Starting phenix.real_space_refine on Mon Apr 6 05:03:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpn_27639/04_2026/8dpn_27639_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpn_27639/04_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_27639/04_2026/8dpn_27639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpn_27639/04_2026/8dpn_27639.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpn_27639/04_2026/8dpn_27639_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpn_27639/04_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-2.1rc1-6017/lib/python3.9/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, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'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, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 4.84, per 1000 atoms: 0.30 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: 1.52 Conformation dependent library (CDL) restraints added in 966.4 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: 0.52 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: 2.80 Time building geometry restraints manager: 1.88 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 2.260 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: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.010 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 covalent geometry : bond 0.02368 (16483) covalent geometry : angle 0.76583 (22243) hydrogen bonds : bond 0.13952 ( 774) hydrogen bonds : angle 6.75035 ( 2226) Misc. bond : bond 0.08787 ( 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 : 0.695 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: 0.8145 (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: 0.8212 time to fit residues: 460.0767 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 : 0.605 ------------------------------------------------------------------------------- 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: 0.1980 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: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 HIS C 432 GLN D 104 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.115801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105344 restraints weight = 18795.029| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.02 r_work: 0.3259 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 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 = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.178 16499 Z= 0.179 Angle : 0.719 28.938 22243 Z= 0.337 Chirality : 0.046 0.136 2336 Planarity : 0.005 0.051 2858 Dihedral : 5.339 59.199 2536 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.79 % Allowed : 20.55 % 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: 0.79 (0.19), residues: 1992 helix: 1.36 (0.17), residues: 1000 sheet: -0.59 (0.36), residues: 190 loop : -0.16 (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 0.015 0.002 TRP A 253 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00398 (16483) covalent geometry : angle 0.71882 (22243) hydrogen bonds : bond 0.05078 ( 774) hydrogen bonds : angle 5.61453 ( 2226) Misc. bond : bond 0.08250 ( 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 555 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 507 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8333 (mt) REVERT: A 393 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: A 474 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7593 (mtpp) REVERT: B 258 GLU cc_start: 0.7500 (pt0) cc_final: 0.7286 (tt0) REVERT: C 35 ASN cc_start: 0.8518 (t0) cc_final: 0.8170 (t0) REVERT: C 221 TYR cc_start: 0.8349 (m-80) cc_final: 0.8147 (m-80) REVERT: D 45 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7647 (tp-100) REVERT: D 256 ASP cc_start: 0.7593 (t0) cc_final: 0.7357 (t0) outliers start: 48 outliers final: 21 residues processed: 522 average time/residue: 0.8028 time to fit residues: 452.9238 Evaluate side-chains 523 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 499 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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: 0.9990 chunk 168 optimal weight: 0.3980 chunk 129 optimal weight: 0.5980 chunk 127 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3505 r_free = 0.3505 target = 0.115446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103587 restraints weight = 27528.392| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.33 r_work: 0.3211 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 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 = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 16499 Z= 0.187 Angle : 0.718 29.169 22243 Z= 0.335 Chirality : 0.047 0.174 2336 Planarity : 0.005 0.049 2858 Dihedral : 5.231 61.019 2527 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.90 % Allowed : 20.72 % Favored : 76.38 % 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: 0.73 (0.19), residues: 1992 helix: 1.36 (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 0.017 0.002 TYR B 88 PHE 0.019 0.001 PHE C 412 TRP 0.014 0.002 TRP A 253 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00421 (16483) covalent geometry : angle 0.71797 (22243) hydrogen bonds : bond 0.05080 ( 774) hydrogen bonds : angle 5.50599 ( 2226) Misc. bond : bond 0.08244 ( 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 562 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 512 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8349 (mt) REVERT: A 334 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: A 393 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: A 408 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7457 (mt-10) REVERT: A 474 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7724 (mtpp) REVERT: B 258 GLU cc_start: 0.7632 (pt0) cc_final: 0.7341 (tt0) REVERT: C 35 ASN cc_start: 0.8519 (t0) cc_final: 0.8267 (t0) REVERT: C 287 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7479 (tp30) REVERT: D 45 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7752 (tp-100) REVERT: D 256 ASP cc_start: 0.7740 (t0) cc_final: 0.7510 (t0) outliers start: 50 outliers final: 27 residues processed: 526 average time/residue: 0.8094 time to fit residues: 459.6183 Evaluate side-chains 534 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 502 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 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 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 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 172 GLU Chi-restraints excluded: chain D residue 258 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: 0.7980 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 190 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 B 477 HIS C 151 GLN ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.115477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103128 restraints weight = 32643.693| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.49 r_work: 0.3195 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 16499 Z= 0.179 Angle : 0.712 29.185 22243 Z= 0.331 Chirality : 0.046 0.144 2336 Planarity : 0.005 0.047 2858 Dihedral : 5.187 62.656 2527 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.19 % Allowed : 20.78 % Favored : 76.03 % 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: 1.39 (0.17), residues: 1000 sheet: -0.44 (0.35), residues: 200 loop : -0.37 (0.21), residues: 792 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 0.020 0.001 PHE C 431 TRP 0.014 0.002 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00403 (16483) covalent geometry : angle 0.71172 (22243) hydrogen bonds : bond 0.04907 ( 774) hydrogen bonds : angle 5.44310 ( 2226) Misc. bond : bond 0.07815 ( 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 567 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 512 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8350 (mt) REVERT: A 332 LYS cc_start: 0.8479 (tttp) cc_final: 0.8274 (tttp) REVERT: A 336 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 393 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: A 474 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7726 (mtpp) REVERT: B 258 GLU cc_start: 0.7661 (pt0) cc_final: 0.7418 (tt0) REVERT: C 35 ASN cc_start: 0.8524 (t0) cc_final: 0.8247 (t0) REVERT: D 45 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7793 (tp-100) REVERT: D 258 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7502 (tt0) outliers start: 55 outliers final: 32 residues processed: 529 average time/residue: 0.7887 time to fit residues: 450.8012 Evaluate side-chains 541 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 505 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 60 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 193 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 180 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3504 r_free = 0.3504 target = 0.115458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.103081 restraints weight = 32710.081| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.49 r_work: 0.3192 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.176 16499 Z= 0.180 Angle : 0.712 29.166 22243 Z= 0.331 Chirality : 0.046 0.171 2336 Planarity : 0.005 0.046 2858 Dihedral : 5.212 63.488 2527 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.96 % Allowed : 21.36 % Favored : 75.68 % 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: 0.68 (0.19), residues: 1992 helix: 1.35 (0.17), residues: 1004 sheet: -0.47 (0.35), residues: 200 loop : -0.39 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 187 TYR 0.017 0.002 TYR D 88 PHE 0.020 0.001 PHE C 431 TRP 0.014 0.002 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00406 (16483) covalent geometry : angle 0.71164 (22243) hydrogen bonds : bond 0.04889 ( 774) hydrogen bonds : angle 5.43458 ( 2226) Misc. bond : bond 0.07737 ( 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 555 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 504 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8335 (mt) REVERT: A 234 ASP cc_start: 0.7628 (m-30) cc_final: 0.7400 (m-30) REVERT: A 320 ILE cc_start: 0.8545 (mm) cc_final: 0.8337 (mm) REVERT: A 332 LYS cc_start: 0.8469 (tttp) cc_final: 0.8233 (tttp) REVERT: A 393 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: A 474 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7788 (mtpp) REVERT: B 258 GLU cc_start: 0.7650 (pt0) cc_final: 0.7414 (tt0) REVERT: C 35 ASN cc_start: 0.8517 (t0) cc_final: 0.8279 (t0) REVERT: C 151 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8137 (mp10) REVERT: D 45 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7818 (tp-100) REVERT: D 221 ASN cc_start: 0.8477 (p0) cc_final: 0.8224 (p0) REVERT: D 258 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7493 (tt0) outliers start: 51 outliers final: 34 residues processed: 521 average time/residue: 0.7823 time to fit residues: 441.2757 Evaluate side-chains 534 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 495 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 334 GLU 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 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: 0.7980 chunk 101 optimal weight: 0.6980 chunk 175 optimal weight: 0.3980 chunk 129 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 184 optimal weight: 0.2980 chunk 180 optimal weight: 0.5980 chunk 154 optimal weight: 0.8980 chunk 167 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 252 GLN A 298 ASN 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 ** 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 = 0.3510 r_free = 0.3510 target = 0.115822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105103 restraints weight = 20952.823| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.10 r_work: 0.3251 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 16499 Z= 0.163 Angle : 0.711 29.164 22243 Z= 0.330 Chirality : 0.045 0.154 2336 Planarity : 0.005 0.046 2858 Dihedral : 5.006 64.223 2525 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.66 % Allowed : 21.24 % Favored : 75.10 % 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: 1.40 (0.17), residues: 1004 sheet: -0.49 (0.35), residues: 200 loop : -0.38 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 187 TYR 0.015 0.002 TYR C 401 PHE 0.019 0.001 PHE C 412 TRP 0.013 0.001 TRP C 335 HIS 0.009 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00361 (16483) covalent geometry : angle 0.71085 (22243) hydrogen bonds : bond 0.04662 ( 774) hydrogen bonds : angle 5.38401 ( 2226) Misc. bond : bond 0.07384 ( 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 559 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 496 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8329 (mt) REVERT: A 234 ASP cc_start: 0.7553 (m-30) cc_final: 0.7346 (m-30) REVERT: A 393 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: A 474 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7700 (mtpp) REVERT: B 258 GLU cc_start: 0.7512 (pt0) cc_final: 0.7244 (tt0) REVERT: C 35 ASN cc_start: 0.8457 (t0) cc_final: 0.8222 (t0) REVERT: C 263 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7582 (mt-10) REVERT: D 45 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7696 (tp-100) REVERT: D 258 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7355 (tt0) outliers start: 63 outliers final: 32 residues processed: 516 average time/residue: 0.8000 time to fit residues: 447.1938 Evaluate side-chains 525 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 489 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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 393 GLU 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 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 392 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 4 optimal weight: 0.0970 chunk 140 optimal weight: 0.4980 chunk 174 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 106 optimal weight: 0.0020 chunk 37 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 252 GLN A 432 GLN B 128 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.104175 restraints weight = 33980.223| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.54 r_work: 0.3208 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 16499 Z= 0.144 Angle : 0.702 29.128 22243 Z= 0.324 Chirality : 0.044 0.152 2336 Planarity : 0.005 0.042 2858 Dihedral : 4.933 64.294 2525 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.96 % Allowed : 22.23 % Favored : 74.81 % 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: 0.77 (0.19), residues: 1992 helix: 1.42 (0.17), residues: 1010 sheet: -0.46 (0.35), residues: 200 loop : -0.34 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 187 TYR 0.017 0.001 TYR C 401 PHE 0.018 0.001 PHE C 431 TRP 0.013 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00311 (16483) covalent geometry : angle 0.70217 (22243) hydrogen bonds : bond 0.04347 ( 774) hydrogen bonds : angle 5.31604 ( 2226) Misc. bond : bond 0.06932 ( 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 537 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 486 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8363 (mt) REVERT: A 234 ASP cc_start: 0.7667 (m-30) cc_final: 0.7460 (m-30) REVERT: A 393 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: A 474 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7778 (mtpp) REVERT: C 35 ASN cc_start: 0.8496 (t0) cc_final: 0.8262 (t0) REVERT: C 323 LYS cc_start: 0.8192 (mtmt) cc_final: 0.7986 (mttp) REVERT: D 45 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7856 (tp-100) REVERT: D 258 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7515 (tt0) outliers start: 51 outliers final: 26 residues processed: 503 average time/residue: 0.7885 time to fit residues: 429.3895 Evaluate side-chains 512 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 482 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 393 GLU 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 131 optimal weight: 0.9980 chunk 146 optimal weight: 0.0070 chunk 88 optimal weight: 0.0370 chunk 4 optimal weight: 0.0770 chunk 100 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 197 optimal weight: 0.5980 chunk 156 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 252 GLN A 362 HIS B 163 ASN B 167 ASN C 98 ASN C 151 GLN ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.108018 restraints weight = 22561.211| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.19 r_work: 0.3289 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 16499 Z= 0.118 Angle : 0.684 29.084 22243 Z= 0.313 Chirality : 0.043 0.143 2336 Planarity : 0.004 0.041 2858 Dihedral : 4.737 63.306 2525 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.55 % Allowed : 22.98 % Favored : 74.46 % 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: 0.99 (0.19), residues: 1992 helix: 1.61 (0.17), residues: 1002 sheet: -0.31 (0.36), residues: 196 loop : -0.24 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 238 TYR 0.018 0.001 TYR C 401 PHE 0.016 0.001 PHE C 431 TRP 0.014 0.001 TRP A 335 HIS 0.006 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00246 (16483) covalent geometry : angle 0.68378 (22243) hydrogen bonds : bond 0.03668 ( 774) hydrogen bonds : angle 5.14572 ( 2226) Misc. bond : bond 0.05740 ( 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 539 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 495 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 336 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7567 (mt-10) REVERT: A 474 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7667 (mtpp) REVERT: B 258 GLU cc_start: 0.7601 (tt0) cc_final: 0.7373 (tt0) REVERT: C 19 VAL cc_start: 0.7618 (OUTLIER) cc_final: 0.7410 (t) REVERT: C 35 ASN cc_start: 0.8470 (t0) cc_final: 0.8214 (t0) REVERT: C 323 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7951 (mttp) REVERT: C 407 TYR cc_start: 0.7649 (t80) cc_final: 0.7386 (t80) REVERT: D 45 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7686 (tp-100) REVERT: D 258 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: D 372 ASP cc_start: 0.7503 (m-30) cc_final: 0.7292 (m-30) outliers start: 44 outliers final: 18 residues processed: 512 average time/residue: 0.7718 time to fit residues: 428.0761 Evaluate side-chains 508 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 487 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL 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 362 HIS 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 351 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 26 LYS 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 400 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 24 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 73 optimal weight: 0.0570 chunk 42 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 98 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 252 GLN A 362 HIS B 163 ASN B 167 ASN C 98 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.117656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.106594 restraints weight = 20528.247| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.11 r_work: 0.3271 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- 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 = 0.35 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 = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1594 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= 0.157 Angle : 0.719 29.134 22243 Z= 0.334 Chirality : 0.045 0.154 2336 Planarity : 0.005 0.044 2858 Dihedral : 4.750 64.597 2523 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.15 % Allowed : 23.68 % Favored : 74.17 % 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: 0.91 (0.19), residues: 1992 helix: 1.52 (0.17), residues: 1002 sheet: -0.29 (0.36), residues: 196 loop : -0.27 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 108 TYR 0.021 0.002 TYR C 221 PHE 0.018 0.001 PHE C 412 TRP 0.014 0.001 TRP A 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00351 (16483) covalent geometry : angle 0.71943 (22243) hydrogen bonds : bond 0.04391 ( 774) hydrogen bonds : angle 5.23995 ( 2226) Misc. bond : bond 0.06725 ( 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 530 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 493 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8614 (mp) cc_final: 0.8358 (mt) REVERT: A 336 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7568 (mt-10) REVERT: A 354 TYR cc_start: 0.8485 (t80) cc_final: 0.8230 (t80) REVERT: A 474 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7637 (mtpp) REVERT: C 35 ASN cc_start: 0.8462 (t0) cc_final: 0.8218 (t0) REVERT: C 151 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8066 (mp10) REVERT: C 263 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7469 (mt-10) REVERT: D 258 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7346 (tt0) REVERT: D 414 PRO cc_start: 0.8542 (Cg_endo) cc_final: 0.8321 (Cg_exo) outliers start: 37 outliers final: 20 residues processed: 501 average time/residue: 0.7996 time to fit residues: 433.0896 Evaluate side-chains 510 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 487 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 77 ASP Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 362 HIS 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 151 GLN 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 109 optimal weight: 0.7980 chunk 152 optimal weight: 0.0770 chunk 133 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 177 optimal weight: 0.1980 chunk 120 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN 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 432 GLN D 167 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.117671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105645 restraints weight = 26500.188| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.33 r_work: 0.3243 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 16499 Z= 0.157 Angle : 0.733 29.140 22243 Z= 0.341 Chirality : 0.046 0.157 2336 Planarity : 0.005 0.043 2858 Dihedral : 4.774 64.570 2523 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.63 % Allowed : 24.20 % Favored : 74.17 % 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: 0.83 (0.19), residues: 1992 helix: 1.47 (0.17), residues: 1004 sheet: -0.30 (0.36), residues: 196 loop : -0.33 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 108 TYR 0.018 0.002 TYR C 401 PHE 0.017 0.001 PHE C 412 TRP 0.017 0.001 TRP A 253 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00350 (16483) covalent geometry : angle 0.73338 (22243) hydrogen bonds : bond 0.04403 ( 774) hydrogen bonds : angle 5.27017 ( 2226) Misc. bond : bond 0.06770 ( 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 520 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 492 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8622 (mp) cc_final: 0.8367 (mt) REVERT: A 336 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7641 (mt-10) REVERT: A 380 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6842 (tp30) REVERT: A 474 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7717 (mtpp) REVERT: B 330 MET cc_start: 0.8649 (mtp) cc_final: 0.8398 (mtp) REVERT: C 35 ASN cc_start: 0.8459 (t0) cc_final: 0.8187 (t0) REVERT: C 263 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7511 (mt-10) REVERT: C 325 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7453 (mm-30) REVERT: D 258 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: D 414 PRO cc_start: 0.8567 (Cg_endo) cc_final: 0.8358 (Cg_exo) outliers start: 28 outliers final: 21 residues processed: 500 average time/residue: 0.8107 time to fit residues: 437.9493 Evaluate side-chains 511 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 488 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 77 ASP Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 432 GLN 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 83 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 chunk 134 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 106 optimal weight: 0.0570 chunk 147 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** D 163 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 = 0.3538 r_free = 0.3538 target = 0.117723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.105723 restraints weight = 26503.270| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.33 r_work: 0.3244 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1635 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= 0.153 Angle : 0.732 29.128 22243 Z= 0.341 Chirality : 0.045 0.156 2336 Planarity : 0.005 0.044 2858 Dihedral : 4.773 64.636 2523 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.92 % Allowed : 23.80 % Favored : 74.29 % 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: 0.82 (0.19), residues: 1992 helix: 1.47 (0.17), residues: 1004 sheet: -0.34 (0.36), residues: 196 loop : -0.34 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 108 TYR 0.019 0.002 TYR C 401 PHE 0.017 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 covalent geometry : bond 0.00337 (16483) covalent geometry : angle 0.73160 (22243) hydrogen bonds : bond 0.04342 ( 774) hydrogen bonds : angle 5.27568 ( 2226) Misc. bond : bond 0.06726 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9222.75 seconds wall clock time: 157 minutes 6.11 seconds (9426.11 seconds total)