 PHE 0.031 0.002 PHE d 11 TRP 0.009 0.001 TRP a 216 HIS 0.014 0.001 HIS d 273 Details of bonding type rmsd covalent geometry : bond 0.00695 (38233) covalent geometry : angle 0.66781 (51891) hydrogen bonds : bond 0.05681 ( 2311) hydrogen bonds : angle 4.73882 ( 6681) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 481 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 128 ASP cc_start: 0.9056 (t0) cc_final: 0.8850 (t0) REVERT: a 161 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7490 (mm) REVERT: a 197 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8212 (mp) REVERT: A 36 ASP cc_start: 0.8152 (p0) cc_final: 0.7848 (p0) REVERT: A 146 LYS cc_start: 0.8361 (ptpt) cc_final: 0.8106 (ptpt) REVERT: A 192 ASN cc_start: 0.8015 (m-40) cc_final: 0.7394 (m-40) REVERT: A 356 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7262 (mt-10) REVERT: B 90 GLN cc_start: 0.8296 (mm110) cc_final: 0.8057 (mm110) REVERT: B 481 GLU cc_start: 0.6397 (mp0) cc_final: 0.5950 (mp0) REVERT: B 485 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6934 (tt0) REVERT: B 499 LYS cc_start: 0.6395 (tttt) cc_final: 0.6057 (tppp) REVERT: C 18 TYR cc_start: 0.7288 (t80) cc_final: 0.6971 (t80) REVERT: C 191 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.7055 (mp-120) REVERT: C 499 LYS cc_start: 0.7167 (ttmt) cc_final: 0.6468 (tptt) REVERT: D 22 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6937 (tpp-160) REVERT: D 37 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7651 (ttm-80) REVERT: D 266 ASN cc_start: 0.7975 (m-40) cc_final: 0.7664 (t0) REVERT: D 468 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8226 (mp) REVERT: D 477 LYS cc_start: 0.7201 (mptm) cc_final: 0.6710 (mptt) REVERT: E 50 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: E 346 ARG cc_start: 0.7371 (ttm-80) cc_final: 0.7014 (ttm-80) REVERT: E 436 GLN cc_start: 0.6488 (mp10) cc_final: 0.6106 (pt0) REVERT: F 214 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7394 (tp30) REVERT: F 343 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8294 (mt-10) REVERT: F 351 LYS cc_start: 0.8341 (mtmt) cc_final: 0.8063 (mtmp) REVERT: G 139 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7610 (mmm) REVERT: G 180 ASP cc_start: 0.8051 (m-30) cc_final: 0.7830 (m-30) REVERT: G 232 SER cc_start: 0.8582 (m) cc_final: 0.8238 (p) REVERT: H 89 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: 5 46 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8527 (tt0) REVERT: d 17 LEU cc_start: 0.9036 (tt) cc_final: 0.8826 (tp) REVERT: d 75 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8285 (tm-30) REVERT: d 195 ASP cc_start: 0.8181 (p0) cc_final: 0.7782 (p0) REVERT: d 235 ARG cc_start: 0.8325 (mmm160) cc_final: 0.7997 (mmm160) REVERT: d 359 GLU cc_start: 0.8088 (tt0) cc_final: 0.7550 (tt0) REVERT: d 360 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7649 (tm-30) REVERT: d 367 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7636 (tm-30) REVERT: d 413 ASP cc_start: 0.8467 (t0) cc_final: 0.8257 (t0) outliers start: 109 outliers final: 47 residues processed: 541 average time/residue: 0.8066 time to fit residues: 515.4603 Evaluate side-chains 518 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 459 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 161 LEU Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 207 TYR Chi-restraints excluded: chain a residue 240 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 214 GLU Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 3 residue 75 VAL Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 46 GLN Chi-restraints excluded: chain 6 residue 51 THR Chi-restraints excluded: chain 7 residue 71 MET Chi-restraints excluded: chain 8 residue 51 THR Chi-restraints excluded: chain b residue 74 SER Chi-restraints excluded: chain b residue 119 GLU Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 220 THR Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 275 SER Chi-restraints excluded: chain d residue 330 VAL Chi-restraints excluded: chain d residue 343 VAL Chi-restraints excluded: chain d residue 404 HIS Chi-restraints excluded: chain d residue 407 THR Chi-restraints excluded: chain d residue 424 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 45 optimal weight: 0.9990 chunk 302 optimal weight: 2.9990 chunk 474 optimal weight: 7.9990 chunk 316 optimal weight: 3.9990 chunk 387 optimal weight: 0.8980 chunk 328 optimal weight: 5.9990 chunk 360 optimal weight: 0.3980 chunk 221 optimal weight: 0.7980 chunk 358 optimal weight: 0.7980 chunk 396 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 130 ASN A 84 ASN A 112 ASN B 192 ASN B 435 GLN B 437 GLN C 335 ASN C 369 ASN E 266 ASN F 256 GLN ** F 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 GLN b 23 ASN b 71 ASN ** b 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 273 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.143576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113376 restraints weight = 46541.402| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.70 r_work: 0.3255 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 38233 Z= 0.127 Angle : 0.559 13.141 51891 Z= 0.283 Chirality : 0.043 0.412 6003 Planarity : 0.004 0.051 6746 Dihedral : 7.559 165.907 5573 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.35 % Favored : 97.61 % Rotamer: Outliers : 2.29 % Allowed : 13.69 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.12), residues: 4858 helix: 1.75 (0.10), residues: 2621 sheet: -0.45 (0.21), residues: 561 loop : -0.73 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 1 48 TYR 0.031 0.001 TYR a 143 PHE 0.035 0.001 PHE d 11 TRP 0.010 0.001 TRP a 216 HIS 0.005 0.001 HIS d 273 Details of bonding type rmsd covalent geometry : bond 0.00278 (38233) covalent geometry : angle 0.55899 (51891) hydrogen bonds : bond 0.04417 ( 2311) hydrogen bonds : angle 4.38187 ( 6681) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 520 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7842 (m-30) cc_final: 0.7212 (t70) REVERT: A 28 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8297 (mpp80) REVERT: A 29 GLU cc_start: 0.7753 (pt0) cc_final: 0.7455 (pt0) REVERT: A 36 ASP cc_start: 0.7995 (p0) cc_final: 0.7717 (p0) REVERT: A 146 LYS cc_start: 0.8378 (ptpt) cc_final: 0.8124 (ptpt) REVERT: A 192 ASN cc_start: 0.7949 (m-40) cc_final: 0.7346 (m-40) REVERT: A 356 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7203 (mt-10) REVERT: A 499 LYS cc_start: 0.7095 (mttp) cc_final: 0.6864 (mtmm) REVERT: B 71 GLU cc_start: 0.7781 (pt0) cc_final: 0.7251 (pm20) REVERT: B 90 GLN cc_start: 0.8286 (mm110) cc_final: 0.8057 (mm110) REVERT: B 485 GLU cc_start: 0.7358 (tm-30) cc_final: 0.6932 (tt0) REVERT: B 499 LYS cc_start: 0.6369 (tttt) cc_final: 0.5936 (tppp) REVERT: C 18 TYR cc_start: 0.7217 (t80) cc_final: 0.6845 (t80) REVERT: C 191 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6991 (mp-120) REVERT: C 498 ASP cc_start: 0.6564 (p0) cc_final: 0.6280 (m-30) REVERT: C 499 LYS cc_start: 0.7081 (ttmt) cc_final: 0.6322 (tptt) REVERT: D 20 SER cc_start: 0.8680 (m) cc_final: 0.8478 (m) REVERT: D 37 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7684 (ttm-80) REVERT: D 73 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7906 (p) REVERT: D 203 GLU cc_start: 0.7892 (tp30) cc_final: 0.7658 (mm-30) REVERT: D 214 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7357 (tm-30) REVERT: D 391 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7749 (ttmt) REVERT: D 394 GLN cc_start: 0.6865 (mt0) cc_final: 0.6495 (mt0) REVERT: D 477 LYS cc_start: 0.7107 (mptm) cc_final: 0.6587 (mptt) REVERT: E 50 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: E 408 GLU cc_start: 0.6326 (mp0) cc_final: 0.5922 (pm20) REVERT: E 436 GLN cc_start: 0.6395 (mp10) cc_final: 0.6009 (pt0) REVERT: E 477 LYS cc_start: 0.6383 (tptp) cc_final: 0.6176 (mtmt) REVERT: F 39 SER cc_start: 0.8366 (m) cc_final: 0.7790 (p) REVERT: F 118 ASP cc_start: 0.7646 (t0) cc_final: 0.7271 (t0) REVERT: F 203 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7971 (mm-30) REVERT: F 214 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7271 (tp30) REVERT: F 345 SER cc_start: 0.8393 (t) cc_final: 0.8162 (p) REVERT: F 351 LYS cc_start: 0.8335 (mtmt) cc_final: 0.8060 (mtmp) REVERT: G 109 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7609 (mt-10) REVERT: G 139 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7729 (mmm) REVERT: G 232 SER cc_start: 0.8530 (m) cc_final: 0.8248 (p) REVERT: H 89 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: 2 50 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8495 (m-10) REVERT: 4 71 MET cc_start: 0.8676 (tmm) cc_final: 0.8272 (tmm) REVERT: 5 46 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: b 109 LYS cc_start: 0.9065 (tmmm) cc_final: 0.8805 (tptt) REVERT: b 113 ASP cc_start: 0.8747 (p0) cc_final: 0.8496 (p0) REVERT: d 75 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8281 (tm-30) REVERT: d 195 ASP cc_start: 0.8216 (p0) cc_final: 0.7868 (p0) REVERT: d 235 ARG cc_start: 0.8230 (mmm160) cc_final: 0.7917 (mmm160) REVERT: d 312 LEU cc_start: 0.8699 (pt) cc_final: 0.8405 (tm) REVERT: d 326 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7337 (mt) REVERT: d 359 GLU cc_start: 0.8001 (tt0) cc_final: 0.7574 (tt0) REVERT: d 360 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7558 (tm-30) REVERT: d 367 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7554 (tm-30) outliers start: 89 outliers final: 32 residues processed: 575 average time/residue: 0.8028 time to fit residues: 546.0170 Evaluate side-chains 518 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 474 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 240 SER Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 266 ASN Chi-restraints excluded: chain F residue 214 GLU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 2 residue 50 PHE Chi-restraints excluded: chain 3 residue 80 VAL Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 46 GLN Chi-restraints excluded: chain 5 residue 51 THR Chi-restraints excluded: chain 6 residue 51 THR Chi-restraints excluded: chain 7 residue 71 MET Chi-restraints excluded: chain 8 residue 51 THR Chi-restraints excluded: chain 9 residue 51 THR Chi-restraints excluded: chain b residue 119 GLU Chi-restraints excluded: chain b residue 147 HIS Chi-restraints excluded: chain d residue 128 GLN Chi-restraints excluded: chain d residue 220 THR Chi-restraints excluded: chain d residue 273 HIS Chi-restraints excluded: chain d residue 275 SER Chi-restraints excluded: chain d residue 326 LEU Chi-restraints excluded: chain d residue 343 VAL Chi-restraints excluded: chain d residue 404 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 374 optimal weight: 0.6980 chunk 282 optimal weight: 0.9990 chunk 379 optimal weight: 4.9990 chunk 111 optimal weight: 0.4980 chunk 444 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 253 optimal weight: 1.9990 chunk 476 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 416 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 26 ASN a 110 GLN a 130 ASN A 84 ASN A 112 ASN B 192 ASN B 435 GLN B 437 GLN C 192 ASN C 335 ASN C 369 ASN ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 GLN ** F 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 67 ASN b 71 ASN b 95 GLN ** b 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 273 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.114079 restraints weight = 46653.664| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.74 r_work: 0.3260 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 38233 Z= 0.125 Angle : 0.549 12.228 51891 Z= 0.276 Chirality : 0.042 0.403 6003 Planarity : 0.004 0.065 6746 Dihedral : 7.391 166.802 5573 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.41 % Favored : 97.57 % Rotamer: Outliers : 2.40 % Allowed : 14.64 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.12), residues: 4858 helix: 2.07 (0.10), residues: 2572 sheet: -0.39 (0.21), residues: 593 loop : -0.62 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG 1 48 TYR 0.027 0.001 TYR a 143 PHE 0.037 0.001 PHE d 11 TRP 0.009 0.001 TRP a 216 HIS 0.006 0.001 HIS d 273 Details of bonding type rmsd covalent geometry : bond 0.00272 (38233) covalent geometry : angle 0.54887 (51891) hydrogen bonds : bond 0.04266 ( 2311) hydrogen bonds : angle 4.25377 ( 6681) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 508 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 71 MET cc_start: 0.8955 (mmt) cc_final: 0.8657 (mmt) REVERT: A 9 ASP cc_start: 0.7826 (m-30) cc_final: 0.7165 (t70) REVERT: A 29 GLU cc_start: 0.7694 (pt0) cc_final: 0.7404 (pt0) REVERT: A 36 ASP cc_start: 0.8002 (p0) cc_final: 0.7719 (p0) REVERT: A 146 LYS cc_start: 0.8350 (ptpt) cc_final: 0.8112 (ptpt) REVERT: A 192 ASN cc_start: 0.7941 (m-40) cc_final: 0.7346 (m-40) REVERT: A 225 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8098 (mm-30) REVERT: A 331 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: A 356 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: B 485 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6997 (tt0) REVERT: B 499 LYS cc_start: 0.6319 (tttt) cc_final: 0.5934 (tppp) REVERT: C 18 TYR cc_start: 0.7177 (t80) cc_final: 0.6782 (t80) REVERT: C 191 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.7006 (mp-120) REVERT: C 498 ASP cc_start: 0.6546 (p0) cc_final: 0.6260 (m-30) REVERT: C 499 LYS cc_start: 0.7098 (ttmt) cc_final: 0.6320 (tptt) REVERT: D 20 SER cc_start: 0.8711 (m) cc_final: 0.8499 (m) REVERT: D 37 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7775 (ttm-80) REVERT: D 214 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7384 (tm-30) REVERT: D 391 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7781 (ttmt) REVERT: D 394 GLN cc_start: 0.6827 (mt0) cc_final: 0.6512 (mt0) REVERT: D 477 LYS cc_start: 0.7086 (mptm) cc_final: 0.6662 (mptt) REVERT: E 50 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: E 346 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.7067 (ttp80) REVERT: E 408 GLU cc_start: 0.6273 (mp0) cc_final: 0.5861 (pm20) REVERT: E 436 GLN cc_start: 0.6360 (mp10) cc_final: 0.5985 (pt0) REVERT: E 477 LYS cc_start: 0.6257 (tptp) cc_final: 0.6051 (mttt) REVERT: F 39 SER cc_start: 0.8366 (m) cc_final: 0.7862 (p) REVERT: F 118 ASP cc_start: 0.7646 (t0) cc_final: 0.7339 (t0) REVERT: F 214 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7291 (tp30) REVERT: F 421 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7290 (mtt90) REVERT: G 109 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7572 (mt-10) REVERT: G 139 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7719 (mmm) REVERT: G 232 SER cc_start: 0.8510 (m) cc_final: 0.8284 (p) REVERT: H 89 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7600 (mm-30) REVERT: 2 50 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8438 (m-10) REVERT: 3 44 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: 4 71 MET cc_start: 0.8675 (tmm) cc_final: 0.8263 (tmm) REVERT: 5 46 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: b 113 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8518 (p0) REVERT: b 141 GLU cc_start: 0.8389 (tp30) cc_final: 0.8118 (tp30) REVERT: d 195 ASP cc_start: 0.8155 (p0) cc_final: 0.7803 (p0) REVERT: d 235 ARG cc_start: 0.8218 (mmm160) cc_final: 0.7918 (mmm160) REVERT: d 326 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7410 (mt) REVERT: d 359 GLU cc_start: 0.8019 (tt0) cc_final: 0.7479 (tt0) REVERT: d 360 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7536 (tm-30) REVERT: d 413 ASP cc_start: 0.8392 (t0) cc_final: 0.8169 (t0) outliers start: 93 outliers final: 41 residues processed: 564 average time/residue: 0.8017 time to fit residues: 533.0305 Evaluate side-chains 528 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 473 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 240 SER Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 214 GLU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 421 ARG Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 2 residue 50 PHE Chi-restraints excluded: chain 3 residue 44 GLU Chi-restraints excluded: chain 3 residue 80 VAL Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 46 GLN Chi-restraints excluded: chain 5 residue 51 THR Chi-restraints excluded: chain 6 residue 51 THR Chi-restraints excluded: chain 7 residue 71 MET Chi-restraints excluded: chain 8 residue 51 THR Chi-restraints excluded: chain 9 residue 51 THR Chi-restraints excluded: chain b residue 90 THR Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain b residue 119 GLU Chi-restraints excluded: chain d residue 128 GLN Chi-restraints excluded: chain d residue 220 THR Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 271 ILE Chi-restraints excluded: chain d residue 273 HIS Chi-restraints excluded: chain d residue 275 SER Chi-restraints excluded: chain d residue 326 LEU Chi-restraints excluded: chain d residue 343 VAL Chi-restraints excluded: chain d residue 404 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 163 optimal weight: 9.9990 chunk 406 optimal weight: 2.9990 chunk 301 optimal weight: 0.0970 chunk 57 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 404 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 303 optimal weight: 0.0030 chunk 207 optimal weight: 0.9980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 26 ASN ** a 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 130 ASN A 84 ASN A 112 ASN B 141 HIS B 192 ASN B 435 GLN B 437 GLN C 68 ASN C 192 ASN C 335 ASN C 369 ASN E 230 GLN ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 HIS 4 42 GLN b 23 ASN b 71 ASN d 273 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.146178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.115578 restraints weight = 46259.039| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.69 r_work: 0.3277 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 38233 Z= 0.114 Angle : 0.541 13.315 51891 Z= 0.271 Chirality : 0.042 0.370 6003 Planarity : 0.004 0.086 6746 Dihedral : 7.213 166.760 5573 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.31 % Favored : 97.67 % Rotamer: Outliers : 2.50 % Allowed : 15.29 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.12), residues: 4858 helix: 2.26 (0.10), residues: 2567 sheet: -0.27 (0.21), residues: 581 loop : -0.49 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 22 TYR 0.033 0.001 TYR a 143 PHE 0.039 0.001 PHE d 297 TRP 0.008 0.001 TRP B 247 HIS 0.007 0.001 HIS d 273 Details of bonding type rmsd covalent geometry : bond 0.00243 (38233) covalent geometry : angle 0.54067 (51891) hydrogen bonds : bond 0.04042 ( 2311) hydrogen bonds : angle 4.15460 ( 6681) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 513 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 71 MET cc_start: 0.8965 (mmt) cc_final: 0.8685 (mmt) REVERT: a 74 GLN cc_start: 0.8207 (mm110) cc_final: 0.7883 (mm-40) REVERT: A 9 ASP cc_start: 0.7729 (m-30) cc_final: 0.7075 (t0) REVERT: A 29 GLU cc_start: 0.7598 (pt0) cc_final: 0.7319 (pt0) REVERT: A 36 ASP cc_start: 0.7925 (p0) cc_final: 0.7654 (p0) REVERT: A 146 LYS cc_start: 0.8331 (ptpt) cc_final: 0.8131 (ptpt) REVERT: A 192 ASN cc_start: 0.7908 (m-40) cc_final: 0.7303 (m-40) REVERT: B 485 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6998 (tt0) REVERT: B 499 LYS cc_start: 0.6266 (tttt) cc_final: 0.5972 (tppp) REVERT: C 18 TYR cc_start: 0.7153 (t80) cc_final: 0.6801 (t80) REVERT: C 191 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6980 (mp-120) REVERT: C 323 SER cc_start: 0.9067 (m) cc_final: 0.8752 (p) REVERT: C 498 ASP cc_start: 0.6565 (p0) cc_final: 0.6289 (m-30) REVERT: C 499 LYS cc_start: 0.7101 (ttmt) cc_final: 0.6322 (tptt) REVERT: D 37 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7652 (ttm-80) REVERT: D 73 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7929 (p) REVERT: D 203 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7799 (mm-30) REVERT: D 214 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7269 (tm-30) REVERT: D 391 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7771 (ttmt) REVERT: D 394 GLN cc_start: 0.6734 (mt0) cc_final: 0.6412 (mt0) REVERT: D 477 LYS cc_start: 0.7090 (mptm) cc_final: 0.6666 (mptt) REVERT: E 50 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: E 95 ARG cc_start: 0.7572 (ptt90) cc_final: 0.6479 (ptp90) REVERT: E 230 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7733 (mp10) REVERT: E 346 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.7103 (ttp80) REVERT: E 408 GLU cc_start: 0.6375 (mp0) cc_final: 0.5994 (pm20) REVERT: E 436 GLN cc_start: 0.6388 (mp10) cc_final: 0.6005 (pt0) REVERT: E 477 LYS cc_start: 0.6218 (tptp) cc_final: 0.5986 (mttt) REVERT: E 485 LYS cc_start: 0.6375 (OUTLIER) cc_final: 0.4847 (pptt) REVERT: F 39 SER cc_start: 0.8327 (m) cc_final: 0.7844 (p) REVERT: F 118 ASP cc_start: 0.7569 (t0) cc_final: 0.7315 (t0) REVERT: F 214 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: G 75 LYS cc_start: 0.6847 (pttm) cc_final: 0.5863 (ptmt) REVERT: G 109 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7585 (mt-10) REVERT: G 139 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7740 (mmm) REVERT: G 180 ASP cc_start: 0.7809 (m-30) cc_final: 0.7589 (m-30) REVERT: H 89 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7578 (mm-30) REVERT: 2 50 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8434 (m-10) REVERT: 4 71 MET cc_start: 0.8697 (tmm) cc_final: 0.8333 (tmm) REVERT: 5 46 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: 5 71 MET cc_start: 0.8720 (tmm) cc_final: 0.8397 (tmt) REVERT: b 109 LYS cc_start: 0.8915 (tptt) cc_final: 0.8501 (tmtp) REVERT: b 141 GLU cc_start: 0.8387 (tp30) cc_final: 0.8085 (tp30) REVERT: d 195 ASP cc_start: 0.8118 (p0) cc_final: 0.7778 (p0) REVERT: d 308 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7809 (ptp-170) REVERT: d 312 LEU cc_start: 0.8651 (pt) cc_final: 0.8288 (tm) REVERT: d 326 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7396 (mt) REVERT: d 360 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7493 (tm-30) REVERT: d 413 ASP cc_start: 0.8424 (t0) cc_final: 0.8160 (t0) outliers start: 97 outliers final: 36 residues processed: 572 average time/residue: 0.8105 time to fit residues: 549.4257 Evaluate side-chains 521 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 472 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 171 ILE Chi-restraints excluded: chain a residue 240 SER Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 230 GLN Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 485 LYS Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 214 GLU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 2 residue 50 PHE Chi-restraints excluded: chain 3 residue 80 VAL Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 46 GLN Chi-restraints excluded: chain 5 residue 51 THR Chi-restraints excluded: chain 6 residue 51 THR Chi-restraints excluded: chain 7 residue 71 MET Chi-restraints excluded: chain 8 residue 51 THR Chi-restraints excluded: chain 9 residue 51 THR Chi-restraints excluded: chain b residue 90 THR Chi-restraints excluded: chain b residue 119 GLU Chi-restraints excluded: chain d residue 128 GLN Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 220 THR Chi-restraints excluded: chain d residue 275 SER Chi-restraints excluded: chain d residue 308 ARG Chi-restraints excluded: chain d residue 326 LEU Chi-restraints excluded: chain d residue 343 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 348 optimal weight: 5.9990 chunk 473 optimal weight: 0.9980 chunk 209 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 392 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 130 ASN A 84 ASN B 84 ASN B 192 ASN B 435 GLN B 437 GLN C 192 ASN C 335 ASN ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 464 GLN G 37 GLN H 14 ASN 1 46 GLN b 71 ASN b 95 GLN d 273 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.113542 restraints weight = 46280.987| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.69 r_work: 0.3252 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38233 Z= 0.141 Angle : 0.566 13.424 51891 Z= 0.284 Chirality : 0.043 0.336 6003 Planarity : 0.004 0.074 6746 Dihedral : 7.310 169.785 5573 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.47 % Favored : 97.51 % Rotamer: Outliers : 2.45 % Allowed : 16.01 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.12), residues: 4858 helix: 2.27 (0.10), residues: 2561 sheet: -0.29 (0.21), residues: 568 loop : -0.40 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG 1 48 TYR 0.032 0.001 TYR a 143 PHE 0.027 0.001 PHE d 297 TRP 0.008 0.001 TRP a 216 HIS 0.003 0.001 HIS D 376 Details of bonding type rmsd covalent geometry : bond 0.00321 (38233) covalent geometry : angle 0.56609 (51891) hydrogen bonds : bond 0.04317 ( 2311) hydrogen bonds : angle 4.18676 ( 6681) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 492 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 71 MET cc_start: 0.8989 (mmt) cc_final: 0.8694 (mmt) REVERT: A 9 ASP cc_start: 0.7695 (m-30) cc_final: 0.7053 (t0) REVERT: A 29 GLU cc_start: 0.7565 (pt0) cc_final: 0.7272 (pt0) REVERT: A 36 ASP cc_start: 0.7987 (p0) cc_final: 0.7708 (p0) REVERT: A 146 LYS cc_start: 0.8370 (ptpt) cc_final: 0.8166 (ptpt) REVERT: A 192 ASN cc_start: 0.7934 (m-40) cc_final: 0.7343 (m-40) REVERT: A 356 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: B 96 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6620 (mt-10) REVERT: B 485 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7045 (tt0) REVERT: B 499 LYS cc_start: 0.6285 (tttt) cc_final: 0.6041 (tppp) REVERT: C 18 TYR cc_start: 0.7112 (t80) cc_final: 0.6749 (t80) REVERT: C 191 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7054 (mp-120) REVERT: C 498 ASP cc_start: 0.6601 (p0) cc_final: 0.6350 (m-30) REVERT: C 499 LYS cc_start: 0.7141 (ttmt) cc_final: 0.6333 (tptt) REVERT: D 37 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7688 (ttm-80) REVERT: D 73 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.7995 (p) REVERT: D 203 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7892 (mm-30) REVERT: D 214 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7396 (tm-30) REVERT: D 391 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7851 (ttmt) REVERT: D 394 GLN cc_start: 0.6903 (mt0) cc_final: 0.6582 (mt0) REVERT: D 477 LYS cc_start: 0.7184 (mptm) cc_final: 0.6758 (mptt) REVERT: D 486 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6706 (mp) REVERT: E 50 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: E 95 ARG cc_start: 0.7712 (ptt90) cc_final: 0.6624 (ptp90) REVERT: E 346 ARG cc_start: 0.7443 (ttm-80) cc_final: 0.7146 (ttp80) REVERT: E 408 GLU cc_start: 0.6462 (mp0) cc_final: 0.6054 (pm20) REVERT: E 436 GLN cc_start: 0.6413 (mp10) cc_final: 0.6016 (pt0) REVERT: E 477 LYS cc_start: 0.6297 (tptp) cc_final: 0.6054 (mttt) REVERT: E 485 LYS cc_start: 0.6449 (OUTLIER) cc_final: 0.4928 (pptt) REVERT: F 39 SER cc_start: 0.8377 (m) cc_final: 0.7919 (p) REVERT: F 118 ASP cc_start: 0.7635 (t0) cc_final: 0.7376 (t0) REVERT: F 214 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7314 (tp30) REVERT: G 75 LYS cc_start: 0.7016 (pttm) cc_final: 0.6019 (ptmt) REVERT: G 109 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7637 (mt-10) REVERT: G 139 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7709 (mmm) REVERT: H 89 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7663 (mm-30) REVERT: 2 50 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8483 (m-10) REVERT: 3 44 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: 4 71 MET cc_start: 0.8711 (tmm) cc_final: 0.8439 (tmm) REVERT: 5 46 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: 7 48 ARG cc_start: 0.8181 (ttp-110) cc_final: 0.7875 (mtm110) REVERT: b 136 GLU cc_start: 0.8367 (tt0) cc_final: 0.8132 (tt0) REVERT: d 195 ASP cc_start: 0.8125 (p0) cc_final: 0.7790 (p0) REVERT: d 312 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8194 (tm) REVERT: d 326 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7462 (mp) REVERT: d 360 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7482 (tm-30) REVERT: d 413 ASP cc_start: 0.8365 (t0) cc_final: 0.8107 (t0) outliers start: 95 outliers final: 43 residues processed: 552 average time/residue: 0.7991 time to fit residues: 522.6981 Evaluate side-chains 533 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 475 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 171 ILE Chi-restraints excluded: chain a residue 240 SER Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 485 LYS Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 214 GLU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 2 residue 50 PHE Chi-restraints excluded: chain 3 residue 44 GLU Chi-restraints excluded: chain 3 residue 80 VAL Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 46 GLN Chi-restraints excluded: chain 5 residue 51 THR Chi-restraints excluded: chain 6 residue 51 THR Chi-restraints excluded: chain 8 residue 51 THR Chi-restraints excluded: chain 9 residue 51 THR Chi-restraints excluded: chain b residue 90 THR Chi-restraints excluded: chain b residue 119 GLU Chi-restraints excluded: chain d residue 128 GLN Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 220 THR Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 273 HIS Chi-restraints excluded: chain d residue 275 SER Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 326 LEU Chi-restraints excluded: chain d residue 343 VAL Chi-restraints excluded: chain d residue 363 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 103 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 378 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 429 optimal weight: 8.9990 chunk 375 optimal weight: 0.7980 chunk 476 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 237 optimal weight: 0.0970 overall best weight: 1.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 26 ASN ** a 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 130 ASN A 84 ASN B 192 ASN B 435 GLN B 437 GLN C 192 ASN C 335 ASN ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN 1 46 GLN b 23 ASN b 71 ASN d 101 GLN d 273 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.143869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112963 restraints weight = 46052.529| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.68 r_work: 0.3244 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38233 Z= 0.151 Angle : 0.580 13.680 51891 Z= 0.290 Chirality : 0.043 0.340 6003 Planarity : 0.004 0.074 6746 Dihedral : 7.379 171.401 5573 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.41 % Favored : 97.57 % Rotamer: Outliers : 2.32 % Allowed : 16.24 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.12), residues: 4858 helix: 2.24 (0.10), residues: 2561 sheet: -0.29 (0.21), residues: 572 loop : -0.39 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG 1 48 TYR 0.030 0.001 TYR a 143 PHE 0.025 0.001 PHE d 297 TRP 0.008 0.001 TRP a 216 HIS 0.013 0.001 HIS d 273 Details of bonding type rmsd covalent geometry : bond 0.00350 (38233) covalent geometry : angle 0.57973 (51891) hydrogen bonds : bond 0.04431 ( 2311) hydrogen bonds : angle 4.23402 ( 6681) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 486 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 71 MET cc_start: 0.8984 (mmt) cc_final: 0.8699 (mmt) REVERT: A 9 ASP cc_start: 0.7671 (m-30) cc_final: 0.7019 (t0) REVERT: A 29 GLU cc_start: 0.7540 (pt0) cc_final: 0.7234 (pt0) REVERT: A 36 ASP cc_start: 0.7984 (p0) cc_final: 0.7689 (p0) REVERT: A 146 LYS cc_start: 0.8367 (ptpt) cc_final: 0.8154 (ptpt) REVERT: A 192 ASN cc_start: 0.7943 (m-40) cc_final: 0.7361 (m-40) REVERT: A 331 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: A 356 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: B 96 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6632 (mt-10) REVERT: B 485 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7060 (tt0) REVERT: B 499 LYS cc_start: 0.6286 (tttt) cc_final: 0.6034 (tppp) REVERT: C 191 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.7061 (mp-120) REVERT: C 498 ASP cc_start: 0.6602 (p0) cc_final: 0.6369 (m-30) REVERT: C 499 LYS cc_start: 0.7175 (ttmt) cc_final: 0.6363 (tptt) REVERT: D 37 ARG cc_start: 0.8025 (ttm-80) cc_final: 0.7698 (ttm-80) REVERT: D 73 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.7998 (p) REVERT: D 203 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7874 (mm-30) REVERT: D 214 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7387 (tm-30) REVERT: D 391 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7881 (ttmt) REVERT: D 394 GLN cc_start: 0.6927 (mt0) cc_final: 0.6598 (mt0) REVERT: D 477 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6775 (mptt) REVERT: D 486 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6719 (mp) REVERT: E 50 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: E 95 ARG cc_start: 0.7699 (ptt90) cc_final: 0.6610 (ptp90) REVERT: E 346 ARG cc_start: 0.7424 (ttm-80) cc_final: 0.7131 (ttp80) REVERT: E 408 GLU cc_start: 0.6452 (mp0) cc_final: 0.6043 (pm20) REVERT: E 436 GLN cc_start: 0.6460 (mp10) cc_final: 0.6034 (pt0) REVERT: E 477 LYS cc_start: 0.6272 (tptp) cc_final: 0.6054 (mttt) REVERT: E 485 LYS cc_start: 0.6458 (OUTLIER) cc_final: 0.4908 (pptt) REVERT: F 39 SER cc_start: 0.8354 (m) cc_final: 0.7901 (p) REVERT: F 118 ASP cc_start: 0.7639 (t0) cc_final: 0.7371 (t0) REVERT: F 214 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7314 (tp30) REVERT: F 482 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7255 (mp) REVERT: G 41 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: G 109 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7622 (mt-10) REVERT: G 139 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7724 (mmm) REVERT: H 89 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7710 (mm-30) REVERT: H 91 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8002 (p0) REVERT: 2 50 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8487 (m-10) REVERT: 4 71 MET cc_start: 0.8724 (tmm) cc_final: 0.8452 (tmm) REVERT: 5 46 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: b 109 LYS cc_start: 0.8906 (tptt) cc_final: 0.8538 (tmtp) REVERT: b 113 ASP cc_start: 0.8552 (p0) cc_final: 0.8338 (p0) REVERT: b 136 GLU cc_start: 0.8352 (tt0) cc_final: 0.8121 (tt0) REVERT: b 141 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7994 (tp30) REVERT: d 195 ASP cc_start: 0.8107 (p0) cc_final: 0.7775 (p0) REVERT: d 308 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7716 (ptp-170) REVERT: d 312 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8211 (tm) REVERT: d 360 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7538 (tm-30) REVERT: d 413 ASP cc_start: 0.8387 (t0) cc_final: 0.8126 (t0) outliers start: 90 outliers final: 44 residues processed: 541 average time/residue: 0.8154 time to fit residues: 521.7697 Evaluate side-chains 536 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 473 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 171 ILE Chi-restraints excluded: chain a residue 240 SER Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 477 LYS Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 485 LYS Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 214 GLU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 2 residue 50 PHE Chi-restraints excluded: chain 3 residue 80 VAL Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 46 GLN Chi-restraints excluded: chain 5 residue 51 THR Chi-restraints excluded: chain 6 residue 51 THR Chi-restraints excluded: chain 8 residue 51 THR Chi-restraints excluded: chain 9 residue 51 THR Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 119 GLU Chi-restraints excluded: chain d residue 79 ASP Chi-restraints excluded: chain d residue 128 GLN Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 220 THR Chi-restraints excluded: chain d residue 241 VAL Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 273 HIS Chi-restraints excluded: chain d residue 275 SER Chi-restraints excluded: chain d residue 308 ARG Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 343 VAL Chi-restraints excluded: chain d residue 363 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 123 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 291 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 306 optimal weight: 0.7980 chunk 234 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 130 ASN A 84 ASN B 192 ASN B 437 GLN C 192 ASN C 335 ASN C 437 GLN E 230 GLN ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN 1 46 GLN b 71 ASN b 95 GLN d 273 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112214 restraints weight = 46463.614| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.69 r_work: 0.3233 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 38233 Z= 0.164 Angle : 0.600 13.918 51891 Z= 0.300 Chirality : 0.044 0.336 6003 Planarity : 0.004 0.054 6746 Dihedral : 7.462 172.578 5573 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.47 % Favored : 97.51 % Rotamer: Outliers : 2.22 % Allowed : 16.45 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.12), residues: 4858 helix: 2.20 (0.10), residues: 2559 sheet: -0.30 (0.21), residues: 572 loop : -0.40 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG d 239 TYR 0.036 0.001 TYR a 143 PHE 0.017 0.001 PHE d 297 TRP 0.008 0.001 TRP a 216 HIS 0.017 0.001 HIS d 273 Details of bonding type rmsd covalent geometry : bond 0.00386 (38233) covalent geometry : angle 0.60000 (51891) hydrogen bonds : bond 0.04564 ( 2311) hydrogen bonds : angle 4.28299 ( 6681) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 488 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 71 MET cc_start: 0.8987 (mmt) cc_final: 0.8719 (mmt) REVERT: A 9 ASP cc_start: 0.7591 (m-30) cc_final: 0.6959 (t0) REVERT: A 29 GLU cc_start: 0.7556 (pt0) cc_final: 0.7341 (pt0) REVERT: A 36 ASP cc_start: 0.8002 (p0) cc_final: 0.7695 (p0) REVERT: A 92 LYS cc_start: 0.8685 (mttm) cc_final: 0.8252 (mtpt) REVERT: A 146 LYS cc_start: 0.8351 (ptpt) cc_final: 0.8124 (ptpt) REVERT: A 192 ASN cc_start: 0.7986 (m-40) cc_final: 0.7409 (m-40) REVERT: A 331 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: A 356 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7222 (mt-10) REVERT: B 96 GLU cc_start: 0.6897 (mm-30) cc_final: 0.6659 (mt-10) REVERT: B 485 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7055 (tt0) REVERT: B 499 LYS cc_start: 0.6295 (tttt) cc_final: 0.5997 (tppp) REVERT: C 12 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6714 (pp30) REVERT: C 191 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.7070 (mp-120) REVERT: C 498 ASP cc_start: 0.6706 (p0) cc_final: 0.6391 (m-30) REVERT: C 499 LYS cc_start: 0.7198 (ttmt) cc_final: 0.6382 (tptt) REVERT: D 37 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7677 (ttm-80) REVERT: D 203 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7869 (mm-30) REVERT: D 214 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7414 (tm-30) REVERT: D 391 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7876 (ttmt) REVERT: D 394 GLN cc_start: 0.6969 (mt0) cc_final: 0.6629 (mt0) REVERT: D 477 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6813 (mptt) REVERT: D 486 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6695 (mp) REVERT: E 50 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: E 95 ARG cc_start: 0.7700 (ptt90) cc_final: 0.6602 (ptp90) REVERT: E 230 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7691 (mp10) REVERT: E 346 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.7134 (ttp80) REVERT: E 436 GLN cc_start: 0.6517 (mp10) cc_final: 0.6076 (pt0) REVERT: E 477 LYS cc_start: 0.6279 (tptp) cc_final: 0.6069 (mtmt) REVERT: E 485 LYS cc_start: 0.6498 (OUTLIER) cc_final: 0.4934 (pptt) REVERT: F 39 SER cc_start: 0.8379 (m) cc_final: 0.7930 (p) REVERT: F 118 ASP cc_start: 0.7652 (t0) cc_final: 0.7378 (t0) REVERT: F 214 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7334 (tp30) REVERT: F 482 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7297 (mp) REVERT: G 41 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: G 109 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7615 (mt-10) REVERT: G 139 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7696 (mmm) REVERT: H 89 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7715 (mm-30) REVERT: H 91 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7994 (p0) REVERT: 1 48 ARG cc_start: 0.8180 (ptt-90) cc_final: 0.7026 (ptt90) REVERT: 2 50 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8512 (m-10) REVERT: 3 44 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: 4 71 MET cc_start: 0.8733 (tmm) cc_final: 0.8442 (tmm) REVERT: 5 46 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8430 (tt0) REVERT: 7 48 ARG cc_start: 0.8174 (ttp-110) cc_final: 0.7884 (mtm110) REVERT: b 136 GLU cc_start: 0.8373 (tt0) cc_final: 0.8148 (tt0) REVERT: d 105 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: d 195 ASP cc_start: 0.8095 (p0) cc_final: 0.7753 (p0) REVERT: d 308 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7737 (ptp-170) REVERT: d 312 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8208 (tm) REVERT: d 360 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7532 (tm-30) REVERT: d 413 ASP cc_start: 0.8396 (t0) cc_final: 0.8123 (t0) outliers start: 86 outliers final: 48 residues processed: 540 average time/residue: 0.8042 time to fit residues: 514.1842 Evaluate side-chains 545 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 475 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 171 ILE Chi-restraints excluded: chain a residue 240 SER Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 477 LYS Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 230 GLN Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 485 LYS Chi-restraints excluded: chain F residue 214 GLU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 2 residue 50 PHE Chi-restraints excluded: chain 3 residue 44 GLU Chi-restraints excluded: chain 3 residue 80 VAL Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 46 GLN Chi-restraints excluded: chain 5 residue 51 THR Chi-restraints excluded: chain 6 residue 51 THR Chi-restraints excluded: chain 8 residue 51 THR Chi-restraints excluded: chain 9 residue 51 THR Chi-restraints excluded: chain b residue 74 SER Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 119 GLU Chi-restraints excluded: chain d residue 79 ASP Chi-restraints excluded: chain d residue 105 GLN Chi-restraints excluded: chain d residue 108 LEU Chi-restraints excluded: chain d residue 128 GLN Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 220 THR Chi-restraints excluded: chain d residue 241 VAL Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 273 HIS Chi-restraints excluded: chain d residue 275 SER Chi-restraints excluded: chain d residue 308 ARG Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 343 VAL Chi-restraints excluded: chain d residue 363 LEU Chi-restraints excluded: chain d residue 404 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 248 optimal weight: 1.9990 chunk 462 optimal weight: 7.9990 chunk 344 optimal weight: 2.9990 chunk 432 optimal weight: 5.9990 chunk 305 optimal weight: 5.9990 chunk 239 optimal weight: 0.0010 chunk 269 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 360 optimal weight: 0.9990 chunk 396 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 130 ASN A 84 ASN B 192 ASN B 437 GLN C 192 ASN C 335 ASN ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN 1 46 GLN b 23 ASN b 71 ASN b 82 GLN d 273 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112626 restraints weight = 46310.668| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.71 r_work: 0.3243 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 38233 Z= 0.156 Angle : 0.599 14.231 51891 Z= 0.299 Chirality : 0.044 0.342 6003 Planarity : 0.004 0.058 6746 Dihedral : 7.462 172.580 5573 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.39 % Favored : 97.57 % Rotamer: Outliers : 2.11 % Allowed : 16.73 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.12), residues: 4858 helix: 2.20 (0.10), residues: 2556 sheet: -0.26 (0.21), residues: 565 loop : -0.38 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG d 239 TYR 0.036 0.001 TYR a 143 PHE 0.015 0.001 PHE d 299 TRP 0.009 0.001 TRP a 216 HIS 0.013 0.001 HIS d 273 Details of bonding type rmsd covalent geometry : bond 0.00362 (38233) covalent geometry : angle 0.59883 (51891) hydrogen bonds : bond 0.04519 ( 2311) hydrogen bonds : angle 4.27854 ( 6681) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 482 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 71 MET cc_start: 0.8947 (mmt) cc_final: 0.8678 (mmt) REVERT: A 36 ASP cc_start: 0.7955 (p0) cc_final: 0.7668 (p0) REVERT: A 92 LYS cc_start: 0.8662 (mttm) cc_final: 0.8212 (mtpt) REVERT: A 146 LYS cc_start: 0.8304 (ptpt) cc_final: 0.8063 (ptpt) REVERT: A 192 ASN cc_start: 0.7914 (m-40) cc_final: 0.7328 (m-40) REVERT: A 331 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: A 356 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7185 (mt-10) REVERT: B 96 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6562 (mt-10) REVERT: B 485 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6993 (tt0) REVERT: B 499 LYS cc_start: 0.6238 (tttt) cc_final: 0.5947 (tppp) REVERT: C 12 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6736 (pp30) REVERT: C 79 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8298 (mt) REVERT: C 191 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.7001 (mp-120) REVERT: C 499 LYS cc_start: 0.7089 (ttmt) cc_final: 0.6392 (tptt) REVERT: D 37 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7663 (ttm-80) REVERT: D 214 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7339 (tm-30) REVERT: D 391 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7792 (ttmt) REVERT: D 394 GLN cc_start: 0.6833 (mt0) cc_final: 0.6496 (mt0) REVERT: D 477 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6704 (mptt) REVERT: D 486 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6647 (mp) REVERT: E 50 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: E 95 ARG cc_start: 0.7698 (ptt90) cc_final: 0.6557 (ptp90) REVERT: E 346 ARG cc_start: 0.7360 (ttm-80) cc_final: 0.7060 (ttp80) REVERT: E 436 GLN cc_start: 0.6483 (mp10) cc_final: 0.6032 (pt0) REVERT: E 477 LYS cc_start: 0.6245 (tptp) cc_final: 0.6036 (mtmt) REVERT: E 485 LYS cc_start: 0.6506 (OUTLIER) cc_final: 0.4903 (pptt) REVERT: F 39 SER cc_start: 0.8333 (m) cc_final: 0.7880 (p) REVERT: F 118 ASP cc_start: 0.7649 (t0) cc_final: 0.7375 (t0) REVERT: F 214 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7278 (tp30) REVERT: F 482 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7188 (mp) REVERT: G 41 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: G 109 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7559 (mt-10) REVERT: G 139 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7698 (mmm) REVERT: H 89 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7667 (mm-30) REVERT: H 91 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8024 (p0) REVERT: 1 48 ARG cc_start: 0.8142 (ptt-90) cc_final: 0.6982 (ptt90) REVERT: 2 50 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8464 (m-10) REVERT: 3 44 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: 4 71 MET cc_start: 0.8723 (tmm) cc_final: 0.8445 (tmm) REVERT: 5 46 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: 7 48 ARG cc_start: 0.8185 (ttp-110) cc_final: 0.7868 (mtm110) REVERT: b 109 LYS cc_start: 0.8993 (tptt) cc_final: 0.8582 (tmtp) REVERT: b 113 ASP cc_start: 0.8616 (p0) cc_final: 0.8387 (p0) REVERT: b 136 GLU cc_start: 0.8424 (tt0) cc_final: 0.8181 (tt0) REVERT: d 105 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: d 195 ASP cc_start: 0.8170 (p0) cc_final: 0.7779 (p0) REVERT: d 239 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7676 (tmm160) REVERT: d 308 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7820 (ptp-170) REVERT: d 312 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8228 (tm) REVERT: d 360 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7661 (tm-30) REVERT: d 413 ASP cc_start: 0.8419 (t0) cc_final: 0.8143 (t0) outliers start: 82 outliers final: 47 residues processed: 530 average time/residue: 0.8130 time to fit residues: 510.1635 Evaluate side-chains 540 residues out of total 3880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 471 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 171 ILE Chi-restraints excluded: chain a residue 240 SER Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 477 LYS Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 485 LYS Chi-restraints excluded: chain F residue 214 GLU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 2 residue 50 PHE Chi-restraints excluded: chain 3 residue 44 GLU Chi-restraints excluded: chain 3 residue 80 VAL Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 46 GLN Chi-restraints excluded: chain 5 residue 51 THR Chi-restraints excluded: chain 6 residue 51 THR Chi-restraints excluded: chain 8 residue 51 THR Chi-restraints excluded: chain 9 residue 51 THR Chi-restraints excluded: chain b residue 74 SER Chi-restraints excluded: chain b residue 119 GLU Chi-restraints excluded: chain d residue 105 GLN Chi-restraints excluded: chain d residue 108 LEU Chi-restraints excluded: chain d residue 128 GLN Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 220 THR Chi-restraints excluded: chain d residue 241 VAL Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 273 HIS Chi-restraints excluded: chain d residue 275 SER Chi-restraints excluded: chain d residue 297 PHE Chi-restraints excluded: chain d residue 308 ARG Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 343 VAL Chi-restraints excluded: chain d residue 363 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 122 optimal weight: 0.0980 chunk 482 optimal weight: 1.9990 chunk 432 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 295 optimal weight: 0.7980 chunk 106 optimal weight: 0.0050 chunk 313 optimal weight: 0.9990 chunk 451 optimal weight: 7.9990 chunk 397 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 110 GLN a 130 ASN A 84 ASN B 192 ASN B 437 GLN C 192 ASN C 335 ASN C 437 GLN ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN 1 46 GLN b 71 ASN b 95 GLN ** d 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.144311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.113894 restraints weight = 46533.618| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.73 r_work: 0.3263 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38233 Z= 0.129 Angle : 0.585 14.479 51891 Z= 0.291 Chirality : 0.043 0.371 6003 Planarity : 0.004 0.059 6746 Dihedral : 7.357 171.635 5573 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.31 % Favored : 97.67 % Rotamer: Outliers : 2.04 % Allowed : 16.86 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.12), residues: 4858 helix: 2.24 (0.10), residues: 2572 sheet: -0.25 (0.21), residues: 575 loop : -0.39 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG d 239 TYR 0.035 0.001 TYR a 143 PHE 0.017 0.001 PHE d 297 TRP 0.009 0.001 TRP a 216 HIS 0.012 0.001 HIS d 273 Details of bonding type rmsd covalent geometry : bond 0.00285 (38233) covalent geometry : angle 0.58507 (51891) hydrogen bonds : bond 0.04290 ( 2311) hydrogen bonds : angle 4.21351 ( 6681) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17109.82 seconds wall clock time: 290 minutes 18.45 seconds (17418.45 seconds total)