Starting phenix.real_space_refine on Sat Jul 4 06:53:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11nd_75857/07_2026/11nd_75857.cif Found real_map, /net/cci-nas-00/data/ceres_data/11nd_75857/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/11nd_75857/07_2026/11nd_75857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11nd_75857/07_2026/11nd_75857.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11nd_75857/07_2026/11nd_75857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11nd_75857/07_2026/11nd_75857.map" } 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-dev-6108/lib/python3.11/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, 15 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "A" Number of atoms: 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: 5.71, per 1000 atoms: 0.31 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: 1.73 Conformation dependent library (CDL) restraints added in 866.5 milliseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 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: 0.59 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: 3.82 Time building geometry restraints manager: 2.19 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 3.000 nonbonded pdb=" OE2 GLU D 109 " pdb="FE FE B 601 " model vdw 2.145 3.000 nonbonded pdb=" O ARG B 108 " pdb="FE FE D 601 " model vdw 2.210 3.000 nonbonded pdb=" O ARG D 108 " pdb="FE FE B 601 " model vdw 2.215 3.000 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: 5.270 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: 0.050 Set scattering table: 0.060 Process input model: 20.460 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 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/Z covalent geometry : bond 0.03765 / 1.89 (16483) covalent geometry : angle 0.94893 / 0.54 (22243) hydrogen bonds : bond 0.14727 / 9.62 ( 780) hydrogen bonds : angle 6.66131 / 4.89 ( 2232) Misc. bond : bond 0.14103 / 10.33 ( 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 : 0.763 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: 0.8984 time to fit residues: 280.7642 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 : 0.763 ------------------------------------------------------------------------------- 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... A 35 ASN A 53 GLN A 145 ASN A 199 ASN A 451 HIS A 469 ASN C 35 ASN C 98 ASN C 199 ASN C 469 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122251 restraints weight = 13685.544| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 0.84 r_work: 0.3340 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 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 = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.391 16499 Z= 0.228 Angle : 0.742 30.981 22243 Z= 0.360 Chirality : 0.046 0.162 2336 Planarity : 0.004 0.039 2858 Dihedral : 5.185 57.713 2518 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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 0.022 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/Z covalent geometry : bond 0.00418 / 0.21 (16483) covalent geometry : angle 0.74184 / 0.36 (22243) hydrogen bonds : bond 0.05791 / 3.87 ( 780) hydrogen bonds : angle 5.61341 / 4.12 ( 2232) Misc. bond : bond 0.15974 / 10.41 ( 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 226 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 0.763 Fit side-chains REVERT: A 15 GLU cc_start: 0.5773 (mt-10) cc_final: 0.5388 (tt0) REVERT: A 18 GLU cc_start: 0.6593 (mt-10) cc_final: 0.5977 (tt0) REVERT: A 26 LYS cc_start: 0.6840 (tttp) cc_final: 0.6636 (tttp) REVERT: A 51 LYS cc_start: 0.7802 (ptmt) cc_final: 0.7373 (pttm) REVERT: A 218 SER cc_start: 0.8571 (p) cc_final: 0.8143 (m) REVERT: A 288 GLU cc_start: 0.6878 (pt0) cc_final: 0.6637 (pt0) REVERT: A 322 LYS cc_start: 0.7655 (tttt) cc_final: 0.7103 (mmpt) REVERT: A 373 GLU cc_start: 0.7231 (mp0) cc_final: 0.6913 (pm20) REVERT: A 391 MET cc_start: 0.6997 (mtt) cc_final: 0.6667 (mtp) REVERT: A 476 GLN cc_start: 0.8266 (tp-100) cc_final: 0.8050 (tp40) REVERT: B 7 LYS cc_start: 0.7825 (tptm) cc_final: 0.7521 (tttm) REVERT: B 50 LYS cc_start: 0.8329 (mttm) cc_final: 0.7979 (mmmt) REVERT: B 214 ASP cc_start: 0.7555 (m-30) cc_final: 0.7236 (p0) REVERT: B 315 LYS cc_start: 0.8627 (tppt) cc_final: 0.8007 (tptp) REVERT: B 417 LYS cc_start: 0.8233 (tttt) cc_final: 0.7966 (ttmm) REVERT: C 15 GLU cc_start: 0.5637 (mt-10) cc_final: 0.5231 (tt0) REVERT: C 18 GLU cc_start: 0.5914 (mm-30) cc_final: 0.5619 (tt0) REVERT: C 51 LYS cc_start: 0.8173 (ptpt) cc_final: 0.7588 (pttm) REVERT: C 288 GLU cc_start: 0.7269 (pt0) cc_final: 0.6931 (pt0) REVERT: C 373 GLU cc_start: 0.7147 (mp0) cc_final: 0.6850 (pm20) REVERT: C 388 ASP cc_start: 0.6788 (m-30) cc_final: 0.6554 (m-30) REVERT: C 393 GLU cc_start: 0.7078 (mm-30) cc_final: 0.5982 (mm-30) REVERT: C 415 ARG cc_start: 0.6337 (tpp80) cc_final: 0.6104 (mmp-170) REVERT: D 50 LYS cc_start: 0.8302 (mttp) cc_final: 0.8044 (mmmt) REVERT: D 60 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7592 (mm-30) REVERT: D 214 ASP cc_start: 0.7577 (m-30) cc_final: 0.7329 (p0) REVERT: D 400 LYS cc_start: 0.8593 (mttm) cc_final: 0.8387 (mptt) outliers start: 15 outliers final: 5 residues processed: 219 average time/residue: 0.7926 time to fit residues: 191.2721 Evaluate side-chains 202 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 197 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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: 0.9990 chunk 69 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3734 r_free = 0.3734 target = 0.148685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118819 restraints weight = 17170.727| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 0.95 r_work: 0.3295 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 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 = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.369 16499 Z= 0.236 Angle : 0.745 30.836 22243 Z= 0.362 Chirality : 0.047 0.156 2336 Planarity : 0.005 0.040 2858 Dihedral : 5.119 53.713 2518 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.93 % Allowed : 6.96 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 1992 helix: 1.36 (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 0.011 0.001 ARG A 277 TYR 0.019 0.002 TYR B 142 PHE 0.019 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/Z covalent geometry : bond 0.00447 / 0.22 (16483) covalent geometry : angle 0.74519 / 0.36 (22243) hydrogen bonds : bond 0.06015 / 4.02 ( 780) hydrogen bonds : angle 5.50750 / 4.04 ( 2232) Misc. bond : bond 0.15325 / 9.92 ( 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 215 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.761 Fit side-chains REVERT: A 15 GLU cc_start: 0.5666 (mt-10) cc_final: 0.5324 (tt0) REVERT: A 18 GLU cc_start: 0.6609 (mt-10) cc_final: 0.5950 (tt0) REVERT: A 26 LYS cc_start: 0.6829 (tttp) cc_final: 0.6604 (tttp) REVERT: A 51 LYS cc_start: 0.7812 (ptmt) cc_final: 0.7356 (pttm) REVERT: A 129 LYS cc_start: 0.8322 (mtmt) cc_final: 0.7977 (mtpp) REVERT: A 218 SER cc_start: 0.8550 (p) cc_final: 0.8121 (m) REVERT: A 322 LYS cc_start: 0.7742 (tttt) cc_final: 0.7216 (ttpt) REVERT: A 358 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7626 (tp) REVERT: A 373 GLU cc_start: 0.7201 (mp0) cc_final: 0.6932 (pm20) REVERT: A 391 MET cc_start: 0.7001 (mtt) cc_final: 0.6672 (mtp) REVERT: A 476 GLN cc_start: 0.8308 (tp-100) cc_final: 0.8063 (tp40) REVERT: B 7 LYS cc_start: 0.7866 (tptm) cc_final: 0.7539 (tttm) REVERT: B 50 LYS cc_start: 0.8406 (mttm) cc_final: 0.7918 (mmmt) REVERT: B 214 ASP cc_start: 0.7574 (m-30) cc_final: 0.7279 (p0) REVERT: B 315 LYS cc_start: 0.8631 (tppt) cc_final: 0.7906 (tptp) REVERT: B 417 LYS cc_start: 0.8266 (tttt) cc_final: 0.7969 (ttmm) REVERT: C 15 GLU cc_start: 0.5695 (mt-10) cc_final: 0.5205 (tt0) REVERT: C 18 GLU cc_start: 0.5983 (mm-30) cc_final: 0.5656 (tt0) REVERT: C 51 LYS cc_start: 0.8209 (ptpt) cc_final: 0.7693 (pttm) REVERT: C 288 GLU cc_start: 0.7374 (pt0) cc_final: 0.7043 (pt0) REVERT: C 322 LYS cc_start: 0.7536 (ttpt) cc_final: 0.7122 (ttpt) REVERT: C 373 GLU cc_start: 0.7196 (mp0) cc_final: 0.6967 (pm20) REVERT: C 391 MET cc_start: 0.7106 (mmm) cc_final: 0.6784 (mmm) REVERT: C 415 ARG cc_start: 0.6348 (tpp80) cc_final: 0.6088 (mmp-170) REVERT: D 50 LYS cc_start: 0.8379 (mttp) cc_final: 0.8089 (mmmt) REVERT: D 60 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7629 (mm-30) REVERT: D 214 ASP cc_start: 0.7655 (m-30) cc_final: 0.7332 (p0) REVERT: D 400 LYS cc_start: 0.8644 (mttm) cc_final: 0.8403 (mptt) REVERT: D 417 LYS cc_start: 0.7999 (ttmm) cc_final: 0.7663 (ttmt) outliers start: 16 outliers final: 4 residues processed: 207 average time/residue: 0.8358 time to fit residues: 190.4807 Evaluate side-chains 195 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 190 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 77 optimal weight: 0.7980 chunk 157 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 53 GLN A 98 ASN B 268 GLN C 35 ASN C 98 ASN D 104 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121035 restraints weight = 15228.463| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 0.90 r_work: 0.3325 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- 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 = 0.44 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 = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.336 16499 Z= 0.213 Angle : 0.714 30.869 22243 Z= 0.342 Chirality : 0.046 0.150 2336 Planarity : 0.004 0.040 2858 Dihedral : 4.968 53.620 2518 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.75 % Allowed : 8.18 % 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: 0.81 (0.19), residues: 1992 helix: 1.48 (0.16), residues: 1010 sheet: -0.47 (0.37), residues: 176 loop : -0.36 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 277 TYR 0.016 0.002 TYR A 229 PHE 0.017 0.002 PHE A 431 TRP 0.013 0.002 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 (16483) covalent geometry : angle 0.71395 / 0.34 (22243) hydrogen bonds : bond 0.05334 / 3.58 ( 780) hydrogen bonds : angle 5.37735 / 3.95 ( 2232) Misc. bond : bond 0.13551 / 8.84 ( 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: 13 poor density : 196 time to evaluate : 0.774 Fit side-chains REVERT: A 15 GLU cc_start: 0.5693 (mt-10) cc_final: 0.5273 (tt0) REVERT: A 18 GLU cc_start: 0.6525 (mt-10) cc_final: 0.6013 (tt0) REVERT: A 51 LYS cc_start: 0.7769 (ptmt) cc_final: 0.7329 (pttm) REVERT: A 129 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7938 (mtpp) REVERT: A 218 SER cc_start: 0.8466 (p) cc_final: 0.8058 (m) REVERT: A 358 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7659 (tp) REVERT: A 373 GLU cc_start: 0.7223 (mp0) cc_final: 0.6989 (pm20) REVERT: A 391 MET cc_start: 0.6942 (mtt) cc_final: 0.6593 (mtp) REVERT: A 417 LYS cc_start: 0.7622 (mttp) cc_final: 0.6843 (mtmt) REVERT: A 476 GLN cc_start: 0.8264 (tp-100) cc_final: 0.8029 (tp40) REVERT: B 7 LYS cc_start: 0.7845 (tptm) cc_final: 0.7495 (tttm) REVERT: B 50 LYS cc_start: 0.8339 (mttm) cc_final: 0.7943 (mmmt) REVERT: B 214 ASP cc_start: 0.7596 (m-30) cc_final: 0.7238 (p0) REVERT: B 315 LYS cc_start: 0.8613 (tppt) cc_final: 0.7904 (tptp) REVERT: B 417 LYS cc_start: 0.8279 (tttt) cc_final: 0.7994 (ttmm) REVERT: C 15 GLU cc_start: 0.5667 (mt-10) cc_final: 0.5156 (tt0) REVERT: C 18 GLU cc_start: 0.5895 (mm-30) cc_final: 0.5597 (tt0) REVERT: C 51 LYS cc_start: 0.8191 (ptpt) cc_final: 0.7683 (pttm) REVERT: C 288 GLU cc_start: 0.7241 (pt0) cc_final: 0.6786 (pt0) REVERT: C 322 LYS cc_start: 0.7513 (ttpt) cc_final: 0.7099 (ttpt) REVERT: C 373 GLU cc_start: 0.7136 (mp0) cc_final: 0.6922 (pm20) REVERT: C 415 ARG cc_start: 0.6337 (tpp80) cc_final: 0.6073 (mmp-170) REVERT: D 50 LYS cc_start: 0.8339 (mttp) cc_final: 0.8085 (mmmt) REVERT: D 60 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7613 (mm-30) REVERT: D 214 ASP cc_start: 0.7631 (m-30) cc_final: 0.7366 (p0) REVERT: D 315 LYS cc_start: 0.8566 (tppt) cc_final: 0.7890 (tptp) REVERT: D 400 LYS cc_start: 0.8628 (mttm) cc_final: 0.8418 (mptt) REVERT: D 417 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7685 (ttmt) outliers start: 13 outliers final: 6 residues processed: 201 average time/residue: 0.8133 time to fit residues: 180.6496 Evaluate side-chains 194 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 31 optimal weight: 0.7980 chunk 159 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN A 98 ASN B 268 GLN C 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.145679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114362 restraints weight = 21036.647| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.07 r_work: 0.3234 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.377 16499 Z= 0.299 Angle : 0.818 30.838 22243 Z= 0.407 Chirality : 0.051 0.200 2336 Planarity : 0.005 0.066 2858 Dihedral : 5.418 55.472 2518 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.45 % Allowed : 8.01 % Favored : 90.54 % 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: -0.56 (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 0.023 0.003 TYR B 142 PHE 0.023 0.003 PHE A 431 TRP 0.014 0.002 TRP C 444 HIS 0.010 0.002 HIS C 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.28 (16483) covalent geometry : angle 0.81782 / 0.41 (22243) hydrogen bonds : bond 0.07292 / 4.88 ( 780) hydrogen bonds : angle 5.61449 / 4.12 ( 2232) Misc. bond : bond 0.17267 / 10.81 ( 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 217 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.810 Fit side-chains REVERT: A 15 GLU cc_start: 0.5676 (mt-10) cc_final: 0.5292 (tt0) REVERT: A 18 GLU cc_start: 0.6553 (mt-10) cc_final: 0.5803 (tt0) REVERT: A 51 LYS cc_start: 0.7836 (ptmt) cc_final: 0.7192 (pttm) REVERT: A 129 LYS cc_start: 0.8457 (mtmt) cc_final: 0.8107 (mtpp) REVERT: A 218 SER cc_start: 0.8520 (p) cc_final: 0.8108 (m) REVERT: A 347 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7661 (tp30) REVERT: A 373 GLU cc_start: 0.7273 (mp0) cc_final: 0.7014 (pm20) REVERT: A 476 GLN cc_start: 0.8330 (tp-100) cc_final: 0.8126 (tp40) REVERT: B 7 LYS cc_start: 0.7960 (tptm) cc_final: 0.7638 (tttm) REVERT: B 50 LYS cc_start: 0.8460 (mttm) cc_final: 0.8085 (mmmt) REVERT: B 172 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: B 214 ASP cc_start: 0.7596 (m-30) cc_final: 0.7185 (p0) REVERT: B 315 LYS cc_start: 0.8638 (tppt) cc_final: 0.7850 (tptp) REVERT: B 417 LYS cc_start: 0.8319 (tttt) cc_final: 0.7971 (ttmm) REVERT: C 15 GLU cc_start: 0.5872 (mt-10) cc_final: 0.5269 (tt0) REVERT: C 18 GLU cc_start: 0.5908 (mm-30) cc_final: 0.5539 (tt0) REVERT: C 51 LYS cc_start: 0.8221 (ptpt) cc_final: 0.7661 (pttm) REVERT: C 322 LYS cc_start: 0.7614 (ttpt) cc_final: 0.7151 (ttpt) REVERT: C 373 GLU cc_start: 0.7248 (mp0) cc_final: 0.6865 (pm20) REVERT: C 415 ARG cc_start: 0.6382 (tpp80) cc_final: 0.6052 (mmp-170) REVERT: D 50 LYS cc_start: 0.8450 (mttp) cc_final: 0.8107 (mmmt) REVERT: D 60 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7669 (mm-30) REVERT: D 214 ASP cc_start: 0.7693 (m-30) cc_final: 0.7354 (p0) REVERT: D 315 LYS cc_start: 0.8606 (tppt) cc_final: 0.7892 (tptp) REVERT: D 400 LYS cc_start: 0.8732 (mttm) cc_final: 0.8489 (mptt) outliers start: 25 outliers final: 8 residues processed: 206 average time/residue: 0.7898 time to fit residues: 180.2726 Evaluate side-chains 197 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 187 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 172 GLU 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 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: 0.9990 chunk 48 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120387 restraints weight = 17498.536| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 0.96 r_work: 0.3317 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.324 16499 Z= 0.204 Angle : 0.706 30.816 22243 Z= 0.337 Chirality : 0.045 0.165 2336 Planarity : 0.004 0.045 2858 Dihedral : 5.032 57.928 2516 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.10 % Allowed : 8.65 % Favored : 90.25 % 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: 1.50 (0.17), residues: 1010 sheet: -0.53 (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 0.002 TYR A 229 PHE 0.018 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/Z covalent geometry : bond 0.00382 / 0.19 (16483) covalent geometry : angle 0.70555 / 0.34 (22243) hydrogen bonds : bond 0.05146 / 3.45 ( 780) hydrogen bonds : angle 5.34257 / 3.92 ( 2232) Misc. bond : bond 0.13089 / 8.49 ( 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: 19 poor density : 189 time to evaluate : 0.773 Fit side-chains REVERT: A 15 GLU cc_start: 0.5618 (mt-10) cc_final: 0.5228 (tt0) REVERT: A 18 GLU cc_start: 0.6355 (mt-10) cc_final: 0.5838 (tt0) REVERT: A 51 LYS cc_start: 0.7768 (ptmt) cc_final: 0.7325 (pttm) REVERT: A 129 LYS cc_start: 0.8316 (mtmt) cc_final: 0.7942 (mtpp) REVERT: A 218 SER cc_start: 0.8469 (p) cc_final: 0.8078 (m) REVERT: A 391 MET cc_start: 0.6824 (mtp) cc_final: 0.6415 (mtp) REVERT: A 415 ARG cc_start: 0.6754 (mmp-170) cc_final: 0.6370 (mmm160) REVERT: A 476 GLN cc_start: 0.8291 (tp-100) cc_final: 0.8054 (tp40) REVERT: B 7 LYS cc_start: 0.7890 (tptm) cc_final: 0.7504 (tttm) REVERT: B 50 LYS cc_start: 0.8401 (mttm) cc_final: 0.8016 (mmmt) REVERT: B 214 ASP cc_start: 0.7544 (m-30) cc_final: 0.7183 (p0) REVERT: B 315 LYS cc_start: 0.8608 (tppt) cc_final: 0.7888 (tptp) REVERT: B 417 LYS cc_start: 0.8331 (tttt) cc_final: 0.8023 (ttmm) REVERT: C 15 GLU cc_start: 0.5815 (mt-10) cc_final: 0.5224 (tt0) REVERT: C 18 GLU cc_start: 0.5831 (mm-30) cc_final: 0.5528 (tt0) REVERT: C 51 LYS cc_start: 0.8190 (ptpt) cc_final: 0.7567 (pttm) REVERT: C 322 LYS cc_start: 0.7527 (ttpt) cc_final: 0.7101 (ttpt) REVERT: C 373 GLU cc_start: 0.7130 (mp0) cc_final: 0.6926 (pm20) REVERT: D 50 LYS cc_start: 0.8388 (mttp) cc_final: 0.8070 (mmmt) REVERT: D 60 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7600 (mm-30) REVERT: D 214 ASP cc_start: 0.7621 (m-30) cc_final: 0.7383 (p0) REVERT: D 315 LYS cc_start: 0.8586 (tppt) cc_final: 0.7888 (tptp) REVERT: D 400 LYS cc_start: 0.8650 (mttm) cc_final: 0.8423 (mptt) outliers start: 19 outliers final: 7 residues processed: 200 average time/residue: 0.8035 time to fit residues: 177.8715 Evaluate side-chains 194 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 401 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 137 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 118 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 73 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3752 r_free = 0.3752 target = 0.150371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120362 restraints weight = 18463.004| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 0.99 r_work: 0.3315 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.318 16499 Z= 0.204 Angle : 0.704 30.832 22243 Z= 0.335 Chirality : 0.045 0.159 2336 Planarity : 0.004 0.044 2858 Dihedral : 4.888 54.469 2516 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.93 % Allowed : 9.00 % 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: 0.88 (0.19), residues: 1992 helix: 1.57 (0.17), residues: 1010 sheet: -0.54 (0.34), 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 0.015 0.002 TYR B 142 PHE 0.016 0.001 PHE A 431 TRP 0.012 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 (16483) covalent geometry : angle 0.70379 / 0.33 (22243) hydrogen bonds : bond 0.05121 / 3.44 ( 780) hydrogen bonds : angle 5.30113 / 3.88 ( 2232) Misc. bond : bond 0.12831 / 8.34 ( 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 208 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.785 Fit side-chains REVERT: A 15 GLU cc_start: 0.5575 (mt-10) cc_final: 0.5170 (tt0) REVERT: A 18 GLU cc_start: 0.6358 (mt-10) cc_final: 0.5819 (tt0) REVERT: A 51 LYS cc_start: 0.7730 (ptmt) cc_final: 0.7268 (pttm) REVERT: A 129 LYS cc_start: 0.8329 (mtmt) cc_final: 0.7994 (mtpp) REVERT: A 218 SER cc_start: 0.8429 (p) cc_final: 0.8076 (m) REVERT: A 243 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8166 (mp0) REVERT: A 322 LYS cc_start: 0.7779 (ttmm) cc_final: 0.6946 (mmmt) REVERT: A 358 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7658 (tt) REVERT: A 373 GLU cc_start: 0.7569 (pm20) cc_final: 0.7317 (pm20) REVERT: A 391 MET cc_start: 0.6647 (mtp) cc_final: 0.6255 (mtm) REVERT: A 415 ARG cc_start: 0.6708 (mmp-170) cc_final: 0.6489 (mmp80) REVERT: A 417 LYS cc_start: 0.7541 (mttp) cc_final: 0.6778 (mtmt) REVERT: A 476 GLN cc_start: 0.8291 (tp-100) cc_final: 0.8049 (tp40) REVERT: B 7 LYS cc_start: 0.7955 (tptm) cc_final: 0.7565 (tttm) REVERT: B 50 LYS cc_start: 0.8399 (mttm) cc_final: 0.7946 (mmmt) REVERT: B 214 ASP cc_start: 0.7533 (m-30) cc_final: 0.7181 (p0) REVERT: B 315 LYS cc_start: 0.8619 (tppt) cc_final: 0.7894 (tptp) REVERT: B 417 LYS cc_start: 0.8312 (tttt) cc_final: 0.7993 (ttmm) REVERT: C 15 GLU cc_start: 0.5755 (mt-10) cc_final: 0.5181 (tt0) REVERT: C 18 GLU cc_start: 0.5775 (mm-30) cc_final: 0.5481 (tt0) REVERT: C 51 LYS cc_start: 0.8183 (ptpt) cc_final: 0.7576 (pttm) REVERT: C 322 LYS cc_start: 0.7537 (ttpt) cc_final: 0.7109 (ttpt) REVERT: C 373 GLU cc_start: 0.7127 (mp0) cc_final: 0.6893 (pm20) REVERT: C 415 ARG cc_start: 0.6318 (tpp80) cc_final: 0.6029 (mmp-170) REVERT: D 50 LYS cc_start: 0.8394 (mttp) cc_final: 0.8085 (mmmt) REVERT: D 60 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7613 (mm-30) REVERT: D 214 ASP cc_start: 0.7630 (m-30) cc_final: 0.7398 (p0) REVERT: D 315 LYS cc_start: 0.8599 (tppt) cc_final: 0.7888 (tptp) REVERT: D 400 LYS cc_start: 0.8662 (mttm) cc_final: 0.8431 (mptt) outliers start: 16 outliers final: 6 residues processed: 201 average time/residue: 0.7879 time to fit residues: 175.3846 Evaluate side-chains 198 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 191 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 153 CYS 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: 0.9990 chunk 83 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 76 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN A 53 GLN A 98 ASN B 268 GLN 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 = 66)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120025 restraints weight = 20340.774| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.04 r_work: 0.3310 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.317 16499 Z= 0.202 Angle : 0.702 30.819 22243 Z= 0.333 Chirality : 0.045 0.150 2336 Planarity : 0.004 0.042 2858 Dihedral : 4.802 50.632 2516 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.99 % Allowed : 9.17 % Favored : 89.84 % 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: 0.90 (0.19), residues: 1992 helix: 1.59 (0.17), residues: 1010 sheet: -0.53 (0.36), residues: 176 loop : -0.35 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 96 TYR 0.015 0.002 TYR B 142 PHE 0.016 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/Z covalent geometry : bond 0.00381 / 0.19 (16483) covalent geometry : angle 0.70175 / 0.33 (22243) hydrogen bonds : bond 0.05064 / 3.40 ( 780) hydrogen bonds : angle 5.28454 / 3.87 ( 2232) Misc. bond : bond 0.12767 / 8.30 ( 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 208 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.772 Fit side-chains REVERT: A 15 GLU cc_start: 0.5598 (mt-10) cc_final: 0.5196 (tt0) REVERT: A 18 GLU cc_start: 0.6374 (mt-10) cc_final: 0.5849 (tt0) REVERT: A 51 LYS cc_start: 0.7731 (ptmt) cc_final: 0.7259 (pttm) REVERT: A 129 LYS cc_start: 0.8318 (mtmt) cc_final: 0.7972 (mtpp) REVERT: A 218 SER cc_start: 0.8418 (p) cc_final: 0.8076 (m) REVERT: A 243 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8176 (mp0) REVERT: A 321 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: A 322 LYS cc_start: 0.7771 (ttmm) cc_final: 0.6976 (mmmt) REVERT: A 358 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7657 (tt) REVERT: A 373 GLU cc_start: 0.7598 (pm20) cc_final: 0.7341 (pm20) REVERT: A 415 ARG cc_start: 0.6689 (mmp-170) cc_final: 0.6489 (mmp80) REVERT: A 476 GLN cc_start: 0.8309 (tp-100) cc_final: 0.8062 (tp40) REVERT: B 7 LYS cc_start: 0.7939 (tptm) cc_final: 0.7543 (tttm) REVERT: B 50 LYS cc_start: 0.8367 (mttm) cc_final: 0.7924 (mmmt) REVERT: B 172 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: B 214 ASP cc_start: 0.7551 (m-30) cc_final: 0.7185 (p0) REVERT: B 315 LYS cc_start: 0.8632 (tppt) cc_final: 0.7844 (tptp) REVERT: B 417 LYS cc_start: 0.8340 (tttt) cc_final: 0.7989 (ttmm) REVERT: C 15 GLU cc_start: 0.5787 (mt-10) cc_final: 0.5212 (tt0) REVERT: C 18 GLU cc_start: 0.5804 (mm-30) cc_final: 0.5513 (tt0) REVERT: C 51 LYS cc_start: 0.8188 (ptpt) cc_final: 0.7582 (pttm) REVERT: C 218 SER cc_start: 0.8619 (p) cc_final: 0.8109 (t) REVERT: C 322 LYS cc_start: 0.7555 (ttpt) cc_final: 0.7114 (ttpt) REVERT: C 373 GLU cc_start: 0.7107 (mp0) cc_final: 0.6874 (pm20) REVERT: C 415 ARG cc_start: 0.6318 (tpp80) cc_final: 0.6073 (mmp-170) REVERT: D 50 LYS cc_start: 0.8402 (mttp) cc_final: 0.8058 (mmmt) REVERT: D 60 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7621 (mm-30) REVERT: D 214 ASP cc_start: 0.7639 (m-30) cc_final: 0.7368 (p0) REVERT: D 315 LYS cc_start: 0.8598 (tppt) cc_final: 0.7876 (tptp) outliers start: 17 outliers final: 8 residues processed: 203 average time/residue: 0.8010 time to fit residues: 179.8941 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 : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN 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 401 TYR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 172 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 197 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN A 98 ASN B 268 GLN C 31 HIS 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 = 0.3691 r_free = 0.3691 target = 0.145013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.115178 restraints weight = 15956.822| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 0.94 r_work: 0.3249 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.403 16499 Z= 0.324 Angle : 0.850 30.735 22243 Z= 0.426 Chirality : 0.053 0.209 2336 Planarity : 0.006 0.063 2858 Dihedral : 5.393 53.718 2516 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.93 % Allowed : 9.46 % 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: 0.55 (0.18), residues: 1992 helix: 1.21 (0.16), residues: 1010 sheet: -0.62 (0.34), residues: 190 loop : -0.38 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 277 TYR 0.024 0.003 TYR B 142 PHE 0.028 0.003 PHE A 431 TRP 0.015 0.003 TRP C 444 HIS 0.011 0.002 HIS C 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.30 (16483) covalent geometry : angle 0.84968 / 0.43 (22243) hydrogen bonds : bond 0.07757 / 5.17 ( 780) hydrogen bonds : angle 5.65900 / 4.15 ( 2232) Misc. bond : bond 0.17784 / 10.98 ( 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: 16 poor density : 193 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.5821 (mt-10) cc_final: 0.5343 (tt0) REVERT: A 18 GLU cc_start: 0.6564 (mt-10) cc_final: 0.5951 (tt0) REVERT: A 51 LYS cc_start: 0.7823 (ptmt) cc_final: 0.7197 (pttm) REVERT: A 129 LYS cc_start: 0.8453 (mtmt) cc_final: 0.8114 (mtpp) REVERT: A 218 SER cc_start: 0.8498 (p) cc_final: 0.8129 (m) REVERT: A 347 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7411 (tp30) REVERT: A 476 GLN cc_start: 0.8288 (tp-100) cc_final: 0.8083 (tp40) REVERT: B 7 LYS cc_start: 0.8032 (tptm) cc_final: 0.7657 (tttm) REVERT: B 50 LYS cc_start: 0.8425 (mttm) cc_final: 0.8110 (mmmt) REVERT: B 214 ASP cc_start: 0.7547 (m-30) cc_final: 0.7234 (p0) REVERT: B 315 LYS cc_start: 0.8601 (tppt) cc_final: 0.7872 (tptp) REVERT: B 417 LYS cc_start: 0.8257 (tttt) cc_final: 0.7930 (ttmm) REVERT: C 15 GLU cc_start: 0.5873 (mt-10) cc_final: 0.5316 (tt0) REVERT: C 18 GLU cc_start: 0.5874 (mm-30) cc_final: 0.5490 (tt0) REVERT: C 51 LYS cc_start: 0.8188 (ptpt) cc_final: 0.7562 (pttm) REVERT: C 322 LYS cc_start: 0.7669 (ttpt) cc_final: 0.7207 (ttpt) REVERT: C 373 GLU cc_start: 0.7201 (mp0) cc_final: 0.6970 (pm20) REVERT: C 415 ARG cc_start: 0.6380 (tpp80) cc_final: 0.6054 (mmp-170) REVERT: D 50 LYS cc_start: 0.8504 (mttp) cc_final: 0.8132 (mmmt) REVERT: D 60 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7659 (mm-30) REVERT: D 214 ASP cc_start: 0.7626 (m-30) cc_final: 0.7396 (p0) REVERT: D 315 LYS cc_start: 0.8594 (tppt) cc_final: 0.7894 (tptp) outliers start: 16 outliers final: 8 residues processed: 204 average time/residue: 0.7826 time to fit residues: 176.8220 Evaluate side-chains 196 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 187 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 401 TYR Chi-restraints excluded: chain B residue 172 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: 9.9990 chunk 53 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.148570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118384 restraints weight = 18186.193| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 0.98 r_work: 0.3289 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.328 16499 Z= 0.227 Angle : 0.736 30.866 22243 Z= 0.356 Chirality : 0.046 0.177 2336 Planarity : 0.004 0.047 2858 Dihedral : 5.135 53.598 2516 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.87 % Allowed : 9.29 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 1992 helix: 1.38 (0.16), residues: 1010 sheet: -0.56 (0.35), residues: 192 loop : -0.37 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 277 TYR 0.018 0.002 TYR B 142 PHE 0.024 0.002 PHE A 431 TRP 0.013 0.002 TRP A 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.21 (16483) covalent geometry : angle 0.73555 / 0.36 (22243) hydrogen bonds : bond 0.05733 / 3.84 ( 780) hydrogen bonds : angle 5.41353 / 3.97 ( 2232) Misc. bond : bond 0.14204 / 9.08 ( 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 207 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.5780 (mt-10) cc_final: 0.5291 (tt0) REVERT: A 18 GLU cc_start: 0.6375 (mt-10) cc_final: 0.5845 (tt0) REVERT: A 51 LYS cc_start: 0.7785 (ptmt) cc_final: 0.7314 (pttm) REVERT: A 129 LYS cc_start: 0.8368 (mtmt) cc_final: 0.8001 (mtpp) REVERT: A 218 SER cc_start: 0.8470 (p) cc_final: 0.8093 (m) REVERT: A 243 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8115 (mp0) REVERT: A 322 LYS cc_start: 0.7780 (ttmm) cc_final: 0.6975 (mmmt) REVERT: A 476 GLN cc_start: 0.8314 (tp-100) cc_final: 0.8112 (tp-100) REVERT: B 7 LYS cc_start: 0.7966 (tptm) cc_final: 0.7551 (tttm) REVERT: B 50 LYS cc_start: 0.8433 (mttm) cc_final: 0.8021 (mmmt) REVERT: B 214 ASP cc_start: 0.7546 (m-30) cc_final: 0.7192 (p0) REVERT: B 315 LYS cc_start: 0.8610 (tppt) cc_final: 0.7873 (tptp) REVERT: B 417 LYS cc_start: 0.8324 (tttt) cc_final: 0.7989 (ttmm) REVERT: B 507 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8843 (tt0) REVERT: C 15 GLU cc_start: 0.5845 (mt-10) cc_final: 0.5297 (tt0) REVERT: C 18 GLU cc_start: 0.5811 (mm-30) cc_final: 0.5476 (tt0) REVERT: C 51 LYS cc_start: 0.8186 (ptpt) cc_final: 0.7570 (pttm) REVERT: C 322 LYS cc_start: 0.7574 (ttpt) cc_final: 0.7124 (ttpt) REVERT: C 373 GLU cc_start: 0.7154 (mp0) cc_final: 0.6943 (pm20) REVERT: C 415 ARG cc_start: 0.6329 (tpp80) cc_final: 0.6034 (mmp-170) REVERT: D 50 LYS cc_start: 0.8454 (mttp) cc_final: 0.8046 (mmmt) REVERT: D 60 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7645 (mm-30) REVERT: D 214 ASP cc_start: 0.7629 (m-30) cc_final: 0.7380 (p0) REVERT: D 315 LYS cc_start: 0.8594 (tppt) cc_final: 0.7889 (tptp) outliers start: 15 outliers final: 8 residues processed: 201 average time/residue: 0.8229 time to fit residues: 182.5202 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 : 0.747 ------------------------------------------------------------------------------- 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 401 TYR 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 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 140 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3749 r_free = 0.3749 target = 0.150110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118647 restraints weight = 23535.895| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.12 r_work: 0.3291 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 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 = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.318 16499 Z= 0.207 Angle : 0.713 30.809 22243 Z= 0.341 Chirality : 0.045 0.159 2336 Planarity : 0.004 0.044 2858 Dihedral : 4.962 54.053 2516 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.64 % Allowed : 9.81 % Favored : 89.55 % 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: 1.50 (0.16), residues: 1010 sheet: -0.56 (0.34), residues: 192 loop : -0.34 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 277 TYR 0.015 0.002 TYR B 142 PHE 0.021 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/Z covalent geometry : bond 0.00391 / 0.19 (16483) covalent geometry : angle 0.71323 / 0.34 (22243) hydrogen bonds : bond 0.05201 / 3.49 ( 780) hydrogen bonds : angle 5.31902 / 3.90 ( 2232) Misc. bond : bond 0.12977 / 8.41 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9423.63 seconds wall clock time: 161 minutes 22.17 seconds (9682.17 seconds total)