Starting phenix.real_space_refine on Fri Jul 3 20:42:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpn_27639/07_2026/8dpn_27639_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpn_27639/07_2026/8dpn_27639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dpn_27639/07_2026/8dpn_27639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpn_27639/07_2026/8dpn_27639.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpn_27639/07_2026/8dpn_27639_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpn_27639/07_2026/8dpn_27639_neut.cif" } resolution = 2.49 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 32 7.16 5 S 139 5.16 5 C 10170 2.51 5 N 2702 2.21 5 O 3022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16067 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} bond proxies already assigned to first conformer: 3874 Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 3790 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 3871 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 30.808 30.303 36.044 1.00 1.48 S ATOM 1170 SG CYS A 154 20.230 46.469 48.234 1.00 21.76 S ATOM 4552 SG CYS B 95 24.819 46.848 51.447 1.00 21.55 S ATOM 465 SG CYS A 62 25.399 43.002 45.862 1.00 28.88 S ATOM 652 SG CYS A 88 25.454 49.823 45.797 1.00 22.99 S ATOM 652 SG CYS A 88 25.454 49.823 45.797 1.00 22.99 S ATOM 5005 SG CYS B 153 21.487 51.056 50.235 1.00 37.45 S ATOM 4372 SG CYS B 70 28.028 52.852 51.365 1.00 18.63 S ATOM 4552 SG CYS B 95 24.819 46.848 51.447 1.00 21.55 S ATOM 10056 SG CYS C 275 87.809 83.318 36.047 1.00 0.00 S ATOM 9134 SG CYS C 154 98.347 67.063 48.206 1.00 10.22 S ATOM 12516 SG CYS D 95 93.792 66.695 51.504 1.00 17.13 S ATOM 8429 SG CYS C 62 93.247 70.580 45.858 1.00 25.65 S ATOM 8616 SG CYS C 88 92.823 64.067 46.115 1.00 31.36 S ATOM 8616 SG CYS C 88 92.823 64.067 46.115 1.00 31.36 S ATOM 12969 SG CYS D 153 97.116 62.566 50.152 1.00 34.07 S ATOM 12336 SG CYS D 70 90.523 60.848 51.443 1.00 26.56 S ATOM 12516 SG CYS D 95 93.792 66.695 51.504 1.00 17.13 S Time building chain proxies: 5.02, per 1000 atoms: 0.31 Number of scatterers: 16067 At special positions: 0 Unit cell: (120.24, 114.395, 95.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mo 2 41.97 Fe 32 26.01 S 139 16.00 O 3022 8.00 N 2702 7.00 C 10170 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 948.3 milliseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 12 sheets defined 59.5% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.998A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.507A pdb=" N GLN A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.591A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.765A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.222A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.311A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 3.562A pdb=" N MET A 279 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 383 through 394 removed outlier: 3.908A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 434 removed outlier: 4.235A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.769A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 32 removed outlier: 3.679A pdb=" N GLU B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 70 through 80 removed outlier: 4.037A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.095A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.883A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 321 through 337 Processing helix chain 'B' and resid 341 through 363 removed outlier: 3.548A pdb=" N THR B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.768A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 447 through 459 removed outlier: 4.487A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.573A pdb=" N ASN B 518 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 30 removed outlier: 3.990A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 93 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 removed outlier: 3.575A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.689A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.200A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 4.560A pdb=" N ARG C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 245 removed outlier: 4.306A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 275 through 291 removed outlier: 3.511A pdb=" N MET C 279 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 315 removed outlier: 4.271A pdb=" N LYS C 304 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 347 Proline residue: C 333 - end of helix Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 363 through 370 Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.247A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 434 removed outlier: 4.348A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.766A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.524A pdb=" N TRP C 472 " --> pdb=" O ASN C 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.689A pdb=" N GLU D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 70 through 80 removed outlier: 4.023A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.097A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.864A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 3.557A pdb=" N THR D 345 " --> pdb=" O PRO D 341 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.558A pdb=" N LYS D 417 " --> pdb=" O PRO D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 447 through 459 removed outlier: 4.390A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.688A pdb=" N ASN D 518 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.501A pdb=" N LEU A 353 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR A 377 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 6.966A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 7.327A pdb=" N ILE A 225 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN A 252 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY A 227 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER A 254 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP A 222 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU A 272 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA A 224 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASN A 271 " --> pdb=" O MET A 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.495A pdb=" N ILE B 224 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.487A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.059A pdb=" N VAL C 351 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 376 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 6.935A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254 removed outlier: 7.166A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE C 225 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP C 222 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU C 272 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA C 224 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.480A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.496A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 16169 1.57 - 1.91: 178 1.91 - 2.26: 42 2.26 - 2.60: 76 2.60 - 2.95: 18 Bond restraints: 16483 Sorted by residual: bond pdb="FE2 CLF B 601 " pdb="FE8 CLF B 601 " ideal model delta sigma weight residual 2.200 2.947 -0.747 2.00e-02 2.50e+03 1.39e+03 bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 2.941 -0.741 2.00e-02 2.50e+03 1.37e+03 bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 2.930 -0.730 2.00e-02 2.50e+03 1.33e+03 bond pdb="FE4 CLF B 601 " pdb="FE5 CLF B 601 " ideal model delta sigma weight residual 2.200 2.922 -0.722 2.00e-02 2.50e+03 1.30e+03 bond pdb="FE6 CLF D 602 " pdb="FE7 CLF D 602 " ideal model delta sigma weight residual 2.200 2.848 -0.648 2.00e-02 2.50e+03 1.05e+03 ... (remaining 16478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.87: 22235 6.87 - 13.74: 2 13.74 - 20.62: 2 20.62 - 27.49: 0 27.49 - 34.36: 4 Bond angle restraints: 22243 Sorted by residual: angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE4 CLF B 601 " ideal model delta sigma weight residual 90.00 55.64 34.36 3.00e+00 1.11e-01 1.31e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.93 34.07 3.00e+00 1.11e-01 1.29e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE1 CLF B 601 " ideal model delta sigma weight residual 90.00 57.18 32.82 3.00e+00 1.11e-01 1.20e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE1 CLF D 602 " ideal model delta sigma weight residual 90.00 57.70 32.30 3.00e+00 1.11e-01 1.16e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE3 CLF D 602 " ideal model delta sigma weight residual 90.00 108.28 -18.28 3.00e+00 1.11e-01 3.71e+01 ... (remaining 22238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8748 17.91 - 35.82: 974 35.82 - 53.73: 299 53.73 - 71.64: 44 71.64 - 89.56: 36 Dihedral angle restraints: 10101 sinusoidal: 4359 harmonic: 5742 Sorted by residual: dihedral pdb=" CA THR B 209 " pdb=" C THR B 209 " pdb=" N LEU B 210 " pdb=" CA LEU B 210 " ideal model delta harmonic sigma weight residual 180.00 -157.42 -22.58 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA THR D 209 " pdb=" C THR D 209 " pdb=" N LEU D 210 " pdb=" CA LEU D 210 " ideal model delta harmonic sigma weight residual -180.00 -157.84 -22.16 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CG ARG A 187 " pdb=" CD ARG A 187 " pdb=" NE ARG A 187 " pdb=" CZ ARG A 187 " ideal model delta sinusoidal sigma weight residual -90.00 -37.70 -52.30 2 1.50e+01 4.44e-03 1.34e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1294 0.030 - 0.059: 644 0.059 - 0.089: 235 0.089 - 0.119: 143 0.119 - 0.148: 20 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA LYS B 26 " pdb=" N LYS B 26 " pdb=" C LYS B 26 " pdb=" CB LYS B 26 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA VAL A 34 " pdb=" N VAL A 34 " pdb=" C VAL A 34 " pdb=" CB VAL A 34 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE C 355 " pdb=" N ILE C 355 " pdb=" C ILE C 355 " pdb=" CB ILE C 355 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 2333 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 152 " -0.010 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C THR B 152 " 0.032 2.00e-02 2.50e+03 pdb=" O THR B 152 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS B 153 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 152 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C THR D 152 " -0.031 2.00e-02 2.50e+03 pdb=" O THR D 152 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS D 153 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 87 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C GLY C 87 " -0.031 2.00e-02 2.50e+03 pdb=" O GLY C 87 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS C 88 " 0.010 2.00e-02 2.50e+03 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 91 2.50 - 3.10: 11558 3.10 - 3.70: 26286 3.70 - 4.30: 40469 4.30 - 4.90: 65649 Nonbonded interactions: 144053 Sorted by model distance: nonbonded pdb=" OE2 GLU D 109 " pdb="FE FE B 602 " model vdw 1.898 3.000 nonbonded pdb=" OE2 GLU B 231 " pdb=" ND2 ASN B 236 " model vdw 2.083 3.120 nonbonded pdb=" O1 HCA A 501 " pdb=" O7 HCA A 501 " model vdw 2.099 3.040 nonbonded pdb=" OD1 ASP D 326 " pdb=" OH TYR D 487 " model vdw 2.138 3.040 nonbonded pdb=" OD1 ASP B 326 " pdb=" OH TYR B 487 " model vdw 2.138 3.040 ... (remaining 144048 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 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 248 or resid 250 through 502)) selection = (chain 'C' and (resid 4 through 248 or resid 250 through 502)) } ncs_group { reference = (chain 'B' and resid 2 through 523) selection = (chain 'D' and resid 2 through 523) } 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=0.41 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: 5.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.390 Find NCS groups from input model: 0.510 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: 0.000 Load rotamer database and sin/cos tables:9.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 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 : 0.024 0.747 16499 Z= 1.200 Angle : 0.766 34.362 22243 Z= 0.367 Chirality : 0.045 0.148 2336 Planarity : 0.004 0.041 2858 Dihedral : 17.034 89.555 6433 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.99 % Allowed : 23.27 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 1992 helix: 1.28 (0.17), residues: 964 sheet: -0.61 (0.37), residues: 188 loop : -0.38 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 187 TYR 0.017 0.001 TYR C 229 PHE 0.021 0.001 PHE C 431 TRP 0.015 0.001 TRP C 253 HIS 0.008 0.001 HIS C 442 Details of bonding type rmsd/Z covalent geometry : bond 0.02368 / 1.18 (16483) covalent geometry : angle 0.76583 / 0.37 (22243) hydrogen bonds : bond 0.13952 / 9.90 ( 774) hydrogen bonds : angle 6.75035 / 4.93 ( 2226) Misc. bond : bond 0.08787 / 6.32 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 511 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8568 (mp) cc_final: 0.8301 (mt) REVERT: A 445 ASP cc_start: 0.7535 (t70) cc_final: 0.7305 (t0) REVERT: C 35 ASN cc_start: 0.8470 (t0) cc_final: 0.8146 (t0) REVERT: D 45 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7624 (tp-100) outliers start: 17 outliers final: 10 residues processed: 519 average time/residue: 0.7700 time to fit residues: 432.8772 Evaluate side-chains 504 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 494 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.0970 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN A 98 ASN A 252 GLN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN B 477 HIS ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 HIS D 104 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.115855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105445 restraints weight = 18807.442| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.02 r_work: 0.3261 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 16499 Z= 0.178 Angle : 0.717 29.289 22243 Z= 0.335 Chirality : 0.046 0.136 2336 Planarity : 0.005 0.050 2858 Dihedral : 5.328 59.226 2536 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.73 % Allowed : 20.60 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.19), residues: 1992 helix: 1.37 (0.17), residues: 1000 sheet: -0.59 (0.36), residues: 190 loop : -0.14 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 187 TYR 0.017 0.002 TYR D 88 PHE 0.019 0.001 PHE C 412 TRP 0.014 0.002 TRP C 253 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (16483) covalent geometry : angle 0.71666 / 0.34 (22243) hydrogen bonds : bond 0.05100 / 3.48 ( 774) hydrogen bonds : angle 5.63976 / 4.09 ( 2226) Misc. bond : bond 0.09065 / 4.99 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 506 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8333 (mt) REVERT: A 393 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: A 474 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7602 (mtpp) REVERT: B 258 GLU cc_start: 0.7499 (pt0) cc_final: 0.7286 (tt0) REVERT: C 35 ASN cc_start: 0.8518 (t0) cc_final: 0.8171 (t0) REVERT: C 221 TYR cc_start: 0.8350 (m-80) cc_final: 0.8148 (m-80) REVERT: D 45 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7654 (tp-100) REVERT: D 256 ASP cc_start: 0.7602 (t0) cc_final: 0.7366 (t0) outliers start: 47 outliers final: 21 residues processed: 520 average time/residue: 0.7935 time to fit residues: 447.0225 Evaluate side-chains 519 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 495 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 369 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 123 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 127 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN A 252 GLN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN C 98 ASN ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.103278 restraints weight = 27481.583| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.33 r_work: 0.3207 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.188 16499 Z= 0.202 Angle : 0.726 29.202 22243 Z= 0.339 Chirality : 0.047 0.184 2336 Planarity : 0.005 0.050 2858 Dihedral : 5.270 61.010 2527 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.73 % Allowed : 20.78 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.19), residues: 1992 helix: 1.35 (0.17), residues: 1000 sheet: -0.45 (0.35), residues: 200 loop : -0.30 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 187 TYR 0.018 0.002 TYR B 88 PHE 0.019 0.002 PHE C 412 TRP 0.014 0.002 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (16483) covalent geometry : angle 0.72604 / 0.34 (22243) hydrogen bonds : bond 0.05244 / 3.58 ( 774) hydrogen bonds : angle 5.56879 / 4.04 ( 2226) Misc. bond : bond 0.08374 / 4.59 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 512 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8354 (mt) REVERT: A 287 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7797 (tp30) REVERT: A 334 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7518 (mm-30) REVERT: A 393 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6727 (mp0) REVERT: A 474 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7681 (mtpp) REVERT: B 258 GLU cc_start: 0.7622 (pt0) cc_final: 0.7404 (tt0) REVERT: C 35 ASN cc_start: 0.8520 (t0) cc_final: 0.8260 (t0) REVERT: C 287 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7473 (tp30) REVERT: D 45 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7754 (tp-100) REVERT: D 256 ASP cc_start: 0.7742 (t0) cc_final: 0.7508 (t0) outliers start: 47 outliers final: 26 residues processed: 525 average time/residue: 0.7958 time to fit residues: 452.3808 Evaluate side-chains 537 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 505 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 400 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 91 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN A 252 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN C 151 GLN ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.102569 restraints weight = 32554.203| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.48 r_work: 0.3186 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.185 16499 Z= 0.204 Angle : 0.726 29.194 22243 Z= 0.340 Chirality : 0.047 0.140 2336 Planarity : 0.005 0.051 2858 Dihedral : 5.273 62.986 2527 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.08 % Allowed : 21.01 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1992 helix: 1.41 (0.17), residues: 988 sheet: -0.49 (0.35), residues: 200 loop : -0.44 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 187 TYR 0.018 0.002 TYR B 88 PHE 0.021 0.002 PHE C 412 TRP 0.014 0.002 TRP A 253 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (16483) covalent geometry : angle 0.72646 / 0.34 (22243) hydrogen bonds : bond 0.05221 / 3.56 ( 774) hydrogen bonds : angle 5.52636 / 4.01 ( 2226) Misc. bond : bond 0.08124 / 4.42 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 516 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8354 (mt) REVERT: A 320 ILE cc_start: 0.8562 (mm) cc_final: 0.8341 (mm) REVERT: A 393 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: A 474 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7726 (mtpp) REVERT: B 258 GLU cc_start: 0.7680 (pt0) cc_final: 0.7381 (tt0) REVERT: C 35 ASN cc_start: 0.8503 (t0) cc_final: 0.8244 (t0) REVERT: C 151 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8159 (mp10) REVERT: D 45 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7802 (tp-100) REVERT: D 221 ASN cc_start: 0.8484 (p0) cc_final: 0.8216 (p0) REVERT: D 256 ASP cc_start: 0.7812 (t0) cc_final: 0.7604 (t0) REVERT: D 258 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7498 (tt0) outliers start: 53 outliers final: 29 residues processed: 532 average time/residue: 0.7741 time to fit residues: 447.5245 Evaluate side-chains 537 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 503 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 400 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 60 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 147 optimal weight: 0.4980 chunk 1 optimal weight: 0.0060 chunk 193 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN A 252 GLN A 362 HIS A 432 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN C 151 GLN ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103547 restraints weight = 32821.410| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.49 r_work: 0.3201 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 16499 Z= 0.155 Angle : 0.701 29.136 22243 Z= 0.325 Chirality : 0.045 0.161 2336 Planarity : 0.005 0.047 2858 Dihedral : 5.178 63.203 2527 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.08 % Allowed : 21.47 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.19), residues: 1992 helix: 1.42 (0.17), residues: 1002 sheet: -0.49 (0.35), residues: 200 loop : -0.42 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 187 TYR 0.015 0.001 TYR D 88 PHE 0.018 0.001 PHE C 431 TRP 0.014 0.001 TRP A 253 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (16483) covalent geometry : angle 0.70050 / 0.32 (22243) hydrogen bonds : bond 0.04598 / 3.14 ( 774) hydrogen bonds : angle 5.41283 / 3.93 ( 2226) Misc. bond : bond 0.07357 / 3.96 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 503 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8332 (mt) REVERT: A 474 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7710 (mtpp) REVERT: B 258 GLU cc_start: 0.7665 (pt0) cc_final: 0.7431 (tt0) REVERT: B 372 ASP cc_start: 0.7903 (m-30) cc_final: 0.7673 (m-30) REVERT: C 35 ASN cc_start: 0.8509 (t0) cc_final: 0.8251 (t0) REVERT: D 45 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7789 (tp-100) REVERT: D 258 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7505 (tt0) outliers start: 53 outliers final: 33 residues processed: 521 average time/residue: 0.7492 time to fit residues: 423.6099 Evaluate side-chains 530 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 494 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 400 LYS Chi-restraints excluded: chain D residue 488 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 92 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 101 optimal weight: 0.0970 chunk 175 optimal weight: 0.0980 chunk 129 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 184 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 chunk 154 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN A 252 GLN ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN C 151 GLN ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN D 167 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105257 restraints weight = 20998.024| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.10 r_work: 0.3253 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 16499 Z= 0.160 Angle : 0.705 29.158 22243 Z= 0.326 Chirality : 0.045 0.150 2336 Planarity : 0.005 0.044 2858 Dihedral : 4.989 63.477 2525 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.19 % Allowed : 21.65 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.19), residues: 1992 helix: 1.39 (0.17), residues: 1010 sheet: -0.53 (0.35), residues: 200 loop : -0.40 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 187 TYR 0.015 0.001 TYR C 401 PHE 0.019 0.001 PHE C 431 TRP 0.013 0.001 TRP C 335 HIS 0.010 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (16483) covalent geometry : angle 0.70453 / 0.33 (22243) hydrogen bonds : bond 0.04592 / 3.14 ( 774) hydrogen bonds : angle 5.39163 / 3.92 ( 2226) Misc. bond : bond 0.07264 / 3.91 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 503 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8337 (mt) REVERT: A 320 ILE cc_start: 0.8504 (mm) cc_final: 0.8297 (mm) REVERT: A 393 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6692 (mp0) REVERT: A 474 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7697 (mtpp) REVERT: B 238 ARG cc_start: 0.8143 (mtt-85) cc_final: 0.7895 (mtt-85) REVERT: B 258 GLU cc_start: 0.7507 (pt0) cc_final: 0.7156 (tt0) REVERT: C 35 ASN cc_start: 0.8456 (t0) cc_final: 0.8195 (t0) REVERT: D 45 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7696 (tp-100) REVERT: D 258 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7368 (tt0) outliers start: 55 outliers final: 33 residues processed: 518 average time/residue: 0.7499 time to fit residues: 421.7781 Evaluate side-chains 525 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 488 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 400 LYS Chi-restraints excluded: chain D residue 488 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 4 optimal weight: 0.4980 chunk 140 optimal weight: 0.6980 chunk 174 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 171 optimal weight: 0.6980 chunk 96 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN A 252 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN C 151 GLN ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN D 167 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103622 restraints weight = 33844.784| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.53 r_work: 0.3200 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 16499 Z= 0.159 Angle : 0.708 29.160 22243 Z= 0.328 Chirality : 0.045 0.160 2336 Planarity : 0.005 0.043 2858 Dihedral : 4.970 64.208 2525 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.96 % Allowed : 22.17 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.19), residues: 1992 helix: 1.39 (0.17), residues: 1008 sheet: -0.51 (0.35), residues: 200 loop : -0.39 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 187 TYR 0.015 0.001 TYR D 88 PHE 0.018 0.001 PHE C 431 TRP 0.014 0.001 TRP A 335 HIS 0.010 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (16483) covalent geometry : angle 0.70757 / 0.33 (22243) hydrogen bonds : bond 0.04565 / 3.12 ( 774) hydrogen bonds : angle 5.37262 / 3.90 ( 2226) Misc. bond : bond 0.07189 / 3.86 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 491 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8376 (mt) REVERT: A 393 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: A 414 LYS cc_start: 0.8242 (mtpp) cc_final: 0.8041 (mtmt) REVERT: A 474 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7749 (mtpp) REVERT: B 258 GLU cc_start: 0.7677 (pt0) cc_final: 0.7396 (tt0) REVERT: C 35 ASN cc_start: 0.8485 (t0) cc_final: 0.8224 (t0) REVERT: D 45 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7841 (tp-100) REVERT: D 258 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7531 (tt0) outliers start: 51 outliers final: 29 residues processed: 508 average time/residue: 0.7698 time to fit residues: 424.8807 Evaluate side-chains 523 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 490 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 400 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 131 optimal weight: 0.7980 chunk 146 optimal weight: 0.0570 chunk 88 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 100 optimal weight: 0.0670 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN A 252 GLN A 362 HIS B 128 GLN B 167 ASN B 268 GLN C 151 GLN C 432 GLN ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.105773 restraints weight = 23088.147| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.18 r_work: 0.3255 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 16499 Z= 0.141 Angle : 0.704 29.123 22243 Z= 0.324 Chirality : 0.045 0.149 2336 Planarity : 0.004 0.042 2858 Dihedral : 4.897 64.076 2525 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.67 % Allowed : 23.22 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.19), residues: 1992 helix: 1.44 (0.17), residues: 1008 sheet: -0.49 (0.35), residues: 200 loop : -0.37 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 187 TYR 0.017 0.001 TYR C 401 PHE 0.018 0.001 PHE C 431 TRP 0.014 0.001 TRP A 335 HIS 0.008 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (16483) covalent geometry : angle 0.70354 / 0.32 (22243) hydrogen bonds : bond 0.04248 / 2.90 ( 774) hydrogen bonds : angle 5.29181 / 3.85 ( 2226) Misc. bond : bond 0.06755 / 3.63 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 495 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8364 (mt) REVERT: A 336 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7602 (mt-10) REVERT: A 474 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7661 (mtpp) REVERT: C 35 ASN cc_start: 0.8471 (t0) cc_final: 0.8252 (t0) REVERT: D 45 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7706 (tp-100) REVERT: D 258 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7391 (tt0) REVERT: D 372 ASP cc_start: 0.7554 (m-30) cc_final: 0.7353 (m-30) outliers start: 46 outliers final: 26 residues processed: 510 average time/residue: 0.7682 time to fit residues: 425.8775 Evaluate side-chains 515 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 486 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 400 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 24 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.0170 chunk 98 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN A 362 HIS A 432 GLN B 163 ASN B 167 ASN C 151 GLN ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN D 167 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.106136 restraints weight = 20519.985| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.11 r_work: 0.3265 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 16499 Z= 0.158 Angle : 0.724 29.139 22243 Z= 0.336 Chirality : 0.045 0.158 2336 Planarity : 0.005 0.056 2858 Dihedral : 4.920 64.416 2525 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.50 % Allowed : 23.45 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1992 helix: 1.46 (0.17), residues: 1004 sheet: -0.48 (0.35), residues: 200 loop : -0.37 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 238 TYR 0.016 0.002 TYR C 401 PHE 0.018 0.001 PHE C 431 TRP 0.014 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (16483) covalent geometry : angle 0.72432 / 0.34 (22243) hydrogen bonds : bond 0.04463 / 3.04 ( 774) hydrogen bonds : angle 5.31412 / 3.87 ( 2226) Misc. bond : bond 0.06972 / 3.74 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 494 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8349 (mt) REVERT: A 336 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7615 (mt-10) REVERT: A 474 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7665 (mtpp) REVERT: C 35 ASN cc_start: 0.8447 (t0) cc_final: 0.8184 (t0) REVERT: D 45 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7651 (tp-100) REVERT: D 221 ASN cc_start: 0.8388 (p0) cc_final: 0.8173 (p0) REVERT: D 258 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: D 414 PRO cc_start: 0.8554 (Cg_endo) cc_final: 0.8340 (Cg_exo) outliers start: 43 outliers final: 26 residues processed: 506 average time/residue: 0.7381 time to fit residues: 405.4771 Evaluate side-chains 517 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 488 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 400 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 109 optimal weight: 0.0570 chunk 152 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 111 optimal weight: 0.0370 chunk 135 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 132 optimal weight: 0.0670 chunk 177 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN A 362 HIS B 163 ASN B 167 ASN C 151 GLN ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.105538 restraints weight = 26521.396| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.33 r_work: 0.3241 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 16499 Z= 0.147 Angle : 0.721 29.128 22243 Z= 0.335 Chirality : 0.045 0.151 2336 Planarity : 0.005 0.042 2858 Dihedral : 4.902 64.395 2525 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.03 % Allowed : 23.85 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1992 helix: 1.45 (0.17), residues: 1004 sheet: -0.40 (0.35), residues: 196 loop : -0.37 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 187 TYR 0.019 0.001 TYR C 221 PHE 0.018 0.001 PHE C 412 TRP 0.014 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (16483) covalent geometry : angle 0.72095 / 0.34 (22243) hydrogen bonds : bond 0.04312 / 2.93 ( 774) hydrogen bonds : angle 5.30311 / 3.87 ( 2226) Misc. bond : bond 0.06791 / 3.63 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 491 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8348 (mt) REVERT: A 336 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7691 (mt-10) REVERT: A 474 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7707 (mtpp) REVERT: C 35 ASN cc_start: 0.8467 (t0) cc_final: 0.8191 (t0) REVERT: D 45 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7698 (tp-100) REVERT: D 258 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: D 414 PRO cc_start: 0.8571 (Cg_endo) cc_final: 0.8356 (Cg_exo) outliers start: 35 outliers final: 25 residues processed: 501 average time/residue: 0.7470 time to fit residues: 406.9970 Evaluate side-chains 514 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 486 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 400 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 83 optimal weight: 0.4980 chunk 127 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 7 optimal weight: 0.0030 chunk 107 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 106 optimal weight: 0.0870 chunk 147 optimal weight: 0.5980 chunk 86 optimal weight: 0.4980 chunk 144 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 overall best weight: 0.2368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN A 362 HIS A 432 GLN B 163 ASN B 167 ASN C 98 ASN C 151 GLN D 167 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.118913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106912 restraints weight = 26637.563| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.33 r_work: 0.3265 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 16499 Z= 0.127 Angle : 0.704 29.099 22243 Z= 0.324 Chirality : 0.044 0.150 2336 Planarity : 0.005 0.051 2858 Dihedral : 4.775 63.850 2525 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.86 % Allowed : 24.32 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1992 helix: 1.52 (0.17), residues: 1006 sheet: -0.38 (0.36), residues: 184 loop : -0.35 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 108 TYR 0.019 0.001 TYR C 401 PHE 0.016 0.001 PHE C 431 TRP 0.014 0.001 TRP A 335 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (16483) covalent geometry : angle 0.70350 / 0.32 (22243) hydrogen bonds : bond 0.03836 / 2.61 ( 774) hydrogen bonds : angle 5.21299 / 3.80 ( 2226) Misc. bond : bond 0.06015 / 3.26 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8874.90 seconds wall clock time: 151 minutes 39.15 seconds (9099.15 seconds total)