Starting phenix.real_space_refine on Tue Aug 26 00:34:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vcj_43138/08_2025/8vcj_43138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vcj_43138/08_2025/8vcj_43138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vcj_43138/08_2025/8vcj_43138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vcj_43138/08_2025/8vcj_43138.map" model { file = "/net/cci-nas-00/data/ceres_data/8vcj_43138/08_2025/8vcj_43138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vcj_43138/08_2025/8vcj_43138.cif" } resolution = 3.32 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= 0.000 sd= 1.000 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 Zn 2 6.06 5 P 116 5.49 5 Mg 7 5.21 5 S 112 5.16 5 C 20066 2.51 5 N 5771 2.21 5 O 6158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32232 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3865 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain: "B" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3865 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain: "C" Number of atoms: 3138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3138 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 14, 'TRANS': 379} Chain breaks: 1 Chain: "Y" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2515 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 15, 'TRANS': 293} Chain: "D" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3865 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain: "E" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3860 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain: "F" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3203 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 14, 'TRANS': 388} Chain: "G" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3142 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 14, 'TRANS': 380} Chain breaks: 1 Chain: "X" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2523 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "H" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1029 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "I" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1021 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "A" 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: "B" 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: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11863 SG CYS Y 124 20.525 82.018 113.832 1.00 70.84 S ATOM 11884 SG CYS Y 127 20.186 85.809 114.341 1.00 69.62 S ATOM 12102 SG CYS Y 152 19.509 83.328 117.286 1.00 95.98 S ATOM 28448 SG CYS X 124 55.531 58.693 57.401 1.00 76.59 S ATOM 28469 SG CYS X 127 58.085 55.831 57.789 1.00 73.57 S ATOM 28687 SG CYS X 152 58.522 58.442 54.968 1.00 98.63 S Time building chain proxies: 6.02, per 1000 atoms: 0.19 Number of scatterers: 32232 At special positions: 0 Unit cell: (183.825, 171, 192.375, 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) Zn 2 29.99 S 112 16.00 P 116 15.00 Mg 7 11.99 O 6158 8.00 N 5771 7.00 C 20066 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: 2.17 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 238.4 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN X 601 " pdb="ZN ZN X 601 " - pdb=" ND1 HIS X 155 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 152 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 124 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 127 " pdb=" ZN Y 601 " pdb="ZN ZN Y 601 " - pdb=" NE2 HIS Y 155 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 124 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 152 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 127 " Number of angles added : 6 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7046 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 20 sheets defined 57.5% alpha, 5.0% beta 44 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 29 through 36 removed outlier: 3.580A pdb=" N ASN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 4.116A pdb=" N LEU A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 53 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 64 removed outlier: 3.619A pdb=" N ARG A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 90 removed outlier: 4.110A pdb=" N LEU A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 78 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 removed outlier: 3.964A pdb=" N HIS A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 151 removed outlier: 3.587A pdb=" N SER A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 196 removed outlier: 3.626A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 188 " --> pdb=" O CYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 209 through 225 removed outlier: 3.573A pdb=" N ALA A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 removed outlier: 3.991A pdb=" N GLY A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.168A pdb=" N PHE A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ASP A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.973A pdb=" N GLY A 287 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 317 removed outlier: 3.631A pdb=" N ILE A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.669A pdb=" N TYR A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 362 removed outlier: 3.653A pdb=" N VAL A 348 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 382 through 392 Processing helix chain 'A' and resid 395 through 400 removed outlier: 3.714A pdb=" N ARG A 399 " --> pdb=" O GLU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 removed outlier: 3.728A pdb=" N ILE A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'A' and resid 471 through 485 removed outlier: 3.544A pdb=" N LEU A 475 " --> pdb=" O THR A 471 " (cutoff:3.500A) Proline residue: A 477 - end of helix removed outlier: 3.848A pdb=" N GLN A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 19 Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 32 through 38 removed outlier: 3.864A pdb=" N ALA B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 41 No H-bonds generated for 'chain 'B' and resid 39 through 41' Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 64 through 69 removed outlier: 3.543A pdb=" N ASP B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 90 removed outlier: 4.065A pdb=" N LEU B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 95 removed outlier: 3.905A pdb=" N ASN B 95 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 115 removed outlier: 3.527A pdb=" N HIS B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.930A pdb=" N THR B 152 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B 153 " --> pdb=" O LEU B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 153' Processing helix chain 'B' and resid 185 through 196 removed outlier: 3.753A pdb=" N ARG B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.507A pdb=" N ARG B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.854A pdb=" N HIS B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 244 through 259 removed outlier: 4.054A pdb=" N PHE B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 removed outlier: 4.250A pdb=" N PHE B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 286 Processing helix chain 'B' and resid 305 through 312 removed outlier: 3.537A pdb=" N ILE B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 343 through 362 removed outlier: 3.672A pdb=" N VAL B 348 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 379 removed outlier: 3.619A pdb=" N LEU B 371 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 379 " --> pdb=" O TYR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 392 Processing helix chain 'B' and resid 393 through 400 Processing helix chain 'B' and resid 408 through 421 Processing helix chain 'B' and resid 426 through 434 Processing helix chain 'B' and resid 437 through 447 removed outlier: 3.505A pdb=" N ARG B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 Processing helix chain 'B' and resid 471 through 485 Proline residue: B 477 - end of helix Processing helix chain 'C' and resid 15 through 19 Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 32 through 41 removed outlier: 3.719A pdb=" N ALA C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.721A pdb=" N LEU C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 63 removed outlier: 3.624A pdb=" N THR C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 89 removed outlier: 4.196A pdb=" N LEU C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 78 " --> pdb=" O GLY C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 115 removed outlier: 3.554A pdb=" N HIS C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN C 106 " --> pdb=" O GLN C 102 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 182 through 194 removed outlier: 4.045A pdb=" N PHE C 188 " --> pdb=" O CYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 209 through 224 removed outlier: 4.224A pdb=" N ALA C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 removed outlier: 3.677A pdb=" N HIS C 236 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 258 removed outlier: 4.230A pdb=" N MET C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 273 removed outlier: 3.727A pdb=" N ARG C 272 " --> pdb=" O PRO C 269 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 273 " --> pdb=" O LYS C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 317 removed outlier: 3.564A pdb=" N ILE C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN C 317 " --> pdb=" O ASP C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 341 Processing helix chain 'C' and resid 343 through 362 removed outlier: 3.650A pdb=" N VAL C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 348 " --> pdb=" O MET C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 379 removed outlier: 3.545A pdb=" N LEU C 379 " --> pdb=" O TYR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 392 removed outlier: 3.516A pdb=" N LEU C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 399 Processing helix chain 'Y' and resid 12 through 24 removed outlier: 3.509A pdb=" N THR Y 16 " --> pdb=" O LEU Y 12 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN Y 24 " --> pdb=" O ALA Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 37 Processing helix chain 'Y' and resid 51 through 59 removed outlier: 4.261A pdb=" N ILE Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA Y 56 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 66 through 74 removed outlier: 3.534A pdb=" N HIS Y 74 " --> pdb=" O LEU Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 84 removed outlier: 3.580A pdb=" N LEU Y 79 " --> pdb=" O LEU Y 76 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA Y 81 " --> pdb=" O PRO Y 78 " (cutoff:3.500A) Proline residue: Y 82 - end of helix Processing helix chain 'Y' and resid 85 through 98 removed outlier: 4.208A pdb=" N GLU Y 97 " --> pdb=" O ILE Y 93 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR Y 98 " --> pdb=" O ARG Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 109 removed outlier: 3.797A pdb=" N HIS Y 105 " --> pdb=" O GLN Y 101 " (cutoff:3.500A) Processing helix chain 'Y' and resid 109 through 114 Processing helix chain 'Y' and resid 124 through 135 removed outlier: 3.557A pdb=" N ALA Y 129 " --> pdb=" O PRO Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 166 through 168 No H-bonds generated for 'chain 'Y' and resid 166 through 168' Processing helix chain 'Y' and resid 189 through 200 removed outlier: 4.029A pdb=" N THR Y 193 " --> pdb=" O LEU Y 189 " (cutoff:3.500A) Processing helix chain 'Y' and resid 201 through 203 No H-bonds generated for 'chain 'Y' and resid 201 through 203' Processing helix chain 'Y' and resid 205 through 210 removed outlier: 3.690A pdb=" N GLN Y 209 " --> pdb=" O PRO Y 206 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU Y 210 " --> pdb=" O ARG Y 207 " (cutoff:3.500A) Processing helix chain 'Y' and resid 214 through 230 Processing helix chain 'Y' and resid 240 through 250 Processing helix chain 'Y' and resid 251 through 258 removed outlier: 3.562A pdb=" N LYS Y 257 " --> pdb=" O GLU Y 253 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU Y 258 " --> pdb=" O ALA Y 254 " (cutoff:3.500A) Processing helix chain 'Y' and resid 269 through 274 Processing helix chain 'Y' and resid 283 through 295 removed outlier: 3.667A pdb=" N HIS Y 287 " --> pdb=" O SER Y 283 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL Y 290 " --> pdb=" O GLN Y 286 " (cutoff:3.500A) Processing helix chain 'Y' and resid 299 through 309 Processing helix chain 'D' and resid 29 through 35 removed outlier: 4.609A pdb=" N ASN D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 41 removed outlier: 3.854A pdb=" N LEU D 40 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS D 41 " --> pdb=" O ALA D 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 37 through 41' Processing helix chain 'D' and resid 47 through 53 removed outlier: 4.352A pdb=" N LEU D 51 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 64 removed outlier: 3.505A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 90 removed outlier: 3.535A pdb=" N LEU D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 80 " --> pdb=" O HIS D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 114 Processing helix chain 'D' and resid 142 through 150 removed outlier: 3.733A pdb=" N ARG D 148 " --> pdb=" O THR D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 196 removed outlier: 3.805A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE D 188 " --> pdb=" O CYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 4.135A pdb=" N ARG D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 224 Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.725A pdb=" N HIS D 236 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 260 removed outlier: 3.837A pdb=" N GLY D 260 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'D' and resid 271 through 281 removed outlier: 4.086A pdb=" N PHE D 275 " --> pdb=" O ALA D 271 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 281 " --> pdb=" O ALA D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 317 removed outlier: 3.544A pdb=" N ASN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 339 removed outlier: 3.921A pdb=" N TRP D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 337 " --> pdb=" O ARG D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 362 removed outlier: 3.506A pdb=" N VAL D 348 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN D 355 " --> pdb=" O PHE D 351 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D 356 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 378 Processing helix chain 'D' and resid 382 through 392 Processing helix chain 'D' and resid 393 through 400 Processing helix chain 'D' and resid 408 through 421 removed outlier: 3.505A pdb=" N ALA D 421 " --> pdb=" O LEU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 434 Processing helix chain 'D' and resid 440 through 447 Processing helix chain 'D' and resid 455 through 467 Processing helix chain 'D' and resid 471 through 484 Proline residue: D 477 - end of helix removed outlier: 3.940A pdb=" N TRP D 482 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET D 484 " --> pdb=" O LEU D 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.502A pdb=" N TYR E 18 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG E 19 " --> pdb=" O GLU E 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 15 through 19' Processing helix chain 'E' and resid 21 through 26 Processing helix chain 'E' and resid 32 through 39 removed outlier: 3.606A pdb=" N SER E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 3.897A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN E 52 " --> pdb=" O SER E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 47 through 52' Processing helix chain 'E' and resid 54 through 64 Processing helix chain 'E' and resid 75 through 90 removed outlier: 3.948A pdb=" N LEU E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY E 90 " --> pdb=" O MET E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 removed outlier: 4.285A pdb=" N ASN E 95 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 115 removed outlier: 3.893A pdb=" N THR E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 151 removed outlier: 3.736A pdb=" N ILE E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 195 removed outlier: 3.739A pdb=" N ILE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE E 188 " --> pdb=" O CYS E 184 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG E 193 " --> pdb=" O ARG E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 209 through 224 removed outlier: 4.013A pdb=" N SER E 218 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 237 removed outlier: 3.639A pdb=" N HIS E 236 " --> pdb=" O GLU E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 259 removed outlier: 3.873A pdb=" N VAL E 256 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 277 removed outlier: 4.100A pdb=" N ALA E 277 " --> pdb=" O ILE E 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 274 through 277' Processing helix chain 'E' and resid 278 through 283 Processing helix chain 'E' and resid 305 through 317 removed outlier: 3.657A pdb=" N ILE E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 341 Processing helix chain 'E' and resid 343 through 362 removed outlier: 3.628A pdb=" N VAL E 348 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS E 349 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU E 359 " --> pdb=" O GLN E 355 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA E 360 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 379 Processing helix chain 'E' and resid 382 through 392 Processing helix chain 'E' and resid 393 through 400 Processing helix chain 'E' and resid 407 through 423 Processing helix chain 'E' and resid 429 through 435 Processing helix chain 'E' and resid 437 through 448 Processing helix chain 'E' and resid 452 through 467 Proline residue: E 458 - end of helix removed outlier: 3.947A pdb=" N LYS E 461 " --> pdb=" O ILE E 457 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS E 462 " --> pdb=" O PRO E 458 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA E 463 " --> pdb=" O THR E 459 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN E 467 " --> pdb=" O ALA E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 485 removed outlier: 3.588A pdb=" N LEU E 476 " --> pdb=" O ARG E 472 " (cutoff:3.500A) Proline residue: E 477 - end of helix Processing helix chain 'F' and resid 21 through 26 Processing helix chain 'F' and resid 32 through 37 Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 64 through 69 Processing helix chain 'F' and resid 75 through 89 removed outlier: 4.137A pdb=" N LEU F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER F 80 " --> pdb=" O HIS F 76 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG F 88 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 115 removed outlier: 3.880A pdb=" N HIS F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 150 removed outlier: 3.638A pdb=" N SER F 145 " --> pdb=" O GLY F 141 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU F 146 " --> pdb=" O LYS F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 153 No H-bonds generated for 'chain 'F' and resid 151 through 153' Processing helix chain 'F' and resid 184 through 195 removed outlier: 4.158A pdb=" N PHE F 188 " --> pdb=" O CYS F 184 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG F 193 " --> pdb=" O ARG F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 217 removed outlier: 3.818A pdb=" N ALA F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 224 removed outlier: 3.691A pdb=" N HIS F 224 " --> pdb=" O ILE F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 removed outlier: 3.732A pdb=" N HIS F 236 " --> pdb=" O GLU F 233 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU F 237 " --> pdb=" O ILE F 234 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER F 238 " --> pdb=" O GLN F 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 233 through 238' Processing helix chain 'F' and resid 248 through 257 removed outlier: 3.818A pdb=" N VAL F 253 " --> pdb=" O LEU F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 271 through 276 removed outlier: 3.630A pdb=" N PHE F 275 " --> pdb=" O ALA F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 286 removed outlier: 3.781A pdb=" N ARG F 284 " --> pdb=" O ARG F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 317 removed outlier: 4.030A pdb=" N ILE F 309 " --> pdb=" O ASN F 305 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN F 317 " --> pdb=" O ASP F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 341 Processing helix chain 'F' and resid 343 through 362 removed outlier: 3.908A pdb=" N VAL F 348 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA F 354 " --> pdb=" O LEU F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 378 Processing helix chain 'F' and resid 382 through 392 Processing helix chain 'F' and resid 393 through 398 Processing helix chain 'G' and resid 21 through 26 Processing helix chain 'G' and resid 32 through 37 removed outlier: 3.674A pdb=" N ALA G 37 " --> pdb=" O SER G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 53 removed outlier: 4.078A pdb=" N LEU G 51 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN G 52 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS G 53 " --> pdb=" O ASP G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 63 removed outlier: 3.735A pdb=" N ILE G 62 " --> pdb=" O ARG G 58 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 69 Processing helix chain 'G' and resid 73 through 89 removed outlier: 4.099A pdb=" N LEU G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU G 78 " --> pdb=" O GLY G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 removed outlier: 3.649A pdb=" N ASN G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU G 110 " --> pdb=" O GLN G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 148 removed outlier: 3.652A pdb=" N ARG G 148 " --> pdb=" O THR G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 153 removed outlier: 3.755A pdb=" N THR G 152 " --> pdb=" O ILE G 149 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR G 153 " --> pdb=" O LEU G 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 149 through 153' Processing helix chain 'G' and resid 180 through 194 removed outlier: 4.195A pdb=" N CYS G 184 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN G 186 " --> pdb=" O GLU G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 218 removed outlier: 3.824A pdb=" N SER G 218 " --> pdb=" O LEU G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 224 removed outlier: 3.807A pdb=" N HIS G 224 " --> pdb=" O ILE G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 240 removed outlier: 3.597A pdb=" N ARG G 239 " --> pdb=" O HIS G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 258 removed outlier: 4.123A pdb=" N GLU G 247 " --> pdb=" O GLY G 243 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET G 248 " --> pdb=" O GLY G 244 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL G 253 " --> pdb=" O LEU G 249 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL G 256 " --> pdb=" O PHE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 270 No H-bonds generated for 'chain 'G' and resid 268 through 270' Processing helix chain 'G' and resid 271 through 278 removed outlier: 3.988A pdb=" N PHE G 275 " --> pdb=" O ALA G 271 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP G 278 " --> pdb=" O ILE G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 317 removed outlier: 3.898A pdb=" N GLN G 317 " --> pdb=" O ASP G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 341 Processing helix chain 'G' and resid 343 through 362 removed outlier: 3.588A pdb=" N VAL G 348 " --> pdb=" O MET G 344 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 360 " --> pdb=" O LEU G 356 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY G 362 " --> pdb=" O ALA G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 379 removed outlier: 3.523A pdb=" N LEU G 379 " --> pdb=" O TYR G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 392 Processing helix chain 'G' and resid 393 through 398 Processing helix chain 'X' and resid 12 through 20 removed outlier: 3.534A pdb=" N THR X 16 " --> pdb=" O LEU X 12 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 37 Processing helix chain 'X' and resid 53 through 59 Processing helix chain 'X' and resid 66 through 74 Processing helix chain 'X' and resid 76 through 85 removed outlier: 4.062A pdb=" N TYR X 80 " --> pdb=" O LEU X 76 " (cutoff:3.500A) Proline residue: X 82 - end of helix removed outlier: 4.061A pdb=" N GLY X 85 " --> pdb=" O ALA X 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 96 removed outlier: 4.226A pdb=" N ASP X 90 " --> pdb=" O LYS X 86 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU X 91 " --> pdb=" O GLU X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 108 removed outlier: 4.035A pdb=" N VAL X 104 " --> pdb=" O ALA X 100 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS X 105 " --> pdb=" O GLN X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 124 through 135 removed outlier: 3.617A pdb=" N VAL X 128 " --> pdb=" O CYS X 124 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA X 129 " --> pdb=" O PRO X 125 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU X 130 " --> pdb=" O ASP X 126 " (cutoff:3.500A) Processing helix chain 'X' and resid 166 through 168 No H-bonds generated for 'chain 'X' and resid 166 through 168' Processing helix chain 'X' and resid 176 through 181 Processing helix chain 'X' and resid 189 through 200 Processing helix chain 'X' and resid 201 through 203 No H-bonds generated for 'chain 'X' and resid 201 through 203' Processing helix chain 'X' and resid 206 through 211 removed outlier: 4.436A pdb=" N GLU X 210 " --> pdb=" O PRO X 206 " (cutoff:3.500A) Processing helix chain 'X' and resid 214 through 230 Processing helix chain 'X' and resid 240 through 250 Processing helix chain 'X' and resid 251 through 258 Processing helix chain 'X' and resid 269 through 276 Processing helix chain 'X' and resid 283 through 295 removed outlier: 3.712A pdb=" N HIS X 287 " --> pdb=" O SER X 283 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 310 removed outlier: 3.774A pdb=" N LEU X 310 " --> pdb=" O GLN X 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 173 removed outlier: 6.675A pdb=" N LEU A 133 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N TRP A 293 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 135 " --> pdb=" O TRP A 293 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.077A pdb=" N ILE B 6 " --> pdb=" O TYR B 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 170 through 173 removed outlier: 6.486A pdb=" N LEU B 132 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N GLY B 267 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 134 " --> pdb=" O GLY B 267 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ILE B 291 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 133 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N TRP B 293 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE B 135 " --> pdb=" O TRP B 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 6 through 7 removed outlier: 6.371A pdb=" N ILE C 6 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 170 through 173 removed outlier: 6.471A pdb=" N LEU C 229 " --> pdb=" O MET C 264 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE C 266 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE C 231 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU C 132 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N GLY C 267 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU C 134 " --> pdb=" O GLY C 267 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ILE C 291 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU C 133 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N TRP C 293 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 135 " --> pdb=" O TRP C 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Y' and resid 120 through 123 removed outlier: 5.742A pdb=" N ARG Y 163 " --> pdb=" O PHE Y 121 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N TYR Y 123 " --> pdb=" O PHE Y 161 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N PHE Y 161 " --> pdb=" O TYR Y 123 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 232 through 233 removed outlier: 3.831A pdb=" N LYS Y 233 " --> pdb=" O HIS Y 236 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS Y 236 " --> pdb=" O LYS Y 233 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 156 through 158 removed outlier: 6.996A pdb=" N LEU D 226 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL D 168 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N MET D 264 " --> pdb=" O GLY D 227 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU D 229 " --> pdb=" O MET D 264 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE D 266 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE D 231 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU D 133 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N TRP D 293 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE D 135 " --> pdb=" O TRP D 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 299 through 300 Processing sheet with id=AB3, first strand: chain 'E' and resid 6 through 7 removed outlier: 6.534A pdb=" N ILE E 6 " --> pdb=" O TYR E 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 171 through 173 removed outlier: 6.623A pdb=" N ILE E 172 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE E 291 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE E 135 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP E 293 " --> pdb=" O ILE E 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 6 through 7 removed outlier: 6.070A pdb=" N ILE F 6 " --> pdb=" O TYR F 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 171 through 173 Processing sheet with id=AB7, first strand: chain 'F' and resid 299 through 300 Processing sheet with id=AB8, first strand: chain 'G' and resid 6 through 7 removed outlier: 6.275A pdb=" N ILE G 6 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 169 through 173 removed outlier: 6.556A pdb=" N LEU G 229 " --> pdb=" O MET G 264 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE G 266 " --> pdb=" O LEU G 229 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE G 231 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY G 136 " --> pdb=" O GLY G 267 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ILE G 291 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU G 133 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N TRP G 293 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE G 135 " --> pdb=" O TRP G 293 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 120 through 121 removed outlier: 6.110A pdb=" N ARG X 163 " --> pdb=" O PHE X 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 151 through 152 1184 hydrogen bonds defined for protein. 3459 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 112 hydrogen bonds 224 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 10750 1.36 - 1.51: 9121 1.51 - 1.65: 13003 1.65 - 1.80: 110 1.80 - 1.95: 76 Bond restraints: 33060 Sorted by residual: bond pdb=" O3' DC H 49 " pdb=" P DG H 50 " ideal model delta sigma weight residual 1.607 1.634 -0.027 1.50e-02 4.44e+03 3.17e+00 bond pdb=" O3' DA H 46 " pdb=" P DG H 47 " ideal model delta sigma weight residual 1.607 1.633 -0.026 1.50e-02 4.44e+03 3.06e+00 bond pdb=" CA ILE D 457 " pdb=" CB ILE D 457 " ideal model delta sigma weight residual 1.534 1.546 -0.012 6.80e-03 2.16e+04 2.91e+00 bond pdb=" CA ILE D 457 " pdb=" C ILE D 457 " ideal model delta sigma weight residual 1.520 1.532 -0.013 8.80e-03 1.29e+04 2.10e+00 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.53e+00 ... (remaining 33055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 44894 3.00 - 6.00: 310 6.00 - 9.00: 13 9.00 - 12.00: 2 12.00 - 15.00: 1 Bond angle restraints: 45220 Sorted by residual: angle pdb=" N ILE G 183 " pdb=" CA ILE G 183 " pdb=" C ILE G 183 " ideal model delta sigma weight residual 111.90 107.72 4.18 8.10e-01 1.52e+00 2.66e+01 angle pdb=" CA LEU D 318 " pdb=" CB LEU D 318 " pdb=" CG LEU D 318 " ideal model delta sigma weight residual 116.30 131.30 -15.00 3.50e+00 8.16e-02 1.84e+01 angle pdb=" CA GLN X 223 " pdb=" CB GLN X 223 " pdb=" CG GLN X 223 " ideal model delta sigma weight residual 114.10 121.88 -7.78 2.00e+00 2.50e-01 1.51e+01 angle pdb=" N GLY E 287 " pdb=" CA GLY E 287 " pdb=" C GLY E 287 " ideal model delta sigma weight residual 115.32 110.84 4.48 1.31e+00 5.83e-01 1.17e+01 angle pdb=" CB MET F 344 " pdb=" CG MET F 344 " pdb=" SD MET F 344 " ideal model delta sigma weight residual 112.70 122.41 -9.71 3.00e+00 1.11e-01 1.05e+01 ... (remaining 45215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 18916 35.05 - 70.11: 819 70.11 - 105.16: 37 105.16 - 140.22: 2 140.22 - 175.27: 5 Dihedral angle restraints: 19779 sinusoidal: 8871 harmonic: 10908 Sorted by residual: dihedral pdb=" C5' ADP B 601 " pdb=" O5' ADP B 601 " pdb=" PA ADP B 601 " pdb=" O2A ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 115.27 -175.27 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP D 601 " pdb=" O5' ADP D 601 " pdb=" PA ADP D 601 " pdb=" O2A ADP D 601 " ideal model delta sinusoidal sigma weight residual -60.00 110.13 -170.13 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PA ADP B 601 " pdb=" PB ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 103.19 -163.19 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 19776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 4150 0.050 - 0.099: 764 0.099 - 0.149: 172 0.149 - 0.199: 4 0.199 - 0.248: 1 Chirality restraints: 5091 Sorted by residual: chirality pdb=" CB ILE D 457 " pdb=" CA ILE D 457 " pdb=" CG1 ILE D 457 " pdb=" CG2 ILE D 457 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB VAL C 382 " pdb=" CA VAL C 382 " pdb=" CG1 VAL C 382 " pdb=" CG2 VAL C 382 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA PRO F 269 " pdb=" N PRO F 269 " pdb=" C PRO F 269 " pdb=" CB PRO F 269 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 5088 not shown) Planarity restraints: 5452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS Y 124 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO Y 125 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO Y 125 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO Y 125 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 405 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO E 406 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO E 406 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 406 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 268 " -0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO F 269 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO F 269 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 269 " -0.031 5.00e-02 4.00e+02 ... (remaining 5449 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 142 2.58 - 3.16: 24569 3.16 - 3.74: 47037 3.74 - 4.32: 63281 4.32 - 4.90: 106713 Nonbonded interactions: 241742 Sorted by model distance: nonbonded pdb=" O3B ADP B 601 " pdb="MG MG B 602 " model vdw 2.002 2.170 nonbonded pdb=" OE2 GLU D 233 " pdb="MG MG D 602 " model vdw 2.010 2.170 nonbonded pdb="MG MG E 603 " pdb=" O1B ADP F 601 " model vdw 2.055 2.170 nonbonded pdb=" O1B ADP E 601 " pdb="MG MG E 602 " model vdw 2.065 2.170 nonbonded pdb=" O2G AGS C 601 " pdb="MG MG C 602 " model vdw 2.067 2.170 ... (remaining 241737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 602) selection = (chain 'B' and resid 4 through 602) selection = (chain 'D' and resid 4 through 602) selection = (chain 'E' and resid 4 through 602) } ncs_group { reference = (chain 'C' and resid 3 through 405) selection = (chain 'F' and (resid 3 through 278 or resid 288 through 405)) selection = (chain 'G' and resid 3 through 405) } ncs_group { reference = (chain 'X' and (resid 1 through 309 or resid 601)) selection = chain 'Y' } 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=0.00 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: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 29.670 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33068 Z= 0.152 Angle : 0.643 15.000 45226 Z= 0.335 Chirality : 0.041 0.248 5091 Planarity : 0.004 0.066 5452 Dihedral : 17.521 175.271 12733 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.03 % Allowed : 0.34 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.13), residues: 3720 helix: 0.11 (0.12), residues: 1860 sheet: 0.73 (0.35), residues: 227 loop : -1.31 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 399 TYR 0.025 0.001 TYR B 375 PHE 0.024 0.002 PHE D 311 TRP 0.032 0.001 TRP E 336 HIS 0.017 0.001 HIS D 442 Details of bonding type rmsd covalent geometry : bond 0.00340 (33060) covalent geometry : angle 0.64264 (45220) hydrogen bonds : bond 0.18036 ( 1296) hydrogen bonds : angle 5.70583 ( 3683) metal coordination : bond 0.00295 ( 8) metal coordination : angle 1.23178 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7541 (mttt) cc_final: 0.6604 (tptt) REVERT: Y 235 LYS cc_start: 0.6691 (ttpt) cc_final: 0.6315 (tmtt) REVERT: D 68 ASP cc_start: 0.6992 (m-30) cc_final: 0.6748 (m-30) REVERT: D 324 LYS cc_start: 0.6101 (ptmm) cc_final: 0.5068 (ptmt) REVERT: E 81 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6999 (tt0) REVERT: E 293 TRP cc_start: 0.7774 (m100) cc_final: 0.6950 (m100) REVERT: F 248 MET cc_start: 0.7145 (ptm) cc_final: 0.6632 (ptt) REVERT: F 314 ASN cc_start: 0.7825 (m110) cc_final: 0.7432 (m110) REVERT: F 344 MET cc_start: 0.7554 (mmm) cc_final: 0.7253 (mmt) outliers start: 1 outliers final: 0 residues processed: 317 average time/residue: 0.1787 time to fit residues: 92.3894 Evaluate side-chains 256 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN Y 239 HIS D 198 ASN D 319 GLN ** F 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN G 383 HIS X 239 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.199007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.135963 restraints weight = 40864.698| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.00 r_work: 0.3409 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33068 Z= 0.149 Angle : 0.594 17.262 45226 Z= 0.300 Chirality : 0.040 0.204 5091 Planarity : 0.004 0.060 5452 Dihedral : 16.757 174.323 5335 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.89 % Allowed : 6.38 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.14), residues: 3720 helix: 0.35 (0.12), residues: 1888 sheet: 0.72 (0.36), residues: 204 loop : -1.35 (0.14), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 58 TYR 0.024 0.001 TYR D 375 PHE 0.013 0.001 PHE X 161 TRP 0.017 0.001 TRP D 336 HIS 0.014 0.001 HIS Y 239 Details of bonding type rmsd covalent geometry : bond 0.00348 (33060) covalent geometry : angle 0.59411 (45220) hydrogen bonds : bond 0.04429 ( 1296) hydrogen bonds : angle 4.40938 ( 3683) metal coordination : bond 0.00287 ( 8) metal coordination : angle 1.60883 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 283 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.5610 (OUTLIER) cc_final: 0.5318 (mp) REVERT: A 206 LYS cc_start: 0.7580 (mttt) cc_final: 0.6578 (tptt) REVERT: A 344 MET cc_start: 0.8519 (mmm) cc_final: 0.8162 (mmm) REVERT: A 375 TYR cc_start: 0.6326 (t80) cc_final: 0.5934 (t80) REVERT: D 68 ASP cc_start: 0.7207 (m-30) cc_final: 0.6897 (m-30) REVERT: E 81 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7508 (tt0) REVERT: F 68 ASP cc_start: 0.8715 (m-30) cc_final: 0.8478 (m-30) REVERT: F 248 MET cc_start: 0.7922 (ptm) cc_final: 0.7546 (ptt) REVERT: F 314 ASN cc_start: 0.7645 (m110) cc_final: 0.7225 (m110) REVERT: F 325 ASP cc_start: 0.6828 (m-30) cc_final: 0.6448 (t0) REVERT: X 282 PHE cc_start: 0.7223 (m-80) cc_final: 0.6923 (m-80) outliers start: 29 outliers final: 19 residues processed: 305 average time/residue: 0.1965 time to fit residues: 96.3991 Evaluate side-chains 276 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 256 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain X residue 48 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 4 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 343 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 332 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 HIS E 76 HIS E 222 ASN ** F 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 341 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN ** G 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.196906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.134232 restraints weight = 40692.983| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.07 r_work: 0.3375 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33068 Z= 0.172 Angle : 0.603 15.992 45226 Z= 0.303 Chirality : 0.040 0.174 5091 Planarity : 0.004 0.067 5452 Dihedral : 16.750 168.122 5335 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.39 % Allowed : 9.03 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.14), residues: 3720 helix: 0.39 (0.12), residues: 1892 sheet: 0.68 (0.35), residues: 216 loop : -1.40 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 82 TYR 0.024 0.002 TYR B 375 PHE 0.020 0.002 PHE X 161 TRP 0.017 0.001 TRP D 336 HIS 0.014 0.001 HIS Y 239 Details of bonding type rmsd covalent geometry : bond 0.00419 (33060) covalent geometry : angle 0.60335 (45220) hydrogen bonds : bond 0.04648 ( 1296) hydrogen bonds : angle 4.26746 ( 3683) metal coordination : bond 0.00379 ( 8) metal coordination : angle 0.52905 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.6959 (m-30) cc_final: 0.6351 (m-30) REVERT: A 206 LYS cc_start: 0.7624 (mttt) cc_final: 0.6580 (tptt) REVERT: A 306 GLN cc_start: 0.7248 (tt0) cc_final: 0.6933 (tp-100) REVERT: A 344 MET cc_start: 0.8551 (mmm) cc_final: 0.8187 (mmm) REVERT: A 443 LEU cc_start: 0.7541 (mt) cc_final: 0.7324 (mt) REVERT: B 418 ASP cc_start: 0.7508 (t70) cc_final: 0.7250 (m-30) REVERT: Y 235 LYS cc_start: 0.6584 (ttpt) cc_final: 0.6118 (tmtt) REVERT: Y 291 TRP cc_start: 0.6967 (m100) cc_final: 0.6688 (m100) REVERT: D 25 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: D 68 ASP cc_start: 0.7181 (m-30) cc_final: 0.6857 (m-30) REVERT: E 81 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7501 (tt0) REVERT: F 67 ASP cc_start: 0.8339 (t0) cc_final: 0.8045 (t0) REVERT: F 73 LEU cc_start: 0.9066 (mt) cc_final: 0.8839 (mt) REVERT: F 248 MET cc_start: 0.8022 (ptm) cc_final: 0.7797 (ptt) REVERT: F 314 ASN cc_start: 0.7601 (m110) cc_final: 0.7175 (m110) REVERT: X 282 PHE cc_start: 0.7355 (m-80) cc_final: 0.7101 (m-80) outliers start: 45 outliers final: 33 residues processed: 308 average time/residue: 0.1892 time to fit residues: 93.8136 Evaluate side-chains 289 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 255 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 235 GLN Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain X residue 48 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 96 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 285 optimal weight: 5.9990 chunk 303 optimal weight: 0.7980 chunk 158 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 373 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 105 HIS Y 239 HIS D 319 GLN D 383 HIS E 76 HIS ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN G 236 HIS X 74 HIS X 239 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.193559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126871 restraints weight = 40476.629| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.02 r_work: 0.3302 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 33068 Z= 0.201 Angle : 0.631 16.362 45226 Z= 0.318 Chirality : 0.041 0.198 5091 Planarity : 0.005 0.071 5452 Dihedral : 16.791 169.352 5335 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.66 % Allowed : 11.37 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.14), residues: 3720 helix: 0.34 (0.12), residues: 1886 sheet: 0.40 (0.35), residues: 217 loop : -1.47 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 247 TYR 0.025 0.002 TYR B 18 PHE 0.022 0.002 PHE X 161 TRP 0.017 0.001 TRP E 336 HIS 0.019 0.001 HIS Y 239 Details of bonding type rmsd covalent geometry : bond 0.00493 (33060) covalent geometry : angle 0.63062 (45220) hydrogen bonds : bond 0.04825 ( 1296) hydrogen bonds : angle 4.29029 ( 3683) metal coordination : bond 0.00408 ( 8) metal coordination : angle 0.49205 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 267 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.7090 (m-30) cc_final: 0.6547 (m-30) REVERT: A 206 LYS cc_start: 0.7589 (mttt) cc_final: 0.6684 (tptt) REVERT: A 306 GLN cc_start: 0.7230 (tt0) cc_final: 0.6921 (tp-100) REVERT: A 344 MET cc_start: 0.8609 (mmm) cc_final: 0.8208 (mmm) REVERT: A 443 LEU cc_start: 0.7541 (mt) cc_final: 0.7319 (mt) REVERT: B 279 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6636 (tt) REVERT: Y 235 LYS cc_start: 0.6615 (ttpt) cc_final: 0.6139 (tmtt) REVERT: D 25 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: D 68 ASP cc_start: 0.7283 (m-30) cc_final: 0.6933 (m-30) REVERT: E 81 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7466 (tt0) REVERT: F 314 ASN cc_start: 0.7544 (m110) cc_final: 0.7134 (m110) REVERT: G 314 ASN cc_start: 0.8525 (m-40) cc_final: 0.8280 (m110) REVERT: G 346 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7913 (mm) REVERT: X 282 PHE cc_start: 0.7417 (m-80) cc_final: 0.7152 (m-80) outliers start: 54 outliers final: 36 residues processed: 308 average time/residue: 0.1914 time to fit residues: 95.8373 Evaluate side-chains 292 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 253 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 99 GLN Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain Y residue 290 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 235 GLN Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 346 ILE Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain X residue 48 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 375 optimal weight: 10.0000 chunk 263 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 284 optimal weight: 0.6980 chunk 276 optimal weight: 0.8980 chunk 265 optimal weight: 10.0000 chunk 296 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 301 optimal weight: 3.9990 chunk 165 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 HIS E 107 ASN E 222 ASN E 319 GLN F 322 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN X 58 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.194522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.127209 restraints weight = 40489.583| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.95 r_work: 0.3323 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33068 Z= 0.165 Angle : 0.593 16.301 45226 Z= 0.297 Chirality : 0.040 0.178 5091 Planarity : 0.004 0.069 5452 Dihedral : 16.661 169.053 5335 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.88 % Allowed : 12.73 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.60 (0.14), residues: 3720 helix: 0.41 (0.12), residues: 1887 sheet: 0.41 (0.35), residues: 215 loop : -1.46 (0.14), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 247 TYR 0.019 0.001 TYR E 375 PHE 0.018 0.001 PHE X 161 TRP 0.017 0.001 TRP E 336 HIS 0.010 0.001 HIS Y 239 Details of bonding type rmsd covalent geometry : bond 0.00400 (33060) covalent geometry : angle 0.59298 (45220) hydrogen bonds : bond 0.04286 ( 1296) hydrogen bonds : angle 4.18297 ( 3683) metal coordination : bond 0.00141 ( 8) metal coordination : angle 0.48550 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 266 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.7186 (m-30) cc_final: 0.6621 (m-30) REVERT: A 206 LYS cc_start: 0.7571 (mttt) cc_final: 0.6726 (tptt) REVERT: A 306 GLN cc_start: 0.7250 (tt0) cc_final: 0.6906 (tp-100) REVERT: A 344 MET cc_start: 0.8573 (mmm) cc_final: 0.8194 (mmm) REVERT: B 418 ASP cc_start: 0.7615 (t70) cc_final: 0.7300 (m-30) REVERT: C 353 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7066 (mp) REVERT: Y 235 LYS cc_start: 0.6642 (ttpt) cc_final: 0.6162 (tmtt) REVERT: D 25 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: D 68 ASP cc_start: 0.7293 (m-30) cc_final: 0.6950 (m-30) REVERT: D 173 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8417 (m-30) REVERT: E 81 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7394 (tt0) REVERT: F 314 ASN cc_start: 0.7552 (m110) cc_final: 0.7143 (m110) REVERT: G 314 ASN cc_start: 0.8532 (m-40) cc_final: 0.8075 (m110) REVERT: G 346 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7849 (mm) outliers start: 61 outliers final: 36 residues processed: 313 average time/residue: 0.2018 time to fit residues: 102.5133 Evaluate side-chains 296 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 256 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain Y residue 290 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 346 ILE Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 359 optimal weight: 9.9990 chunk 286 optimal weight: 1.9990 chunk 283 optimal weight: 0.6980 chunk 336 optimal weight: 0.4980 chunk 348 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 chunk 311 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 338 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 HIS E 319 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 HIS ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.193925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129291 restraints weight = 40391.667| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.15 r_work: 0.3333 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33068 Z= 0.172 Angle : 0.604 16.480 45226 Z= 0.301 Chirality : 0.040 0.189 5091 Planarity : 0.004 0.070 5452 Dihedral : 16.610 167.959 5335 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.06 % Allowed : 13.31 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.14), residues: 3720 helix: 0.40 (0.12), residues: 1898 sheet: 0.32 (0.35), residues: 217 loop : -1.51 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 58 TYR 0.019 0.001 TYR D 375 PHE 0.018 0.001 PHE X 161 TRP 0.017 0.001 TRP E 336 HIS 0.010 0.001 HIS Y 239 Details of bonding type rmsd covalent geometry : bond 0.00422 (33060) covalent geometry : angle 0.60396 (45220) hydrogen bonds : bond 0.04368 ( 1296) hydrogen bonds : angle 4.17769 ( 3683) metal coordination : bond 0.00221 ( 8) metal coordination : angle 0.41394 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 265 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.7209 (m-30) cc_final: 0.6693 (m-30) REVERT: A 206 LYS cc_start: 0.7509 (mttt) cc_final: 0.6646 (tptt) REVERT: A 306 GLN cc_start: 0.7209 (tt0) cc_final: 0.6887 (tp-100) REVERT: A 344 MET cc_start: 0.8549 (mmm) cc_final: 0.8177 (mmm) REVERT: C 353 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.6918 (mp) REVERT: Y 235 LYS cc_start: 0.6621 (ttpt) cc_final: 0.6123 (tmtt) REVERT: D 25 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: D 68 ASP cc_start: 0.7329 (m-30) cc_final: 0.6952 (m-30) REVERT: D 173 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8445 (m-30) REVERT: E 81 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7320 (tt0) REVERT: F 252 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.6440 (t80) REVERT: F 314 ASN cc_start: 0.7519 (m110) cc_final: 0.7094 (m110) REVERT: F 389 LEU cc_start: 0.5454 (OUTLIER) cc_final: 0.4861 (tt) REVERT: G 346 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7844 (mm) outliers start: 67 outliers final: 44 residues processed: 318 average time/residue: 0.1810 time to fit residues: 94.2910 Evaluate side-chains 306 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 256 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 99 GLN Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain Y residue 290 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 346 ILE Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 212 optimal weight: 8.9990 chunk 304 optimal weight: 6.9990 chunk 264 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 340 optimal weight: 2.9990 chunk 357 optimal weight: 6.9990 chunk 330 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 78 optimal weight: 0.2980 chunk 252 optimal weight: 6.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 HIS E 222 ASN E 319 GLN E 322 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 HIS ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.192653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126585 restraints weight = 40690.691| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.90 r_work: 0.3292 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33068 Z= 0.209 Angle : 0.642 16.193 45226 Z= 0.322 Chirality : 0.041 0.224 5091 Planarity : 0.005 0.061 5452 Dihedral : 16.661 167.050 5335 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.40 % Allowed : 14.05 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.76 (0.14), residues: 3720 helix: 0.30 (0.12), residues: 1903 sheet: 0.24 (0.35), residues: 217 loop : -1.58 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 82 TYR 0.020 0.002 TYR E 375 PHE 0.019 0.002 PHE X 161 TRP 0.017 0.001 TRP E 336 HIS 0.010 0.001 HIS Y 239 Details of bonding type rmsd covalent geometry : bond 0.00520 (33060) covalent geometry : angle 0.64249 (45220) hydrogen bonds : bond 0.04862 ( 1296) hydrogen bonds : angle 4.25693 ( 3683) metal coordination : bond 0.00273 ( 8) metal coordination : angle 0.55580 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 265 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.7306 (m-30) cc_final: 0.6797 (m-30) REVERT: A 206 LYS cc_start: 0.7564 (mttt) cc_final: 0.6699 (tptt) REVERT: A 306 GLN cc_start: 0.7227 (tt0) cc_final: 0.6901 (tp-100) REVERT: A 344 MET cc_start: 0.8563 (mmm) cc_final: 0.8173 (mmm) REVERT: C 353 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7020 (mp) REVERT: Y 235 LYS cc_start: 0.6666 (ttpt) cc_final: 0.6129 (tmtt) REVERT: D 25 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: D 68 ASP cc_start: 0.7368 (m-30) cc_final: 0.6983 (m-30) REVERT: D 173 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8455 (m-30) REVERT: E 81 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7376 (tt0) REVERT: F 252 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.6442 (t80) REVERT: F 314 ASN cc_start: 0.7541 (m110) cc_final: 0.7109 (m110) REVERT: F 385 MET cc_start: 0.5846 (ttt) cc_final: 0.5623 (ttm) REVERT: F 389 LEU cc_start: 0.5461 (OUTLIER) cc_final: 0.4834 (tt) REVERT: G 346 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7915 (mm) outliers start: 78 outliers final: 50 residues processed: 328 average time/residue: 0.1846 time to fit residues: 98.0485 Evaluate side-chains 317 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 261 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 99 GLN Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain Y residue 177 HIS Chi-restraints excluded: chain Y residue 290 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 346 ILE Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 313 optimal weight: 5.9990 chunk 361 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 325 optimal weight: 8.9990 chunk 169 optimal weight: 0.0770 chunk 132 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 338 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN C 208 HIS Y 239 HIS E 319 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.196003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131769 restraints weight = 40482.030| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.92 r_work: 0.3380 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33068 Z= 0.116 Angle : 0.557 16.878 45226 Z= 0.278 Chirality : 0.038 0.155 5091 Planarity : 0.004 0.063 5452 Dihedral : 16.410 165.975 5335 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.48 % Allowed : 15.22 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.52 (0.14), residues: 3720 helix: 0.49 (0.13), residues: 1914 sheet: 0.39 (0.34), residues: 217 loop : -1.48 (0.14), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 55 TYR 0.026 0.001 TYR Y 123 PHE 0.013 0.001 PHE X 161 TRP 0.016 0.001 TRP E 336 HIS 0.010 0.001 HIS D 442 Details of bonding type rmsd covalent geometry : bond 0.00267 (33060) covalent geometry : angle 0.55675 (45220) hydrogen bonds : bond 0.03437 ( 1296) hydrogen bonds : angle 4.03747 ( 3683) metal coordination : bond 0.00181 ( 8) metal coordination : angle 0.84444 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 276 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.7191 (m-30) cc_final: 0.6665 (m-30) REVERT: A 206 LYS cc_start: 0.7493 (mttt) cc_final: 0.6631 (tptt) REVERT: A 344 MET cc_start: 0.8431 (mmm) cc_final: 0.8121 (mmm) REVERT: B 418 ASP cc_start: 0.7480 (t70) cc_final: 0.7124 (m-30) REVERT: C 55 ARG cc_start: 0.7226 (ttm170) cc_final: 0.7019 (ttm170) REVERT: Y 235 LYS cc_start: 0.6628 (ttpt) cc_final: 0.6104 (tmtt) REVERT: D 20 ASP cc_start: 0.7614 (t0) cc_final: 0.6690 (t0) REVERT: D 68 ASP cc_start: 0.7282 (m-30) cc_final: 0.6932 (m-30) REVERT: D 173 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8427 (m-30) REVERT: E 81 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7197 (tt0) REVERT: F 252 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.6165 (t80) REVERT: F 385 MET cc_start: 0.5960 (ttt) cc_final: 0.5755 (ttm) REVERT: F 389 LEU cc_start: 0.5321 (OUTLIER) cc_final: 0.5108 (tt) outliers start: 48 outliers final: 31 residues processed: 314 average time/residue: 0.2058 time to fit residues: 104.7202 Evaluate side-chains 295 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.8587 > 50: distance: 98 - 101: 18.219 distance: 101 - 102: 7.893 distance: 102 - 103: 8.036 distance: 102 - 105: 17.959 distance: 103 - 104: 35.647 distance: 103 - 108: 9.111 distance: 105 - 106: 24.841 distance: 105 - 107: 17.096 distance: 108 - 109: 11.726 distance: 109 - 110: 24.411 distance: 109 - 112: 30.184 distance: 110 - 111: 22.527 distance: 110 - 120: 18.790 distance: 112 - 113: 13.465 distance: 113 - 114: 27.129 distance: 113 - 115: 39.185 distance: 114 - 116: 22.415 distance: 115 - 117: 24.999 distance: 116 - 118: 11.728 distance: 117 - 118: 27.113 distance: 118 - 119: 8.269 distance: 120 - 121: 10.935 distance: 120 - 126: 4.014 distance: 121 - 122: 13.292 distance: 121 - 124: 21.987 distance: 122 - 123: 22.129 distance: 122 - 127: 12.009 distance: 124 - 125: 28.780 distance: 125 - 126: 19.501 distance: 127 - 128: 16.098 distance: 128 - 129: 18.921 distance: 128 - 131: 33.815 distance: 129 - 130: 13.236 distance: 129 - 136: 21.825 distance: 131 - 132: 33.337 distance: 132 - 133: 8.411 distance: 133 - 134: 13.010 distance: 133 - 135: 14.407 distance: 136 - 137: 17.978 distance: 137 - 138: 18.377 distance: 137 - 140: 32.002 distance: 138 - 139: 14.274 distance: 138 - 143: 27.010 distance: 140 - 141: 45.841 distance: 140 - 142: 51.859 distance: 143 - 222: 5.958 distance: 144 - 145: 16.856 distance: 144 - 147: 3.621 distance: 145 - 146: 9.363 distance: 145 - 151: 3.357 distance: 146 - 219: 11.273 distance: 147 - 148: 9.269 distance: 147 - 149: 22.137 distance: 148 - 150: 25.708 distance: 151 - 152: 13.631 distance: 152 - 153: 14.874 distance: 152 - 155: 5.593 distance: 153 - 154: 6.429 distance: 153 - 163: 13.502 distance: 155 - 156: 6.039 distance: 156 - 158: 18.587 distance: 157 - 159: 3.853 distance: 158 - 160: 10.921 distance: 159 - 161: 12.944 distance: 160 - 161: 17.489 distance: 161 - 162: 9.894 distance: 163 - 164: 12.498 distance: 164 - 165: 11.329 distance: 164 - 167: 10.308 distance: 165 - 166: 11.947 distance: 165 - 173: 11.139 distance: 167 - 168: 17.919 distance: 168 - 169: 15.959 distance: 168 - 170: 15.074 distance: 169 - 171: 15.701 distance: 170 - 172: 10.103 distance: 171 - 172: 8.839 distance: 173 - 174: 9.294 distance: 174 - 175: 11.290 distance: 174 - 177: 8.585 distance: 175 - 176: 4.580 distance: 175 - 184: 16.510 distance: 177 - 178: 9.108 distance: 178 - 179: 11.293 distance: 179 - 180: 15.641 distance: 180 - 181: 11.360 distance: 181 - 182: 8.841 distance: 181 - 183: 16.242 distance: 184 - 185: 10.914 distance: 185 - 186: 7.272 distance: 185 - 188: 7.309 distance: 186 - 187: 23.750 distance: 186 - 193: 6.736 distance: 188 - 189: 23.180 distance: 189 - 190: 10.981 distance: 190 - 191: 13.517 distance: 190 - 192: 12.229