Starting phenix.real_space_refine on Mon May 4 06:37:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11nd_75857/05_2026/11nd_75857.cif Found real_map, /net/cci-nas-00/data/ceres_data/11nd_75857/05_2026/11nd_75857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11nd_75857/05_2026/11nd_75857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11nd_75857/05_2026/11nd_75857.map" model { file = "/net/cci-nas-00/data/ceres_data/11nd_75857/05_2026/11nd_75857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11nd_75857/05_2026/11nd_75857.cif" } resolution = 2.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 5607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18652 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: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 660 Classifications: {'water': 660} Link IDs: {None: 659} Chain: "B" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 655 Classifications: {'water': 655} Link IDs: {None: 654} Chain: "C" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 671 Classifications: {'water': 671} Link IDs: {None: 670} Chain: "D" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 639 Classifications: {'water': 639} Link IDs: {None: 638} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 30.613 45.757 60.431 1.00 29.16 S ATOM 1170 SG CYS A 154 36.633 27.415 48.317 1.00 13.66 S ATOM 4552 SG CYS B 95 39.772 30.599 45.132 1.00 15.65 S ATOM 465 SG CYS A 62 36.998 33.372 50.578 1.00 8.44 S ATOM 652 SG CYS A 88 42.348 29.241 50.626 1.00 11.52 S ATOM 652 SG CYS A 88 42.348 29.241 50.626 1.00 11.52 S ATOM 5005 SG CYS B 153 40.960 25.219 46.669 1.00 12.62 S ATOM 4372 SG CYS B 70 46.578 29.555 45.054 1.00 11.06 S ATOM 4552 SG CYS B 95 39.772 30.599 45.132 1.00 15.65 S ATOM 10056 SG CYS C 275 107.529 57.124 60.463 1.00 29.99 S ATOM 12516 SG CYS D 95 98.306 72.345 45.063 1.00 18.23 S ATOM 9134 SG CYS C 154 101.625 75.565 48.308 1.00 13.03 S ATOM 8429 SG CYS C 62 101.226 69.506 50.679 1.00 8.65 S ATOM 8616 SG CYS C 88 95.773 73.746 50.699 1.00 14.75 S ATOM 8616 SG CYS C 88 95.773 73.746 50.699 1.00 14.75 S ATOM 12969 SG CYS D 153 97.199 77.674 46.655 1.00 15.68 S ATOM 12336 SG CYS D 70 91.709 73.492 45.231 1.00 14.61 S ATOM 12516 SG CYS D 95 98.306 72.345 45.063 1.00 18.23 S Time building chain proxies: 6.36, per 1000 atoms: 0.34 Number of scatterers: 18652 At special positions: 0 Unit cell: (138.915, 103.635, 99.96, 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 5607 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: 1.74 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 109 helices and 12 sheets defined 59.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 29 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 92 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: 3.839A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.613A 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: 4.006A 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: 5.972A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.686A pdb=" N LYS A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 343 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.883A pdb=" N HIS A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 383 through 394 removed outlier: 3.954A 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: 4.556A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.673A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.820A 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 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 80 removed outlier: 4.084A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.027A 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 212 through 216 removed outlier: 4.040A pdb=" N ASP B 215 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.845A 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 320 through 337 removed outlier: 4.230A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.131A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.919A 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: 3.512A pdb=" N GLY B 416 " --> pdb=" O SER B 413 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 413 through 417' Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 447 through 459 removed outlier: 4.412A 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 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 29 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 92 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: 3.873A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.700A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.251A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (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: 4.019A 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: 5.937A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 315 removed outlier: 3.651A pdb=" N LYS C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 343 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 344 through 346 No H-bonds generated for 'chain 'C' and resid 344 through 346' Processing helix chain 'C' and resid 358 through 363 removed outlier: 3.891A pdb=" N HIS C 362 " --> pdb=" O LEU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 370 Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.458A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 435 removed outlier: 4.082A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.382A 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: 3.660A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.879A pdb=" N LYS C 474 " --> pdb=" O CYS C 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 70 through 80 removed outlier: 4.056A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.065A 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 212 through 216 removed outlier: 4.127A pdb=" N ASP D 215 " --> pdb=" O SER D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.845A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 4.183A pdb=" N THR D 263 " --> pdb=" O VAL D 260 " (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: 5.151A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.964A 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: 3.515A pdb=" N GLY D 416 " --> pdb=" O SER D 413 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS D 417 " --> pdb=" O PRO D 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 413 through 417' Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 447 through 459 removed outlier: 4.370A 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 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.265A pdb=" N LYS A 349 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL A 375 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 351 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N THR A 377 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 353 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N TYR A 379 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.356A 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: 6.944A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.190A 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: 7.030A pdb=" N VAL A 223 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N TRP A 253 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE A 225 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASP A 222 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU A 272 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA A 224 " --> pdb=" O LEU A 272 " (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: 6.606A pdb=" N ILE B 224 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.406A 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: 8.538A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET B 442 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.519A pdb=" N LEU C 353 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR C 377 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.387A 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: 6.952A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.197A 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: 7.181A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE C 225 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASP C 222 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU C 272 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 6.386A 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: 6.628A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.398A 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: 8.499A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N MET D 442 " --> pdb=" O ILE D 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 780 hydrogen bonds defined for protein. 2232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.85: 16347 1.85 - 2.48: 104 2.48 - 3.12: 25 3.12 - 3.75: 5 3.75 - 4.39: 2 Bond restraints: 16483 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 4.389 -2.189 2.00e-02 2.50e+03 1.20e+04 bond pdb="FE5 CLF D 602 " pdb="FE6 CLF D 602 " ideal model delta sigma weight residual 2.200 3.895 -1.695 2.00e-02 2.50e+03 7.19e+03 bond pdb=" S1 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 3.627 -1.427 2.00e-02 2.50e+03 5.09e+03 bond pdb=" S1 CLF D 602 " pdb="FE6 CLF D 602 " ideal model delta sigma weight residual 2.200 3.612 -1.412 2.00e-02 2.50e+03 4.98e+03 bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 3.560 -1.360 2.00e-02 2.50e+03 4.62e+03 ... (remaining 16478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.90: 22235 6.90 - 13.79: 2 13.79 - 20.69: 2 20.69 - 27.58: 0 27.58 - 34.48: 4 Bond angle restraints: 22243 Sorted by residual: angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE4 CLF B 602 " ideal model delta sigma weight residual 90.00 55.52 34.48 3.00e+00 1.11e-01 1.32e+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 55.54 34.46 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE1 CLF B 602 " ideal model delta sigma weight residual 90.00 57.08 32.92 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 60.93 29.07 3.00e+00 1.11e-01 9.39e+01 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE3 CLF D 602 " ideal model delta sigma weight residual 90.00 108.21 -18.21 3.00e+00 1.11e-01 3.69e+01 ... (remaining 22238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 9226 17.94 - 35.88: 708 35.88 - 53.82: 102 53.82 - 71.76: 31 71.76 - 89.69: 34 Dihedral angle restraints: 10101 sinusoidal: 4359 harmonic: 5742 Sorted by residual: dihedral pdb=" CA SER D 11 " pdb=" C SER D 11 " pdb=" N TYR D 12 " pdb=" CA TYR D 12 " ideal model delta harmonic sigma weight residual 180.00 159.98 20.02 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA SER B 11 " pdb=" C SER B 11 " pdb=" N TYR B 12 " pdb=" CA TYR B 12 " ideal model delta harmonic sigma weight residual 180.00 160.36 19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" C TYR A 379 " pdb=" N TYR A 379 " pdb=" CA TYR A 379 " pdb=" CB TYR A 379 " ideal model delta harmonic sigma weight residual -122.60 -113.42 -9.18 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1641 0.053 - 0.105: 533 0.105 - 0.158: 128 0.158 - 0.210: 29 0.210 - 0.263: 5 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA TYR A 379 " pdb=" N TYR A 379 " pdb=" C TYR A 379 " pdb=" CB TYR A 379 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA GLN A 321 " pdb=" N GLN A 321 " pdb=" C GLN A 321 " pdb=" CB GLN A 321 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA LEU A 400 " pdb=" N LEU A 400 " pdb=" C LEU A 400 " pdb=" CB LEU A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2333 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP C 253 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" C TRP C 253 " -0.046 2.00e-02 2.50e+03 pdb=" O TRP C 253 " 0.017 2.00e-02 2.50e+03 pdb=" N SER C 254 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 400 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.33e+00 pdb=" C LEU C 400 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU C 400 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR C 401 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 469 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" CG ASN A 469 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 469 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 469 " -0.013 2.00e-02 2.50e+03 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1268 2.69 - 3.24: 19673 3.24 - 3.79: 35838 3.79 - 4.35: 49588 4.35 - 4.90: 73278 Nonbonded interactions: 179645 Sorted by model distance: nonbonded pdb=" OE2 GLU B 109 " pdb="FE FE D 601 " model vdw 2.136 2.260 nonbonded pdb=" OE2 GLU D 109 " pdb="FE FE B 601 " model vdw 2.145 2.260 nonbonded pdb=" O ARG B 108 " pdb="FE FE D 601 " model vdw 2.210 2.260 nonbonded pdb=" O ARG D 108 " pdb="FE FE B 601 " model vdw 2.215 2.260 nonbonded pdb=" OE2 GLU B 306 " pdb=" O HOH B 701 " model vdw 2.302 3.040 ... (remaining 179640 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' selection = chain 'D' } 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=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.710 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 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 : 0.038 2.189 16499 Z= 1.919 Angle : 0.949 34.478 22243 Z= 0.541 Chirality : 0.056 0.263 2336 Planarity : 0.006 0.070 2858 Dihedral : 14.002 89.695 6433 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.17 % Allowed : 1.86 % Favored : 97.97 % 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: 0.30 (0.18), residues: 1992 helix: 1.04 (0.16), residues: 984 sheet: -0.45 (0.37), residues: 174 loop : -0.59 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 277 TYR 0.024 0.003 TYR C 379 PHE 0.028 0.003 PHE A 429 TRP 0.032 0.003 TRP C 444 HIS 0.014 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.03765 (16483) covalent geometry : angle 0.94893 (22243) hydrogen bonds : bond 0.14727 ( 780) hydrogen bonds : angle 6.66131 ( 2232) Misc. bond : bond 0.14103 ( 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 287 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 284 time to evaluate : 0.726 Fit side-chains REVERT: A 15 GLU cc_start: 0.5762 (mt-10) cc_final: 0.5397 (tt0) REVERT: A 18 GLU cc_start: 0.6552 (mt-10) cc_final: 0.5846 (tt0) REVERT: A 26 LYS cc_start: 0.6768 (tttp) cc_final: 0.5935 (mmtt) REVERT: A 51 LYS cc_start: 0.7812 (ptmt) cc_final: 0.7391 (pttm) REVERT: A 129 LYS cc_start: 0.8272 (mttp) cc_final: 0.8023 (mtpp) REVERT: A 218 SER cc_start: 0.8489 (p) cc_final: 0.8087 (m) REVERT: A 243 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8194 (mp0) REVERT: A 322 LYS cc_start: 0.7968 (tttt) cc_final: 0.7391 (mmpt) REVERT: A 373 GLU cc_start: 0.7294 (mp0) cc_final: 0.6848 (pm20) REVERT: A 391 MET cc_start: 0.7142 (mtt) cc_final: 0.6808 (mtm) REVERT: A 415 ARG cc_start: 0.6217 (tpp80) cc_final: 0.5927 (mpt180) REVERT: A 476 GLN cc_start: 0.8325 (tp-100) cc_final: 0.8113 (tp40) REVERT: B 7 LYS cc_start: 0.7755 (tptm) cc_final: 0.7420 (tttm) REVERT: B 50 LYS cc_start: 0.8372 (mttm) cc_final: 0.8011 (mmmt) REVERT: B 177 ASP cc_start: 0.7725 (m-30) cc_final: 0.7524 (t70) REVERT: B 214 ASP cc_start: 0.7563 (m-30) cc_final: 0.7120 (p0) REVERT: B 315 LYS cc_start: 0.8501 (tppt) cc_final: 0.7747 (tptp) REVERT: B 400 LYS cc_start: 0.8593 (mttm) cc_final: 0.8377 (mptt) REVERT: B 417 LYS cc_start: 0.8102 (tttt) cc_final: 0.7801 (ttmm) REVERT: C 15 GLU cc_start: 0.5860 (mt-10) cc_final: 0.5414 (tt0) REVERT: C 18 GLU cc_start: 0.6000 (mm-30) cc_final: 0.5619 (tt0) REVERT: C 26 LYS cc_start: 0.6856 (mmpt) cc_final: 0.6219 (tttp) REVERT: C 51 LYS cc_start: 0.8248 (ptpt) cc_final: 0.7692 (pttm) REVERT: C 218 SER cc_start: 0.8479 (p) cc_final: 0.8028 (m) REVERT: C 373 GLU cc_start: 0.7355 (mp0) cc_final: 0.7024 (mp0) REVERT: C 415 ARG cc_start: 0.6393 (tpp80) cc_final: 0.6052 (mmp-170) REVERT: D 50 LYS cc_start: 0.8264 (mttp) cc_final: 0.7896 (mmmt) REVERT: D 60 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7547 (mm-30) REVERT: D 214 ASP cc_start: 0.7559 (m-30) cc_final: 0.7080 (p0) REVERT: D 315 LYS cc_start: 0.8166 (tptm) cc_final: 0.7927 (tppt) REVERT: D 400 LYS cc_start: 0.8530 (mttm) cc_final: 0.8202 (mptt) REVERT: D 417 LYS cc_start: 0.7994 (ttpp) cc_final: 0.7673 (ttmm) outliers start: 3 outliers final: 1 residues processed: 286 average time/residue: 0.8998 time to fit residues: 280.3404 Evaluate side-chains 212 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.2980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 53 GLN A 145 ASN A 199 ASN A 451 HIS A 469 ASN C 35 ASN C 53 GLN C 98 ASN C 199 ASN C 469 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.149716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122009 restraints weight = 13900.139| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 0.85 r_work: 0.3338 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.392 16499 Z= 0.228 Angle : 0.742 30.378 22243 Z= 0.360 Chirality : 0.046 0.163 2336 Planarity : 0.004 0.039 2858 Dihedral : 5.185 57.830 2518 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.87 % Allowed : 6.21 % Favored : 92.92 % 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: 0.65 (0.18), residues: 1992 helix: 1.28 (0.16), residues: 1008 sheet: -0.39 (0.38), residues: 176 loop : -0.37 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 277 TYR 0.019 0.002 TYR A 229 PHE 0.023 0.002 PHE A 431 TRP 0.014 0.002 TRP A 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00417 (16483) covalent geometry : angle 0.74156 (22243) hydrogen bonds : bond 0.05791 ( 780) hydrogen bonds : angle 5.58723 ( 2232) Misc. bond : bond 0.15858 ( 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 225 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.628 Fit side-chains REVERT: A 15 GLU cc_start: 0.5709 (mt-10) cc_final: 0.5311 (tt0) REVERT: A 18 GLU cc_start: 0.6546 (mt-10) cc_final: 0.5921 (tt0) REVERT: A 26 LYS cc_start: 0.6800 (tttp) cc_final: 0.6590 (tttp) REVERT: A 51 LYS cc_start: 0.7782 (ptmt) cc_final: 0.7356 (pttm) REVERT: A 218 SER cc_start: 0.8575 (p) cc_final: 0.8142 (m) REVERT: A 322 LYS cc_start: 0.7651 (tttt) cc_final: 0.7084 (mmpt) REVERT: A 373 GLU cc_start: 0.7215 (mp0) cc_final: 0.6886 (pm20) REVERT: A 391 MET cc_start: 0.6974 (mtt) cc_final: 0.6637 (mtp) REVERT: A 476 GLN cc_start: 0.8279 (tp-100) cc_final: 0.8064 (tp40) REVERT: B 7 LYS cc_start: 0.7818 (tptm) cc_final: 0.7521 (tttm) REVERT: B 50 LYS cc_start: 0.8333 (mttm) cc_final: 0.8013 (mmmt) REVERT: B 214 ASP cc_start: 0.7544 (m-30) cc_final: 0.7235 (p0) REVERT: B 315 LYS cc_start: 0.8624 (tppt) cc_final: 0.8010 (tptp) REVERT: B 417 LYS cc_start: 0.8236 (tttt) cc_final: 0.7977 (ttmm) REVERT: C 15 GLU cc_start: 0.5593 (mt-10) cc_final: 0.5181 (tt0) REVERT: C 18 GLU cc_start: 0.5871 (mm-30) cc_final: 0.5568 (tt0) REVERT: C 51 LYS cc_start: 0.8154 (ptpt) cc_final: 0.7566 (pttm) REVERT: C 288 GLU cc_start: 0.7275 (pt0) cc_final: 0.6949 (pt0) REVERT: C 373 GLU cc_start: 0.7132 (mp0) cc_final: 0.6828 (pm20) REVERT: C 388 ASP cc_start: 0.6738 (m-30) cc_final: 0.6499 (m-30) REVERT: C 393 GLU cc_start: 0.7047 (mm-30) cc_final: 0.5944 (mm-30) REVERT: C 415 ARG cc_start: 0.6320 (tpp80) cc_final: 0.6066 (mmp-170) REVERT: D 50 LYS cc_start: 0.8293 (mttp) cc_final: 0.8058 (mmmt) REVERT: D 60 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7596 (mm-30) REVERT: D 214 ASP cc_start: 0.7556 (m-30) cc_final: 0.7331 (p0) outliers start: 15 outliers final: 5 residues processed: 217 average time/residue: 0.8153 time to fit residues: 194.2766 Evaluate side-chains 198 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 193 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 130 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN A 362 HIS A 451 HIS B 104 ASN B 268 GLN C 53 GLN C 98 ASN D 268 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.148122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117965 restraints weight = 17417.487| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 0.98 r_work: 0.3285 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.382 16499 Z= 0.244 Angle : 0.756 30.887 22243 Z= 0.368 Chirality : 0.048 0.161 2336 Planarity : 0.005 0.042 2858 Dihedral : 5.178 55.813 2518 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.93 % Allowed : 7.02 % Favored : 92.05 % 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 (0.18), residues: 1992 helix: 1.33 (0.16), residues: 1008 sheet: -0.41 (0.38), residues: 176 loop : -0.39 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 277 TYR 0.020 0.002 TYR B 142 PHE 0.020 0.002 PHE A 431 TRP 0.013 0.002 TRP C 335 HIS 0.008 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00461 (16483) covalent geometry : angle 0.75551 (22243) hydrogen bonds : bond 0.06210 ( 780) hydrogen bonds : angle 5.51907 ( 2232) Misc. bond : bond 0.15971 ( 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 218 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.767 Fit side-chains REVERT: A 15 GLU cc_start: 0.5592 (mt-10) cc_final: 0.5247 (tt0) REVERT: A 18 GLU cc_start: 0.6553 (mt-10) cc_final: 0.5881 (tt0) REVERT: A 26 LYS cc_start: 0.6769 (tttp) cc_final: 0.6537 (tttp) REVERT: A 51 LYS cc_start: 0.7792 (ptmt) cc_final: 0.7329 (pttm) REVERT: A 129 LYS cc_start: 0.8338 (mtmt) cc_final: 0.7987 (mtpp) REVERT: A 218 SER cc_start: 0.8555 (p) cc_final: 0.8118 (m) REVERT: A 322 LYS cc_start: 0.7741 (tttt) cc_final: 0.7184 (ttpt) REVERT: A 358 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7588 (tp) REVERT: A 373 GLU cc_start: 0.7185 (mp0) cc_final: 0.6893 (pm20) REVERT: A 391 MET cc_start: 0.6973 (mtt) cc_final: 0.6627 (mtp) REVERT: A 476 GLN cc_start: 0.8319 (tp-100) cc_final: 0.8074 (tp40) REVERT: B 7 LYS cc_start: 0.7878 (tptm) cc_final: 0.7551 (tttm) REVERT: B 50 LYS cc_start: 0.8390 (mttm) cc_final: 0.7913 (mmmt) REVERT: B 214 ASP cc_start: 0.7564 (m-30) cc_final: 0.7260 (p0) REVERT: B 315 LYS cc_start: 0.8619 (tppt) cc_final: 0.7964 (tptp) REVERT: B 417 LYS cc_start: 0.8271 (tttt) cc_final: 0.7961 (ttmm) REVERT: C 15 GLU cc_start: 0.5654 (mt-10) cc_final: 0.5144 (tt0) REVERT: C 18 GLU cc_start: 0.5928 (mm-30) cc_final: 0.5579 (tt0) REVERT: C 51 LYS cc_start: 0.8192 (ptpt) cc_final: 0.7659 (pttm) REVERT: C 288 GLU cc_start: 0.7353 (pt0) cc_final: 0.7034 (pt0) REVERT: C 322 LYS cc_start: 0.7510 (ttpt) cc_final: 0.7088 (ttpt) REVERT: C 373 GLU cc_start: 0.7191 (mp0) cc_final: 0.6934 (pm20) REVERT: C 415 ARG cc_start: 0.6310 (tpp80) cc_final: 0.6023 (mmp-170) REVERT: D 50 LYS cc_start: 0.8372 (mttp) cc_final: 0.8093 (mmmt) REVERT: D 60 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7629 (mm-30) REVERT: D 214 ASP cc_start: 0.7639 (m-30) cc_final: 0.7292 (p0) REVERT: D 417 LYS cc_start: 0.8037 (ttmm) cc_final: 0.7682 (ttmt) outliers start: 16 outliers final: 5 residues processed: 208 average time/residue: 0.8156 time to fit residues: 186.3121 Evaluate side-chains 197 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 33 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 157 optimal weight: 8.9990 chunk 176 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 164 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 53 GLN A 98 ASN A 362 HIS B 268 GLN C 35 ASN C 53 GLN C 98 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.148049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118769 restraints weight = 15342.719| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 0.91 r_work: 0.3295 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.356 16499 Z= 0.239 Angle : 0.746 30.940 22243 Z= 0.363 Chirality : 0.047 0.169 2336 Planarity : 0.005 0.043 2858 Dihedral : 5.196 58.175 2518 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.87 % Allowed : 8.07 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.18), residues: 1992 helix: 1.39 (0.16), residues: 1008 sheet: -0.47 (0.35), residues: 192 loop : -0.36 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 277 TYR 0.019 0.002 TYR B 142 PHE 0.018 0.002 PHE A 431 TRP 0.013 0.002 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00455 (16483) covalent geometry : angle 0.74641 (22243) hydrogen bonds : bond 0.06025 ( 780) hydrogen bonds : angle 5.46216 ( 2232) Misc. bond : bond 0.15075 ( 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 209 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.743 Fit side-chains REVERT: A 15 GLU cc_start: 0.5672 (mt-10) cc_final: 0.5250 (tt0) REVERT: A 18 GLU cc_start: 0.6519 (mt-10) cc_final: 0.5931 (tt0) REVERT: A 26 LYS cc_start: 0.6756 (tttp) cc_final: 0.6517 (tttp) REVERT: A 51 LYS cc_start: 0.7773 (ptmt) cc_final: 0.7330 (pttm) REVERT: A 218 SER cc_start: 0.8488 (p) cc_final: 0.8079 (m) REVERT: A 322 LYS cc_start: 0.7697 (tttt) cc_final: 0.7187 (ttpt) REVERT: A 358 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7622 (tt) REVERT: A 373 GLU cc_start: 0.7200 (mp0) cc_final: 0.6961 (pm20) REVERT: A 476 GLN cc_start: 0.8299 (tp-100) cc_final: 0.8056 (tp40) REVERT: B 7 LYS cc_start: 0.7926 (tptm) cc_final: 0.7551 (tttm) REVERT: B 50 LYS cc_start: 0.8367 (mttm) cc_final: 0.7970 (mmmt) REVERT: B 214 ASP cc_start: 0.7599 (m-30) cc_final: 0.7245 (p0) REVERT: B 315 LYS cc_start: 0.8615 (tppt) cc_final: 0.7855 (tptp) REVERT: B 417 LYS cc_start: 0.8289 (tttt) cc_final: 0.8001 (ttmm) REVERT: C 15 GLU cc_start: 0.5715 (mt-10) cc_final: 0.5199 (tt0) REVERT: C 18 GLU cc_start: 0.5895 (mm-30) cc_final: 0.5565 (tt0) REVERT: C 51 LYS cc_start: 0.8189 (ptpt) cc_final: 0.7670 (pttm) REVERT: C 288 GLU cc_start: 0.7267 (pt0) cc_final: 0.6805 (pt0) REVERT: C 322 LYS cc_start: 0.7525 (ttpt) cc_final: 0.7101 (ttpt) REVERT: C 345 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7640 (mtp180) REVERT: C 373 GLU cc_start: 0.7181 (mp0) cc_final: 0.6959 (pm20) REVERT: C 391 MET cc_start: 0.7005 (mmm) cc_final: 0.6693 (mmm) REVERT: C 415 ARG cc_start: 0.6313 (tpp80) cc_final: 0.6039 (mmp-170) REVERT: D 50 LYS cc_start: 0.8383 (mttp) cc_final: 0.8106 (mmmt) REVERT: D 60 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7634 (mm-30) REVERT: D 214 ASP cc_start: 0.7647 (m-30) cc_final: 0.7377 (p0) outliers start: 15 outliers final: 6 residues processed: 202 average time/residue: 0.7951 time to fit residues: 177.1752 Evaluate side-chains 199 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 191 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 chunk 159 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN A 362 HIS B 268 GLN C 98 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114609 restraints weight = 21266.652| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.08 r_work: 0.3237 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.368 16499 Z= 0.282 Angle : 0.801 30.914 22243 Z= 0.396 Chirality : 0.050 0.192 2336 Planarity : 0.005 0.062 2858 Dihedral : 5.389 52.487 2518 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.28 % Allowed : 8.13 % Favored : 90.60 % 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: 0.60 (0.18), residues: 1992 helix: 1.26 (0.16), residues: 1010 sheet: -0.54 (0.35), residues: 192 loop : -0.38 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 277 TYR 0.022 0.002 TYR B 142 PHE 0.022 0.002 PHE A 431 TRP 0.013 0.002 TRP C 444 HIS 0.010 0.002 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00552 (16483) covalent geometry : angle 0.80051 (22243) hydrogen bonds : bond 0.07028 ( 780) hydrogen bonds : angle 5.58239 ( 2232) Misc. bond : bond 0.16844 ( 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 216 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.841 Fit side-chains REVERT: A 15 GLU cc_start: 0.5676 (mt-10) cc_final: 0.5289 (tt0) REVERT: A 18 GLU cc_start: 0.6546 (mt-10) cc_final: 0.5815 (tt0) REVERT: A 26 LYS cc_start: 0.6761 (tttp) cc_final: 0.6000 (mmtt) REVERT: A 51 LYS cc_start: 0.7801 (ptmt) cc_final: 0.7322 (pttm) REVERT: A 129 LYS cc_start: 0.8446 (mtmt) cc_final: 0.8092 (mtpp) REVERT: A 218 SER cc_start: 0.8512 (p) cc_final: 0.8102 (m) REVERT: A 322 LYS cc_start: 0.7772 (tttt) cc_final: 0.7259 (ttpt) REVERT: A 347 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7672 (tp30) REVERT: A 358 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7686 (tp) REVERT: A 373 GLU cc_start: 0.7268 (mp0) cc_final: 0.7014 (pm20) REVERT: A 391 MET cc_start: 0.6912 (mtp) cc_final: 0.6524 (mtp) REVERT: A 476 GLN cc_start: 0.8342 (tp-100) cc_final: 0.8136 (tp40) REVERT: B 7 LYS cc_start: 0.7963 (tptm) cc_final: 0.7588 (tttm) REVERT: B 50 LYS cc_start: 0.8456 (mttm) cc_final: 0.8070 (mmmt) REVERT: B 172 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: B 214 ASP cc_start: 0.7587 (m-30) cc_final: 0.7191 (p0) REVERT: B 315 LYS cc_start: 0.8631 (tppt) cc_final: 0.7835 (tptp) REVERT: B 417 LYS cc_start: 0.8328 (tttt) cc_final: 0.7990 (ttmm) REVERT: C 15 GLU cc_start: 0.5842 (mt-10) cc_final: 0.5241 (tt0) REVERT: C 18 GLU cc_start: 0.5871 (mm-30) cc_final: 0.5518 (tt0) REVERT: C 51 LYS cc_start: 0.8227 (ptpt) cc_final: 0.7668 (pttm) REVERT: C 322 LYS cc_start: 0.7601 (ttpt) cc_final: 0.7141 (ttpt) REVERT: C 373 GLU cc_start: 0.7231 (mp0) cc_final: 0.7004 (pm20) REVERT: C 391 MET cc_start: 0.6990 (mmm) cc_final: 0.6705 (mmm) REVERT: C 415 ARG cc_start: 0.6378 (tpp80) cc_final: 0.6036 (mmp-170) REVERT: D 50 LYS cc_start: 0.8467 (mttp) cc_final: 0.8112 (mmmt) REVERT: D 60 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7684 (mm-30) REVERT: D 214 ASP cc_start: 0.7682 (m-30) cc_final: 0.7369 (p0) REVERT: D 315 LYS cc_start: 0.8605 (tppt) cc_final: 0.7882 (tptp) outliers start: 22 outliers final: 5 residues processed: 203 average time/residue: 0.7933 time to fit residues: 177.6051 Evaluate side-chains 199 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 191 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 141 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN B 268 GLN C 35 ASN C 98 ASN D 104 ASN D 268 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.149987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.120230 restraints weight = 17695.847| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 0.97 r_work: 0.3313 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.323 16499 Z= 0.203 Angle : 0.706 30.813 22243 Z= 0.337 Chirality : 0.045 0.163 2336 Planarity : 0.004 0.044 2858 Dihedral : 5.082 57.518 2518 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.04 % Allowed : 8.53 % Favored : 90.42 % 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: 0.80 (0.19), residues: 1992 helix: 1.48 (0.17), residues: 1010 sheet: -0.53 (0.35), residues: 192 loop : -0.36 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.016 0.002 TYR A 229 PHE 0.017 0.001 PHE A 431 TRP 0.014 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00382 (16483) covalent geometry : angle 0.70551 (22243) hydrogen bonds : bond 0.05149 ( 780) hydrogen bonds : angle 5.33729 ( 2232) Misc. bond : bond 0.13041 ( 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 208 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.615 Fit side-chains REVERT: A 15 GLU cc_start: 0.5638 (mt-10) cc_final: 0.5218 (tt0) REVERT: A 18 GLU cc_start: 0.6347 (mt-10) cc_final: 0.5833 (tt0) REVERT: A 51 LYS cc_start: 0.7712 (ptmt) cc_final: 0.7270 (pttm) REVERT: A 129 LYS cc_start: 0.8324 (mtmt) cc_final: 0.7954 (mtpp) REVERT: A 218 SER cc_start: 0.8469 (p) cc_final: 0.8076 (m) REVERT: A 322 LYS cc_start: 0.7644 (tttt) cc_final: 0.7138 (ttpt) REVERT: A 358 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7626 (tp) REVERT: A 391 MET cc_start: 0.6670 (mtp) cc_final: 0.6283 (mtp) REVERT: A 415 ARG cc_start: 0.6734 (mmp-170) cc_final: 0.6346 (mmm160) REVERT: A 476 GLN cc_start: 0.8297 (tp-100) cc_final: 0.8057 (tp40) REVERT: B 7 LYS cc_start: 0.7939 (tptm) cc_final: 0.7502 (tttm) REVERT: B 50 LYS cc_start: 0.8406 (mttm) cc_final: 0.8007 (mmmt) REVERT: B 214 ASP cc_start: 0.7560 (m-30) cc_final: 0.7189 (p0) REVERT: B 315 LYS cc_start: 0.8620 (tppt) cc_final: 0.7893 (tptp) REVERT: B 417 LYS cc_start: 0.8322 (tttt) cc_final: 0.8014 (ttmm) REVERT: C 15 GLU cc_start: 0.5827 (mt-10) cc_final: 0.5233 (tt0) REVERT: C 18 GLU cc_start: 0.5846 (mm-30) cc_final: 0.5536 (tt0) REVERT: C 51 LYS cc_start: 0.8178 (ptpt) cc_final: 0.7558 (pttm) REVERT: C 322 LYS cc_start: 0.7528 (ttpt) cc_final: 0.7097 (ttpt) REVERT: C 345 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7578 (mtp180) REVERT: C 373 GLU cc_start: 0.7126 (mp0) cc_final: 0.6924 (pm20) REVERT: D 50 LYS cc_start: 0.8396 (mttp) cc_final: 0.8075 (mmmt) REVERT: D 60 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7620 (mm-30) REVERT: D 214 ASP cc_start: 0.7612 (m-30) cc_final: 0.7380 (p0) REVERT: D 315 LYS cc_start: 0.8593 (tppt) cc_final: 0.7888 (tptp) outliers start: 18 outliers final: 7 residues processed: 201 average time/residue: 0.8180 time to fit residues: 180.8384 Evaluate side-chains 198 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 189 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 401 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 137 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN B 268 GLN C 98 ASN D 268 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.145554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114983 restraints weight = 18434.701| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.01 r_work: 0.3244 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.370 16499 Z= 0.291 Angle : 0.808 30.883 22243 Z= 0.400 Chirality : 0.050 0.206 2336 Planarity : 0.005 0.060 2858 Dihedral : 5.375 59.539 2518 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.04 % Allowed : 8.88 % Favored : 90.08 % 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: 0.60 (0.18), residues: 1992 helix: 1.27 (0.16), residues: 1010 sheet: -0.59 (0.34), residues: 192 loop : -0.39 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 277 TYR 0.023 0.003 TYR B 142 PHE 0.024 0.002 PHE A 431 TRP 0.013 0.002 TRP C 444 HIS 0.010 0.002 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00569 (16483) covalent geometry : angle 0.80761 (22243) hydrogen bonds : bond 0.07170 ( 780) hydrogen bonds : angle 5.57672 ( 2232) Misc. bond : bond 0.16945 ( 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 213 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 0.722 Fit side-chains REVERT: A 15 GLU cc_start: 0.5834 (mt-10) cc_final: 0.5332 (tt0) REVERT: A 18 GLU cc_start: 0.6574 (mt-10) cc_final: 0.5956 (tt0) REVERT: A 51 LYS cc_start: 0.7797 (ptmt) cc_final: 0.7325 (pttm) REVERT: A 129 LYS cc_start: 0.8466 (mtmt) cc_final: 0.8120 (mtpp) REVERT: A 218 SER cc_start: 0.8529 (p) cc_final: 0.8137 (m) REVERT: A 322 LYS cc_start: 0.7776 (tttt) cc_final: 0.7264 (ttpt) REVERT: A 391 MET cc_start: 0.6832 (mtp) cc_final: 0.6499 (mmm) REVERT: A 476 GLN cc_start: 0.8311 (tp-100) cc_final: 0.8103 (tp40) REVERT: B 7 LYS cc_start: 0.8010 (tptm) cc_final: 0.7585 (tttm) REVERT: B 50 LYS cc_start: 0.8487 (mttm) cc_final: 0.8069 (mmmt) REVERT: B 214 ASP cc_start: 0.7569 (m-30) cc_final: 0.7176 (p0) REVERT: B 315 LYS cc_start: 0.8618 (tppt) cc_final: 0.7821 (tptp) REVERT: B 417 LYS cc_start: 0.8308 (tttt) cc_final: 0.7960 (ttmm) REVERT: C 15 GLU cc_start: 0.5876 (mt-10) cc_final: 0.5299 (tt0) REVERT: C 18 GLU cc_start: 0.5873 (mm-30) cc_final: 0.5490 (tt0) REVERT: C 51 LYS cc_start: 0.8195 (ptpt) cc_final: 0.7557 (pttm) REVERT: C 322 LYS cc_start: 0.7616 (ttpt) cc_final: 0.7144 (ttpt) REVERT: C 373 GLU cc_start: 0.7193 (mp0) cc_final: 0.6980 (pm20) REVERT: C 415 ARG cc_start: 0.6354 (tpp80) cc_final: 0.6060 (mmp-170) REVERT: D 50 LYS cc_start: 0.8493 (mttp) cc_final: 0.8087 (mmmt) REVERT: D 60 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7677 (mm-30) REVERT: D 214 ASP cc_start: 0.7637 (m-30) cc_final: 0.7354 (p0) REVERT: D 315 LYS cc_start: 0.8604 (tppt) cc_final: 0.7879 (tptp) outliers start: 18 outliers final: 9 residues processed: 207 average time/residue: 0.7882 time to fit residues: 179.8431 Evaluate side-chains 199 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 401 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 6 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 76 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN B 268 GLN C 35 ASN C 98 ASN D 268 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119995 restraints weight = 20659.692| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.05 r_work: 0.3310 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.312 16499 Z= 0.197 Angle : 0.699 30.794 22243 Z= 0.332 Chirality : 0.045 0.164 2336 Planarity : 0.004 0.044 2858 Dihedral : 4.979 56.281 2516 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.99 % Allowed : 9.34 % Favored : 89.67 % 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: 0.82 (0.19), residues: 1992 helix: 1.51 (0.17), residues: 1010 sheet: -0.56 (0.35), residues: 192 loop : -0.35 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.016 0.001 TYR A 229 PHE 0.018 0.001 PHE A 431 TRP 0.015 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00371 (16483) covalent geometry : angle 0.69891 (22243) hydrogen bonds : bond 0.04923 ( 780) hydrogen bonds : angle 5.31237 ( 2232) Misc. bond : bond 0.12508 ( 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 211 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.721 Fit side-chains REVERT: A 15 GLU cc_start: 0.5660 (mt-10) cc_final: 0.5197 (tt0) REVERT: A 18 GLU cc_start: 0.6316 (mt-10) cc_final: 0.5819 (tt0) REVERT: A 51 LYS cc_start: 0.7715 (ptmt) cc_final: 0.7257 (pttm) REVERT: A 129 LYS cc_start: 0.8323 (mtmt) cc_final: 0.7950 (mtpp) REVERT: A 218 SER cc_start: 0.8466 (p) cc_final: 0.8079 (m) REVERT: A 243 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8086 (mp0) REVERT: A 322 LYS cc_start: 0.7679 (tttt) cc_final: 0.7140 (ttpt) REVERT: A 391 MET cc_start: 0.6642 (mtp) cc_final: 0.6409 (mmm) REVERT: B 7 LYS cc_start: 0.7938 (tptm) cc_final: 0.7543 (tttm) REVERT: B 50 LYS cc_start: 0.8401 (mttm) cc_final: 0.7965 (mmmt) REVERT: B 51 GLU cc_start: 0.8062 (mp0) cc_final: 0.7804 (mp0) REVERT: B 214 ASP cc_start: 0.7544 (m-30) cc_final: 0.7195 (p0) REVERT: B 315 LYS cc_start: 0.8627 (tppt) cc_final: 0.7891 (tptp) REVERT: B 417 LYS cc_start: 0.8344 (tttt) cc_final: 0.8012 (ttmm) REVERT: C 15 GLU cc_start: 0.5824 (mt-10) cc_final: 0.5234 (tt0) REVERT: C 18 GLU cc_start: 0.5808 (mm-30) cc_final: 0.5495 (tt0) REVERT: C 51 LYS cc_start: 0.8169 (ptpt) cc_final: 0.7550 (pttm) REVERT: C 322 LYS cc_start: 0.7553 (ttpt) cc_final: 0.7107 (ttpt) REVERT: C 373 GLU cc_start: 0.7131 (mp0) cc_final: 0.6892 (pm20) REVERT: D 50 LYS cc_start: 0.8395 (mttp) cc_final: 0.8019 (mmmt) REVERT: D 60 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7597 (mm-30) REVERT: D 154 MET cc_start: 0.9234 (ttt) cc_final: 0.8978 (ttt) REVERT: D 214 ASP cc_start: 0.7617 (m-30) cc_final: 0.7385 (p0) REVERT: D 315 LYS cc_start: 0.8592 (tppt) cc_final: 0.7874 (tptp) outliers start: 17 outliers final: 9 residues processed: 204 average time/residue: 0.7885 time to fit residues: 177.4555 Evaluate side-chains 200 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 401 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 197 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN B 268 GLN C 98 ASN D 268 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.150550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.121156 restraints weight = 16504.294| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 0.95 r_work: 0.3328 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.308 16499 Z= 0.199 Angle : 0.699 30.810 22243 Z= 0.332 Chirality : 0.045 0.153 2336 Planarity : 0.004 0.043 2858 Dihedral : 4.871 56.995 2516 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.87 % Allowed : 9.52 % Favored : 89.61 % 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: 0.89 (0.19), residues: 1992 helix: 1.58 (0.17), residues: 1010 sheet: -0.52 (0.34), residues: 192 loop : -0.33 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.015 0.001 TYR B 88 PHE 0.015 0.001 PHE A 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 0.00376 (16483) covalent geometry : angle 0.69898 (22243) hydrogen bonds : bond 0.04996 ( 780) hydrogen bonds : angle 5.27775 ( 2232) Misc. bond : bond 0.12413 ( 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 209 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.758 Fit side-chains REVERT: A 15 GLU cc_start: 0.5596 (mt-10) cc_final: 0.5195 (tt0) REVERT: A 18 GLU cc_start: 0.6337 (mt-10) cc_final: 0.5818 (tt0) REVERT: A 51 LYS cc_start: 0.7682 (ptmt) cc_final: 0.7234 (pttm) REVERT: A 129 LYS cc_start: 0.8325 (mtmt) cc_final: 0.7981 (mtpp) REVERT: A 218 SER cc_start: 0.8430 (p) cc_final: 0.8091 (m) REVERT: A 243 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8074 (mp0) REVERT: A 322 LYS cc_start: 0.7621 (tttt) cc_final: 0.7095 (ttpt) REVERT: A 347 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7358 (tp30) REVERT: A 391 MET cc_start: 0.6668 (mtp) cc_final: 0.6421 (mmm) REVERT: A 415 ARG cc_start: 0.6666 (mmp-170) cc_final: 0.6460 (mmp80) REVERT: B 7 LYS cc_start: 0.7909 (tptm) cc_final: 0.7512 (tttm) REVERT: B 50 LYS cc_start: 0.8337 (mttm) cc_final: 0.7923 (mmmt) REVERT: B 51 GLU cc_start: 0.8059 (mp0) cc_final: 0.7815 (mp0) REVERT: B 214 ASP cc_start: 0.7526 (m-30) cc_final: 0.7185 (p0) REVERT: B 315 LYS cc_start: 0.8606 (tppt) cc_final: 0.7874 (tptp) REVERT: B 417 LYS cc_start: 0.8307 (tttt) cc_final: 0.7975 (ttmm) REVERT: C 15 GLU cc_start: 0.5812 (mt-10) cc_final: 0.5223 (tt0) REVERT: C 18 GLU cc_start: 0.5790 (mm-30) cc_final: 0.5512 (tt0) REVERT: C 51 LYS cc_start: 0.8162 (ptpt) cc_final: 0.7560 (pttm) REVERT: C 218 SER cc_start: 0.8591 (p) cc_final: 0.8106 (t) REVERT: C 322 LYS cc_start: 0.7511 (ttpt) cc_final: 0.7069 (ttpt) REVERT: C 347 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7581 (tp30) REVERT: C 373 GLU cc_start: 0.7073 (mp0) cc_final: 0.6868 (pm20) REVERT: C 415 ARG cc_start: 0.6305 (tpp80) cc_final: 0.6050 (mmp-170) REVERT: D 50 LYS cc_start: 0.8364 (mttp) cc_final: 0.8011 (mmmt) REVERT: D 60 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7589 (mm-30) REVERT: D 214 ASP cc_start: 0.7590 (m-30) cc_final: 0.7382 (p0) REVERT: D 315 LYS cc_start: 0.8586 (tppt) cc_final: 0.7881 (tptp) outliers start: 15 outliers final: 9 residues processed: 204 average time/residue: 0.8275 time to fit residues: 186.0338 Evaluate side-chains 202 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 401 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 142 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN B 268 GLN C 98 ASN D 268 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.147299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116831 restraints weight = 18440.489| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.01 r_work: 0.3270 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.346 16499 Z= 0.250 Angle : 0.759 30.902 22243 Z= 0.370 Chirality : 0.048 0.174 2336 Planarity : 0.005 0.053 2858 Dihedral : 5.118 55.705 2516 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.04 % Allowed : 9.58 % Favored : 89.38 % 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: 0.76 (0.18), residues: 1992 helix: 1.43 (0.16), residues: 1010 sheet: -0.51 (0.35), residues: 192 loop : -0.35 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 277 TYR 0.020 0.002 TYR B 142 PHE 0.020 0.002 PHE A 431 TRP 0.011 0.002 TRP A 335 HIS 0.008 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00480 (16483) covalent geometry : angle 0.75933 (22243) hydrogen bonds : bond 0.06292 ( 780) hydrogen bonds : angle 5.44290 ( 2232) Misc. bond : bond 0.15472 ( 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 210 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.722 Fit side-chains REVERT: A 15 GLU cc_start: 0.5786 (mt-10) cc_final: 0.5269 (tt0) REVERT: A 18 GLU cc_start: 0.6392 (mt-10) cc_final: 0.5848 (tt0) REVERT: A 51 LYS cc_start: 0.7759 (ptmt) cc_final: 0.7293 (pttm) REVERT: A 129 LYS cc_start: 0.8404 (mtmt) cc_final: 0.8041 (mtpp) REVERT: A 218 SER cc_start: 0.8482 (p) cc_final: 0.8108 (m) REVERT: A 322 LYS cc_start: 0.7744 (tttt) cc_final: 0.7215 (ttpt) REVERT: A 347 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: A 391 MET cc_start: 0.6732 (mtp) cc_final: 0.6438 (mmm) REVERT: B 7 LYS cc_start: 0.8016 (tptm) cc_final: 0.7582 (tttm) REVERT: B 50 LYS cc_start: 0.8385 (mttm) cc_final: 0.7957 (mmmt) REVERT: B 214 ASP cc_start: 0.7557 (m-30) cc_final: 0.7196 (p0) REVERT: B 315 LYS cc_start: 0.8613 (tppt) cc_final: 0.7854 (tptp) REVERT: B 417 LYS cc_start: 0.8316 (tttt) cc_final: 0.7968 (ttmm) REVERT: C 15 GLU cc_start: 0.5851 (mt-10) cc_final: 0.5273 (tt0) REVERT: C 18 GLU cc_start: 0.5785 (mm-30) cc_final: 0.5447 (tt0) REVERT: C 51 LYS cc_start: 0.8166 (ptpt) cc_final: 0.7538 (pttm) REVERT: C 322 LYS cc_start: 0.7595 (ttpt) cc_final: 0.7132 (ttpt) REVERT: C 347 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7581 (tp30) REVERT: C 415 ARG cc_start: 0.6332 (tpp80) cc_final: 0.6039 (mmp-170) REVERT: D 50 LYS cc_start: 0.8465 (mttp) cc_final: 0.8059 (mmmt) REVERT: D 60 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7621 (mm-30) REVERT: D 214 ASP cc_start: 0.7636 (m-30) cc_final: 0.7393 (p0) REVERT: D 315 LYS cc_start: 0.8595 (tppt) cc_final: 0.7874 (tptp) REVERT: D 507 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8893 (tt0) outliers start: 18 outliers final: 8 residues processed: 203 average time/residue: 0.7950 time to fit residues: 177.9373 Evaluate side-chains 201 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 140 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN B 268 GLN C 98 ASN D 268 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116466 restraints weight = 23825.242| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.13 r_work: 0.3261 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.333 16499 Z= 0.233 Angle : 0.742 30.910 22243 Z= 0.359 Chirality : 0.047 0.168 2336 Planarity : 0.005 0.050 2858 Dihedral : 5.048 52.031 2516 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.87 % Allowed : 9.75 % Favored : 89.38 % 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: 0.77 (0.18), residues: 1992 helix: 1.45 (0.16), residues: 1008 sheet: -0.52 (0.34), residues: 192 loop : -0.35 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 277 TYR 0.018 0.002 TYR B 142 PHE 0.023 0.002 PHE A 431 TRP 0.012 0.002 TRP A 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00445 (16483) covalent geometry : angle 0.74208 (22243) hydrogen bonds : bond 0.05880 ( 780) hydrogen bonds : angle 5.40387 ( 2232) Misc. bond : bond 0.14520 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9139.60 seconds wall clock time: 156 minutes 10.34 seconds (9370.34 seconds total)