Starting phenix.real_space_refine on Thu Aug 6 16:33:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10zl_75567/08_2026/10zl_75567.cif Found real_map, /net/cci-nas-00/data/ceres_data/10zl_75567/08_2026/10zl_75567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10zl_75567/08_2026/10zl_75567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10zl_75567/08_2026/10zl_75567.map" model { file = "/net/cci-nas-00/data/ceres_data/10zl_75567/08_2026/10zl_75567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10zl_75567/08_2026/10zl_75567.cif" } resolution = 2.15 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= 0.040 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 118 5.16 5 C 9979 2.51 5 N 2685 2.21 5 O 2947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15763 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4006 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 484} Chain: "D" Number of atoms: 4006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4006 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 484} Chain: "A" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3830 Classifications: {'peptide': 483} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "C" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3825 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 460} Chain breaks: 1 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 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: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9225 SG CYS A 170 22.746 49.719 50.077 1.00 54.23 S ATOM 733 SG CYS B 94 26.983 49.589 53.142 1.00 62.72 S ATOM 8507 SG CYS A 78 26.974 45.652 47.765 1.00 51.19 S ATOM 8692 SG CYS A 104 27.757 51.942 47.714 1.00 52.05 S ATOM 8692 SG CYS A 104 27.757 51.942 47.714 1.00 52.05 S ATOM 1175 SG CYS B 152 23.962 53.972 51.681 1.00 59.90 S ATOM 551 SG CYS B 69 30.884 55.017 53.144 1.00 57.59 S ATOM 733 SG CYS B 94 26.983 49.589 53.142 1.00 62.72 S ATOM 13050 SG CYS C 170 102.466 60.626 50.173 1.00 52.73 S ATOM 4739 SG CYS D 94 98.365 60.888 53.140 1.00 64.55 S ATOM 12332 SG CYS C 78 98.277 64.761 47.750 1.00 51.29 S ATOM 12517 SG CYS C 104 97.476 57.761 47.889 1.00 57.68 S ATOM 12517 SG CYS C 104 97.476 57.761 47.889 1.00 57.68 S ATOM 5181 SG CYS D 152 101.310 56.481 51.684 1.00 62.50 S ATOM 4557 SG CYS D 69 94.441 55.288 53.023 1.00 57.43 S ATOM 4739 SG CYS D 94 98.365 60.888 53.140 1.00 64.55 S ATOM 10160 SG CYS A 291 31.039 32.663 37.821 1.00 62.31 S ATOM 13985 SG CYS C 291 94.412 77.675 37.556 1.00 63.14 S Time building chain proxies: 2.80, per 1000 atoms: 0.18 Number of scatterers: 15763 At special positions: 0 Unit cell: (126.225, 112.2, 97.24, 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 118 16.00 O 2947 8.00 N 2685 7.00 C 9979 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: 1.16 Conformation dependent library (CDL) restraints added in 629.4 milliseconds 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3610 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 13 sheets defined 57.8% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 29 Processing helix chain 'B' and resid 35 through 46 Processing helix chain 'B' and resid 48 through 57 Processing helix chain 'B' and resid 69 through 79 removed outlier: 4.019A pdb=" N GLY B 73 " --> pdb=" O CYS B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 107 removed outlier: 4.082A pdb=" N VAL B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 126 through 142 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 160 through 172 Processing helix chain 'B' and resid 191 through 209 Processing helix chain 'B' and resid 228 through 244 removed outlier: 3.715A pdb=" N ARG B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 259 removed outlier: 4.270A pdb=" N THR B 259 " --> pdb=" O GLN B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 290 through 293 Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.721A pdb=" N LEU B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 332 removed outlier: 4.229A pdb=" N ALA B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 354 Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 367 through 381 Processing helix chain 'B' and resid 394 through 407 Processing helix chain 'B' and resid 408 through 412 removed outlier: 4.031A pdb=" N VAL B 412 " --> pdb=" O PRO B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'B' and resid 440 through 442 No H-bonds generated for 'chain 'B' and resid 440 through 442' Processing helix chain 'B' and resid 443 through 451 Processing helix chain 'B' and resid 466 through 470 removed outlier: 3.616A pdb=" N ARG B 469 " --> pdb=" O HIS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 496 Processing helix chain 'B' and resid 503 through 507 removed outlier: 3.718A pdb=" N SER B 506 " --> pdb=" O THR B 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 35 through 47 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 69 through 79 removed outlier: 4.033A pdb=" N GLY D 73 " --> pdb=" O CYS D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 107 removed outlier: 4.195A pdb=" N VAL D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 126 through 142 removed outlier: 3.531A pdb=" N TYR D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 158 Processing helix chain 'D' and resid 160 through 172 Processing helix chain 'D' and resid 191 through 209 Processing helix chain 'D' and resid 228 through 244 Processing helix chain 'D' and resid 273 through 280 Processing helix chain 'D' and resid 290 through 293 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 315 through 332 removed outlier: 4.147A pdb=" N ALA D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 358 removed outlier: 5.361A pdb=" N ALA D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TYR D 356 " --> pdb=" O ASP D 352 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU D 357 " --> pdb=" O SER D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 382 Processing helix chain 'D' and resid 394 through 407 Processing helix chain 'D' and resid 408 through 412 removed outlier: 3.960A pdb=" N VAL D 412 " --> pdb=" O PRO D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 440 through 442 No H-bonds generated for 'chain 'D' and resid 440 through 442' Processing helix chain 'D' and resid 443 through 451 Processing helix chain 'D' and resid 466 through 470 removed outlier: 3.623A pdb=" N ARG D 469 " --> pdb=" O HIS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 496 Processing helix chain 'D' and resid 503 through 507 removed outlier: 3.715A pdb=" N SER D 506 " --> pdb=" O THR D 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 26 through 34 Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 135 through 141 Processing helix chain 'A' and resid 143 through 158 Processing helix chain 'A' and resid 169 through 176 removed outlier: 4.100A pdb=" N GLY A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 174 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 removed outlier: 3.504A pdb=" N VAL A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 222 removed outlier: 3.730A pdb=" N HIS A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 262 removed outlier: 3.958A pdb=" N LEU A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 291 through 307 removed outlier: 5.888A pdb=" N TYR A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 330 removed outlier: 4.266A pdb=" N GLN A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 363 removed outlier: 3.612A pdb=" N GLU A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) Proline residue: A 349 - end of helix Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 379 through 386 removed outlier: 3.583A pdb=" N LEU A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 407 removed outlier: 3.879A pdb=" N GLY A 407 " --> pdb=" O TYR A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 433 Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 443 through 449 removed outlier: 3.962A pdb=" N VAL A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 467 through 484 removed outlier: 3.875A pdb=" N ALA A 473 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 474 " --> pdb=" O ASP A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 491 removed outlier: 3.738A pdb=" N TRP A 488 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 491 " --> pdb=" O TRP A 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.869A pdb=" N ALA C 24 " --> pdb=" O GLU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 35 removed outlier: 3.640A pdb=" N ARG C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 85 Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 135 through 142 Processing helix chain 'C' and resid 143 through 158 Processing helix chain 'C' and resid 169 through 176 removed outlier: 4.187A pdb=" N GLY C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C 174 " --> pdb=" O CYS C 170 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C 176 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 191 removed outlier: 3.544A pdb=" N VAL C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 222 Processing helix chain 'C' and resid 249 through 261 removed outlier: 4.019A pdb=" N LEU C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 281 Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 291 through 307 removed outlier: 3.564A pdb=" N MET C 295 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TYR C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 298 " --> pdb=" O SER C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 331 removed outlier: 4.272A pdb=" N GLN C 320 " --> pdb=" O PHE C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 363 Proline residue: C 349 - end of helix Proline residue: C 360 - end of helix Processing helix chain 'C' and resid 374 through 379 Processing helix chain 'C' and resid 379 through 385 Processing helix chain 'C' and resid 399 through 407 removed outlier: 3.691A pdb=" N GLY C 407 " --> pdb=" O TYR C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 433 Processing helix chain 'C' and resid 440 through 449 removed outlier: 4.512A pdb=" N TYR C 445 " --> pdb=" O ILE C 441 " (cutoff:3.500A) Proline residue: C 446 - end of helix Processing helix chain 'C' and resid 459 through 463 Processing helix chain 'C' and resid 467 through 484 removed outlier: 3.881A pdb=" N ALA C 473 " --> pdb=" O TYR C 469 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 474 " --> pdb=" O ASP C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 491 removed outlier: 3.988A pdb=" N PHE C 491 " --> pdb=" O TRP C 488 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 62 through 63 removed outlier: 4.142A pdb=" N PHE A 130 " --> pdb=" O HIS A 96 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 95 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN A 167 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A 97 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE A 164 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL A 197 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 166 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'B' and resid 247 through 249 Processing sheet with id=AA4, first strand: chain 'B' and resid 415 through 418 removed outlier: 8.305A pdb=" N LYS B 415 " --> pdb=" O GLU B 384 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS B 386 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N TRP B 417 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N CYS B 388 " --> pdb=" O TRP B 417 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE B 364 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS B 388 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR B 361 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE B 438 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA B 363 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 437 " --> pdb=" O ILE B 455 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 62 through 63 removed outlier: 4.099A pdb=" N PHE C 130 " --> pdb=" O HIS C 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 113 through 114 removed outlier: 8.586A pdb=" N VAL D 113 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER D 86 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 247 through 249 removed outlier: 4.777A pdb=" N ALA D 283 " --> pdb=" O ASN D 216 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER D 218 " --> pdb=" O ALA D 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 415 through 418 removed outlier: 8.311A pdb=" N LYS D 415 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS D 386 " --> pdb=" O LYS D 415 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N TRP D 417 " --> pdb=" O LYS D 386 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS D 388 " --> pdb=" O TRP D 417 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR D 362 " --> pdb=" O HIS D 387 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LEU D 389 " --> pdb=" O TYR D 362 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE D 364 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR D 361 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE D 438 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA D 363 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU D 437 " --> pdb=" O ILE D 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 37 through 39 removed outlier: 9.890A pdb=" N LEU A 415 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 391 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N TYR A 417 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR A 393 " --> pdb=" O TYR A 417 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL A 367 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 392 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS A 366 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N GLY A 438 " --> pdb=" O LYS A 366 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N MET A 368 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 437 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 264 through 270 removed outlier: 7.112A pdb=" N VAL A 239 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N TRP A 269 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A 241 " --> pdb=" O TRP A 269 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASP A 238 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 288 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASN A 240 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 37 through 39 removed outlier: 7.336A pdb=" N VAL C 367 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR C 393 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU C 369 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS C 366 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N GLY C 438 " --> pdb=" O LYS C 366 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N MET C 368 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AB4, first strand: chain 'C' and resid 264 through 270 removed outlier: 7.153A pdb=" N VAL C 239 " --> pdb=" O GLY C 267 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N TRP C 269 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL C 241 " --> pdb=" O TRP C 269 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASP C 238 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU C 288 " --> pdb=" O ASP C 238 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ASN C 240 " --> pdb=" O LEU C 288 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 2169 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.56: 15939 1.56 - 1.90: 144 1.90 - 2.24: 32 2.24 - 2.59: 86 2.59 - 2.93: 18 Bond restraints: 16219 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 2.931 -0.731 2.00e-02 2.50e+03 1.34e+03 bond pdb="FE2 CLF B 602 " pdb="FE8 CLF B 602 " ideal model delta sigma weight residual 2.200 2.916 -0.716 2.00e-02 2.50e+03 1.28e+03 bond pdb="FE6 CLF D 602 " pdb="FE7 CLF D 602 " ideal model delta sigma weight residual 2.200 2.855 -0.655 2.00e-02 2.50e+03 1.07e+03 bond pdb="FE6 CLF B 602 " pdb="FE7 CLF B 602 " ideal model delta sigma weight residual 2.200 2.854 -0.654 2.00e-02 2.50e+03 1.07e+03 bond pdb="FE4 CLF B 602 " pdb="FE5 CLF B 602 " ideal model delta sigma weight residual 2.200 2.840 -0.640 2.00e-02 2.50e+03 1.02e+03 ... (remaining 16214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.89: 21905 6.89 - 13.79: 2 13.79 - 20.68: 2 20.68 - 27.57: 0 27.57 - 34.47: 4 Bond angle restraints: 21913 Sorted by residual: angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.53 34.47 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE4 CLF B 602 " ideal model delta sigma weight residual 90.00 55.58 34.42 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 57.05 32.95 3.00e+00 1.11e-01 1.21e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE1 CLF D 602 " ideal model delta sigma weight residual 90.00 57.06 32.94 3.00e+00 1.11e-01 1.21e+02 angle pdb=" CA HIS C 458 " pdb=" CB HIS C 458 " pdb=" CG HIS C 458 " ideal model delta sigma weight residual 113.80 119.57 -5.77 1.00e+00 1.00e+00 3.33e+01 ... (remaining 21908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 9097 17.91 - 35.83: 617 35.83 - 53.74: 101 53.74 - 71.65: 36 71.65 - 89.57: 8 Dihedral angle restraints: 9859 sinusoidal: 4180 harmonic: 5679 Sorted by residual: dihedral pdb=" CA SER A 124 " pdb=" C SER A 124 " pdb=" N PHE A 125 " pdb=" CA PHE A 125 " ideal model delta harmonic sigma weight residual -180.00 -162.59 -17.41 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA SER C 124 " pdb=" C SER C 124 " pdb=" N PHE C 125 " pdb=" CA PHE C 125 " ideal model delta harmonic sigma weight residual 180.00 -163.48 -16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA TYR B 313 " pdb=" C TYR B 313 " pdb=" N PRO B 314 " pdb=" CA PRO B 314 " ideal model delta harmonic sigma weight residual -180.00 -163.65 -16.35 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 9856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1563 0.042 - 0.083: 532 0.083 - 0.125: 164 0.125 - 0.166: 16 0.166 - 0.208: 8 Chirality restraints: 2283 Sorted by residual: chirality pdb=" CA VAL C 379 " pdb=" N VAL C 379 " pdb=" C VAL C 379 " pdb=" CB VAL C 379 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA GLU A 396 " pdb=" N GLU A 396 " pdb=" C GLU A 396 " pdb=" CB GLU A 396 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CA MET C 368 " pdb=" N MET C 368 " pdb=" C MET C 368 " pdb=" CB MET C 368 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 2280 not shown) Planarity restraints: 2839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 293 " -0.413 9.50e-02 1.11e+02 1.85e-01 2.10e+01 pdb=" NE ARG C 293 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG C 293 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 293 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 293 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 291 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C CYS C 291 " -0.044 2.00e-02 2.50e+03 pdb=" O CYS C 291 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR C 292 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 125 " -0.017 2.00e-02 2.50e+03 1.66e-02 4.83e+00 pdb=" CG PHE A 125 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 125 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 125 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 125 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 125 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 125 " -0.003 2.00e-02 2.50e+03 ... (remaining 2836 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 64 2.66 - 3.22: 14783 3.22 - 3.78: 25982 3.78 - 4.34: 38210 4.34 - 4.90: 61067 Nonbonded interactions: 140106 Sorted by model distance: nonbonded pdb=" OD2 ASP D 352 " pdb="FE FE D 601 " model vdw 2.101 2.260 nonbonded pdb=" OD2 ASP B 352 " pdb="FE FE B 601 " model vdw 2.138 2.260 nonbonded pdb=" OE2 GLU B 108 " pdb="FE FE D 601 " model vdw 2.154 2.260 nonbonded pdb=" O LYS D 107 " pdb="FE FE B 601 " model vdw 2.352 2.260 nonbonded pdb=" O LYS B 107 " pdb="FE FE D 601 " model vdw 2.379 2.260 ... (remaining 140101 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 6 through 44 or resid 54 through 502)) selection = chain 'C' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.370 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 : 0.025 0.788 16235 Z= 1.436 Angle : 0.773 34.466 21913 Z= 0.387 Chirality : 0.046 0.208 2283 Planarity : 0.006 0.185 2839 Dihedral : 12.744 89.568 6249 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.18 % Allowed : 0.54 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.11 % 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: 0.06 (0.19), residues: 1973 helix: 1.04 (0.17), residues: 964 sheet: -0.27 (0.38), residues: 191 loop : -1.06 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 58 TYR 0.022 0.002 TYR C 445 PHE 0.038 0.002 PHE A 125 TRP 0.011 0.001 TRP A 269 HIS 0.014 0.001 HIS C 458 Details of bonding type rmsd/Z covalent geometry : bond 0.02336 / 1.17 (16219) covalent geometry : angle 0.77283 / 0.39 (21913) hydrogen bonds : bond 0.16601 / 11.18 ( 747) hydrogen bonds : angle 7.27091 / 5.38 ( 2169) Misc. bond : bond 0.31536 / 17.91 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 353 time to evaluate : 0.591 Fit side-chains REVERT: B 7 LYS cc_start: 0.6209 (tttp) cc_final: 0.5377 (ttpt) REVERT: B 32 ASN cc_start: 0.6936 (t0) cc_final: 0.5903 (m-40) REVERT: B 44 ASP cc_start: 0.7214 (m-30) cc_final: 0.6964 (m-30) REVERT: B 50 GLU cc_start: 0.6981 (tt0) cc_final: 0.6023 (mp0) REVERT: B 53 GLU cc_start: 0.6255 (mt-10) cc_final: 0.5455 (tm-30) REVERT: B 59 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6761 (tt0) REVERT: B 117 MET cc_start: 0.8108 (mtp) cc_final: 0.7694 (mtp) REVERT: B 153 MET cc_start: 0.7806 (ttt) cc_final: 0.7580 (ttt) REVERT: B 177 GLU cc_start: 0.7050 (pm20) cc_final: 0.6644 (pm20) REVERT: B 209 LYS cc_start: 0.7547 (tttt) cc_final: 0.7194 (ttmm) REVERT: B 217 ARG cc_start: 0.6999 (mmm160) cc_final: 0.6616 (mmm160) REVERT: B 246 GLN cc_start: 0.7174 (mm110) cc_final: 0.6580 (tt0) REVERT: B 285 TYR cc_start: 0.7621 (m-80) cc_final: 0.7245 (m-80) REVERT: B 299 GLU cc_start: 0.7136 (tt0) cc_final: 0.6690 (mt-10) REVERT: B 307 LYS cc_start: 0.7636 (mtmt) cc_final: 0.6862 (mtmm) REVERT: B 329 GLU cc_start: 0.7148 (tt0) cc_final: 0.6751 (tt0) REVERT: B 333 LYS cc_start: 0.7018 (mttp) cc_final: 0.6670 (mttt) REVERT: B 337 GLN cc_start: 0.6473 (tp-100) cc_final: 0.6139 (tm-30) REVERT: B 338 GLU cc_start: 0.6771 (mp0) cc_final: 0.6383 (mp0) REVERT: B 386 LYS cc_start: 0.7330 (ttmm) cc_final: 0.7105 (tttt) REVERT: B 395 LYS cc_start: 0.7486 (mmmm) cc_final: 0.7254 (mmtm) REVERT: B 415 LYS cc_start: 0.7498 (tptm) cc_final: 0.6463 (mttp) REVERT: B 421 ASP cc_start: 0.6389 (m-30) cc_final: 0.6149 (p0) REVERT: B 425 MET cc_start: 0.7939 (tpp) cc_final: 0.7470 (tpp) REVERT: B 433 LYS cc_start: 0.7753 (ttpp) cc_final: 0.6492 (mppt) REVERT: B 447 GLU cc_start: 0.6859 (tt0) cc_final: 0.6636 (tt0) REVERT: B 476 GLN cc_start: 0.6995 (mm110) cc_final: 0.6762 (mm110) REVERT: B 480 ARG cc_start: 0.6944 (mtt90) cc_final: 0.5463 (tmt90) REVERT: D 7 LYS cc_start: 0.6155 (mmpt) cc_final: 0.5580 (ttpp) REVERT: D 10 ASP cc_start: 0.6261 (m-30) cc_final: 0.5741 (p0) REVERT: D 21 GLN cc_start: 0.6142 (tt0) cc_final: 0.5808 (mm110) REVERT: D 22 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6188 (tt0) REVERT: D 32 ASN cc_start: 0.7087 (t0) cc_final: 0.6827 (t0) REVERT: D 41 GLU cc_start: 0.7023 (tt0) cc_final: 0.6754 (tm-30) REVERT: D 50 GLU cc_start: 0.6158 (mp0) cc_final: 0.5608 (tt0) REVERT: D 53 GLU cc_start: 0.6354 (mt-10) cc_final: 0.5566 (tm-30) REVERT: D 54 LYS cc_start: 0.7337 (mtpp) cc_final: 0.7022 (mtmm) REVERT: D 59 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7179 (mt-10) REVERT: D 86 SER cc_start: 0.8204 (m) cc_final: 0.7975 (t) REVERT: D 139 LYS cc_start: 0.7006 (tppt) cc_final: 0.6510 (tptp) REVERT: D 176 GLU cc_start: 0.6871 (tp30) cc_final: 0.6658 (tp30) REVERT: D 177 GLU cc_start: 0.6877 (pm20) cc_final: 0.6618 (pm20) REVERT: D 209 LYS cc_start: 0.7560 (tttp) cc_final: 0.6346 (ptpp) REVERT: D 246 GLN cc_start: 0.7027 (mm110) cc_final: 0.6416 (tt0) REVERT: D 267 MET cc_start: 0.7881 (ttm) cc_final: 0.7595 (ttm) REVERT: D 285 TYR cc_start: 0.7461 (m-80) cc_final: 0.7127 (m-80) REVERT: D 296 LYS cc_start: 0.6698 (mmtp) cc_final: 0.6399 (mttt) REVERT: D 299 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6679 (mt-10) REVERT: D 307 LYS cc_start: 0.7739 (mtmm) cc_final: 0.6870 (mtmm) REVERT: D 329 GLU cc_start: 0.7058 (tt0) cc_final: 0.6635 (tt0) REVERT: D 333 LYS cc_start: 0.6909 (mtmm) cc_final: 0.6590 (ptmt) REVERT: D 338 GLU cc_start: 0.6431 (mp0) cc_final: 0.5853 (pm20) REVERT: D 340 GLU cc_start: 0.6282 (mt-10) cc_final: 0.5982 (tt0) REVERT: D 377 PHE cc_start: 0.6835 (t80) cc_final: 0.6391 (t80) REVERT: D 384 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6540 (tt0) REVERT: D 395 LYS cc_start: 0.7301 (mttp) cc_final: 0.7076 (mmtm) REVERT: D 403 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6112 (tt0) REVERT: D 415 LYS cc_start: 0.7553 (tptp) cc_final: 0.6528 (mttp) REVERT: D 425 MET cc_start: 0.7791 (tpp) cc_final: 0.7324 (tpp) REVERT: D 433 LYS cc_start: 0.7549 (mmtt) cc_final: 0.7323 (mptp) REVERT: D 491 ASP cc_start: 0.7058 (m-30) cc_final: 0.6838 (m-30) REVERT: D 492 LYS cc_start: 0.6855 (tptm) cc_final: 0.6403 (tptm) REVERT: A 16 ARG cc_start: 0.6091 (ttp-110) cc_final: 0.5834 (mtm110) REVERT: A 23 GLU cc_start: 0.5476 (mt-10) cc_final: 0.5067 (mm-30) REVERT: A 27 ASP cc_start: 0.6710 (t70) cc_final: 0.6367 (m-30) REVERT: A 31 LYS cc_start: 0.6574 (mmmm) cc_final: 0.6321 (mttp) REVERT: A 67 LYS cc_start: 0.6440 (ptmt) cc_final: 0.6001 (pttp) REVERT: A 136 GLU cc_start: 0.6484 (mt-10) cc_final: 0.5939 (tp30) REVERT: A 145 LYS cc_start: 0.6928 (mttm) cc_final: 0.6558 (mttm) REVERT: A 188 LYS cc_start: 0.7642 (mtmt) cc_final: 0.7317 (mttm) REVERT: A 203 ARG cc_start: 0.6608 (ttt180) cc_final: 0.6203 (mtm-85) REVERT: A 295 MET cc_start: 0.7667 (mmt) cc_final: 0.7438 (mmt) REVERT: A 303 GLU cc_start: 0.7336 (tt0) cc_final: 0.6499 (tp30) REVERT: A 334 GLU cc_start: 0.6524 (mp0) cc_final: 0.6171 (mp0) REVERT: A 338 GLU cc_start: 0.6827 (pt0) cc_final: 0.6507 (mt-10) REVERT: A 356 GLU cc_start: 0.6603 (mt-10) cc_final: 0.6156 (tt0) REVERT: A 361 ARG cc_start: 0.7227 (mtm180) cc_final: 0.6370 (mtp85) REVERT: A 366 LYS cc_start: 0.7001 (mtmt) cc_final: 0.6298 (mmtm) REVERT: A 368 MET cc_start: 0.8441 (mtp) cc_final: 0.8212 (mtp) REVERT: A 378 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.5916 (m90) REVERT: A 389 GLU cc_start: 0.6776 (pt0) cc_final: 0.6215 (tp30) REVERT: A 400 ASN cc_start: 0.6726 (t0) cc_final: 0.6513 (t0) REVERT: A 411 ARG cc_start: 0.6461 (mpt-90) cc_final: 0.5573 (ptt-90) REVERT: A 423 TYR cc_start: 0.6703 (t80) cc_final: 0.6453 (t80) REVERT: A 430 GLU cc_start: 0.6548 (tt0) cc_final: 0.6002 (tt0) REVERT: A 490 MET cc_start: 0.7697 (mmt) cc_final: 0.7406 (mmm) REVERT: C 23 GLU cc_start: 0.5913 (tp30) cc_final: 0.5644 (mm-30) REVERT: C 31 LYS cc_start: 0.6956 (mttp) cc_final: 0.6737 (mttp) REVERT: C 34 GLN cc_start: 0.6652 (tt0) cc_final: 0.5873 (pt0) REVERT: C 35 LYS cc_start: 0.6592 (pttt) cc_final: 0.5712 (mmpt) REVERT: C 67 LYS cc_start: 0.6844 (ptpt) cc_final: 0.6374 (pttm) REVERT: C 119 ASN cc_start: 0.7352 (t0) cc_final: 0.6745 (m-40) REVERT: C 135 GLN cc_start: 0.7560 (mm110) cc_final: 0.7052 (mm-40) REVERT: C 136 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6699 (tp30) REVERT: C 137 LYS cc_start: 0.6942 (tttm) cc_final: 0.6602 (ttpt) REVERT: C 144 ASP cc_start: 0.6886 (m-30) cc_final: 0.6626 (m-30) REVERT: C 188 LYS cc_start: 0.7698 (mttt) cc_final: 0.7453 (mttm) REVERT: C 233 GLU cc_start: 0.6501 (tt0) cc_final: 0.5722 (mp0) REVERT: C 237 TYR cc_start: 0.7886 (m-80) cc_final: 0.7479 (m-80) REVERT: C 260 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7605 (mt-10) REVERT: C 307 ASN cc_start: 0.7089 (t0) cc_final: 0.6806 (m-40) REVERT: C 334 GLU cc_start: 0.6744 (tt0) cc_final: 0.5871 (mp0) REVERT: C 366 LYS cc_start: 0.7761 (mmtm) cc_final: 0.7516 (mmtt) REVERT: C 378 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.6178 (m90) REVERT: C 389 GLU cc_start: 0.7508 (tt0) cc_final: 0.6579 (tp30) REVERT: C 400 ASN cc_start: 0.6497 (t0) cc_final: 0.5946 (t0) REVERT: C 404 GLN cc_start: 0.6788 (mt0) cc_final: 0.6565 (mt0) REVERT: C 423 TYR cc_start: 0.6940 (t80) cc_final: 0.6666 (t80) REVERT: C 430 GLU cc_start: 0.6448 (tt0) cc_final: 0.5927 (tt0) REVERT: C 479 MET cc_start: 0.7702 (mmp) cc_final: 0.7232 (mmp) REVERT: C 492 LYS cc_start: 0.7271 (ttmm) cc_final: 0.6616 (ttpt) outliers start: 3 outliers final: 1 residues processed: 356 average time/residue: 0.7410 time to fit residues: 284.2258 Evaluate side-chains 243 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 240 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.0270 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.4980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 387 HIS A 34 GLN A 320 GLN A 381 ASN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 ASN C 287 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.117338 restraints weight = 12468.161| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 0.90 r_work: 0.3262 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.228 16235 Z= 0.160 Angle : 0.701 28.956 21913 Z= 0.327 Chirality : 0.042 0.142 2283 Planarity : 0.005 0.060 2839 Dihedral : 4.965 59.930 2520 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.03 % Allowed : 5.61 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.11 % 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: 0.45 (0.19), residues: 1973 helix: 1.44 (0.17), residues: 963 sheet: -0.28 (0.38), residues: 186 loop : -0.92 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 16 TYR 0.016 0.002 TYR A 462 PHE 0.032 0.002 PHE A 125 TRP 0.008 0.001 TRP A 460 HIS 0.008 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (16219) covalent geometry : angle 0.70073 / 0.33 (21913) hydrogen bonds : bond 0.05055 / 3.42 ( 747) hydrogen bonds : angle 5.91434 / 4.38 ( 2169) Misc. bond : bond 0.10867 / 6.31 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 0.533 Fit side-chains REVERT: B 7 LYS cc_start: 0.7684 (tttp) cc_final: 0.7169 (ttpt) REVERT: B 32 ASN cc_start: 0.8054 (t0) cc_final: 0.7345 (m110) REVERT: B 117 MET cc_start: 0.8678 (mtp) cc_final: 0.8382 (mtp) REVERT: B 211 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.6962 (mtm-85) REVERT: B 285 TYR cc_start: 0.8610 (m-80) cc_final: 0.8360 (m-80) REVERT: B 307 LYS cc_start: 0.8658 (mtmt) cc_final: 0.8342 (mtmm) REVERT: B 338 GLU cc_start: 0.7955 (mp0) cc_final: 0.7674 (pm20) REVERT: B 425 MET cc_start: 0.9253 (tpp) cc_final: 0.8947 (tpp) REVERT: B 433 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8200 (mppt) REVERT: B 447 GLU cc_start: 0.8085 (tt0) cc_final: 0.7841 (tt0) REVERT: B 480 ARG cc_start: 0.8104 (mtt90) cc_final: 0.7813 (tmt90) REVERT: D 32 ASN cc_start: 0.7879 (t0) cc_final: 0.7320 (m-40) REVERT: D 209 LYS cc_start: 0.8450 (tttp) cc_final: 0.7817 (ptpp) REVERT: D 267 MET cc_start: 0.9019 (ttm) cc_final: 0.8764 (ttm) REVERT: D 299 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7832 (mt-10) REVERT: D 338 GLU cc_start: 0.7958 (mp0) cc_final: 0.7665 (pm20) REVERT: D 425 MET cc_start: 0.9137 (tpp) cc_final: 0.8874 (tpp) REVERT: A 16 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.7395 (mtm110) REVERT: A 145 LYS cc_start: 0.8280 (mttm) cc_final: 0.8053 (mttm) REVERT: A 283 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8682 (mttm) REVERT: A 303 GLU cc_start: 0.8139 (tt0) cc_final: 0.7819 (tp30) REVERT: A 378 HIS cc_start: 0.8910 (OUTLIER) cc_final: 0.6782 (m90) REVERT: A 411 ARG cc_start: 0.7156 (mpt-90) cc_final: 0.6703 (ptt-90) REVERT: A 423 TYR cc_start: 0.8201 (t80) cc_final: 0.7994 (t80) REVERT: C 34 GLN cc_start: 0.7565 (tt0) cc_final: 0.7322 (pt0) REVERT: C 35 LYS cc_start: 0.7667 (pttt) cc_final: 0.7427 (mmpt) REVERT: C 67 LYS cc_start: 0.7953 (ptpt) cc_final: 0.7753 (pttm) REVERT: C 237 TYR cc_start: 0.8693 (m-80) cc_final: 0.8457 (m-80) REVERT: C 378 HIS cc_start: 0.8824 (OUTLIER) cc_final: 0.6655 (m90) REVERT: C 400 ASN cc_start: 0.7991 (t0) cc_final: 0.7774 (t0) REVERT: C 479 MET cc_start: 0.8758 (mmp) cc_final: 0.8253 (mmp) REVERT: C 492 LYS cc_start: 0.8458 (ttmm) cc_final: 0.8152 (ttpt) REVERT: C 496 LYS cc_start: 0.7630 (mtpp) cc_final: 0.7365 (mmtt) outliers start: 17 outliers final: 5 residues processed: 252 average time/residue: 0.7849 time to fit residues: 213.0132 Evaluate side-chains 199 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 125 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 157 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 HIS ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN A 404 GLN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN C 320 GLN C 381 ASN C 404 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113657 restraints weight = 12680.952| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 0.90 r_work: 0.3208 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.218 16235 Z= 0.158 Angle : 0.705 29.286 21913 Z= 0.331 Chirality : 0.043 0.138 2283 Planarity : 0.005 0.060 2839 Dihedral : 4.954 58.482 2520 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.63 % Allowed : 7.66 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.11 % 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: 0.54 (0.19), residues: 1973 helix: 1.53 (0.17), residues: 970 sheet: -0.28 (0.38), residues: 186 loop : -0.90 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 411 TYR 0.019 0.002 TYR A 462 PHE 0.034 0.002 PHE A 125 TRP 0.009 0.001 TRP C 460 HIS 0.010 0.002 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (16219) covalent geometry : angle 0.70504 / 0.33 (21913) hydrogen bonds : bond 0.04818 / 3.27 ( 747) hydrogen bonds : angle 5.67215 / 4.20 ( 2169) Misc. bond : bond 0.10109 / 5.85 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.569 Fit side-chains REVERT: B 7 LYS cc_start: 0.7651 (tttp) cc_final: 0.7108 (ttpt) REVERT: B 32 ASN cc_start: 0.8082 (t0) cc_final: 0.7399 (m110) REVERT: B 117 MET cc_start: 0.8664 (mtp) cc_final: 0.8337 (mtp) REVERT: B 211 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.6961 (mtm-85) REVERT: B 285 TYR cc_start: 0.8618 (m-80) cc_final: 0.8373 (m-80) REVERT: B 307 LYS cc_start: 0.8638 (mtmt) cc_final: 0.8293 (mtmm) REVERT: B 338 GLU cc_start: 0.7957 (mp0) cc_final: 0.7752 (mp0) REVERT: B 425 MET cc_start: 0.9265 (tpp) cc_final: 0.8988 (tpp) REVERT: B 433 LYS cc_start: 0.8564 (ttpp) cc_final: 0.8235 (mppt) REVERT: B 447 GLU cc_start: 0.8131 (tt0) cc_final: 0.7910 (tt0) REVERT: B 480 ARG cc_start: 0.8049 (mtt90) cc_final: 0.7790 (tmt90) REVERT: D 32 ASN cc_start: 0.8086 (t0) cc_final: 0.7435 (m-40) REVERT: D 209 LYS cc_start: 0.8466 (tttp) cc_final: 0.7838 (ptpp) REVERT: D 338 GLU cc_start: 0.8010 (mp0) cc_final: 0.7735 (pm20) REVERT: D 425 MET cc_start: 0.9212 (tpp) cc_final: 0.8904 (tpp) REVERT: D 447 GLU cc_start: 0.8341 (tt0) cc_final: 0.8041 (tt0) REVERT: A 16 ARG cc_start: 0.7736 (ttp-110) cc_final: 0.7408 (mtm110) REVERT: A 145 LYS cc_start: 0.8369 (mttm) cc_final: 0.8154 (mttm) REVERT: A 283 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8628 (mttm) REVERT: A 430 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: C 67 LYS cc_start: 0.8071 (ptpt) cc_final: 0.7840 (pttm) REVERT: C 237 TYR cc_start: 0.8825 (m-80) cc_final: 0.8607 (m-80) REVERT: C 303 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.6707 (tp30) REVERT: C 400 ASN cc_start: 0.7990 (t0) cc_final: 0.7777 (t0) REVERT: C 479 MET cc_start: 0.8792 (mmp) cc_final: 0.8177 (mmp) REVERT: C 490 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.8096 (mtp) REVERT: C 492 LYS cc_start: 0.8470 (ttmm) cc_final: 0.8240 (ttpt) REVERT: C 496 LYS cc_start: 0.7693 (mtpp) cc_final: 0.7447 (mmtt) outliers start: 27 outliers final: 11 residues processed: 220 average time/residue: 0.7530 time to fit residues: 179.7616 Evaluate side-chains 214 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 490 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 193 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 176 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 157 optimal weight: 0.0470 chunk 123 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN A 381 ASN A 404 GLN C 34 GLN C 114 ASN C 381 ASN C 404 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.131444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114336 restraints weight = 12642.746| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 0.90 r_work: 0.3226 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 16235 Z= 0.138 Angle : 0.675 29.272 21913 Z= 0.312 Chirality : 0.042 0.135 2283 Planarity : 0.004 0.054 2839 Dihedral : 4.827 58.091 2520 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.69 % Allowed : 7.78 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1973 helix: 1.66 (0.17), residues: 969 sheet: -0.25 (0.38), residues: 186 loop : -0.86 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 16 TYR 0.022 0.002 TYR A 423 PHE 0.023 0.001 PHE A 125 TRP 0.008 0.001 TRP A 460 HIS 0.006 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (16219) covalent geometry : angle 0.67511 / 0.31 (21913) hydrogen bonds : bond 0.04282 / 2.90 ( 747) hydrogen bonds : angle 5.50973 / 4.07 ( 2169) Misc. bond : bond 0.08939 / 5.16 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.571 Fit side-chains REVERT: B 7 LYS cc_start: 0.7682 (tttp) cc_final: 0.7074 (ttpt) REVERT: B 32 ASN cc_start: 0.8102 (t0) cc_final: 0.7364 (m110) REVERT: B 211 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.6990 (mtm-85) REVERT: B 285 TYR cc_start: 0.8614 (m-80) cc_final: 0.8384 (m-80) REVERT: B 307 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8266 (mtmm) REVERT: B 425 MET cc_start: 0.9264 (tpp) cc_final: 0.9028 (tpp) REVERT: B 433 LYS cc_start: 0.8541 (ttpp) cc_final: 0.8208 (mppt) REVERT: B 447 GLU cc_start: 0.8146 (tt0) cc_final: 0.7927 (tt0) REVERT: B 480 ARG cc_start: 0.7992 (mtt90) cc_final: 0.7760 (tmt90) REVERT: D 32 ASN cc_start: 0.8098 (t0) cc_final: 0.7438 (m-40) REVERT: D 50 GLU cc_start: 0.7653 (mp0) cc_final: 0.7362 (pm20) REVERT: D 209 LYS cc_start: 0.8480 (tttp) cc_final: 0.7812 (ptpp) REVERT: D 338 GLU cc_start: 0.7981 (mp0) cc_final: 0.7696 (pm20) REVERT: D 425 MET cc_start: 0.9208 (tpp) cc_final: 0.8990 (tpp) REVERT: D 447 GLU cc_start: 0.8289 (tt0) cc_final: 0.8045 (tt0) REVERT: A 16 ARG cc_start: 0.7669 (ttp-110) cc_final: 0.7331 (mtm110) REVERT: A 145 LYS cc_start: 0.8348 (mttm) cc_final: 0.8132 (mttm) REVERT: A 283 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8628 (mttm) REVERT: A 361 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.6620 (mtp85) REVERT: A 430 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: C 67 LYS cc_start: 0.8081 (ptpt) cc_final: 0.7836 (pttm) REVERT: C 303 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.6684 (tp30) REVERT: C 400 ASN cc_start: 0.8017 (t0) cc_final: 0.7816 (t0) REVERT: C 401 ASP cc_start: 0.7838 (p0) cc_final: 0.7460 (p0) REVERT: C 411 ARG cc_start: 0.7595 (mmt180) cc_final: 0.7335 (mpt180) REVERT: C 479 MET cc_start: 0.8785 (mmp) cc_final: 0.8211 (mmp) REVERT: C 490 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7963 (mmm) REVERT: C 492 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8213 (ttpt) REVERT: C 496 LYS cc_start: 0.7739 (mtpp) cc_final: 0.7441 (mmtt) outliers start: 28 outliers final: 13 residues processed: 224 average time/residue: 0.7373 time to fit residues: 178.6466 Evaluate side-chains 218 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 461 ASP Chi-restraints excluded: chain C residue 490 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 125 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 151 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN A 381 ASN A 404 GLN C 114 ASN C 381 ASN C 404 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112416 restraints weight = 12429.612| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 0.88 r_work: 0.3198 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.228 16235 Z= 0.170 Angle : 0.717 29.376 21913 Z= 0.339 Chirality : 0.043 0.140 2283 Planarity : 0.005 0.060 2839 Dihedral : 5.003 58.698 2520 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.69 % Allowed : 8.14 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.19), residues: 1973 helix: 1.63 (0.16), residues: 967 sheet: -0.27 (0.38), residues: 186 loop : -0.72 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 16 TYR 0.020 0.002 TYR A 462 PHE 0.029 0.002 PHE A 125 TRP 0.009 0.002 TRP C 460 HIS 0.010 0.002 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (16219) covalent geometry : angle 0.71658 / 0.34 (21913) hydrogen bonds : bond 0.05026 / 3.41 ( 747) hydrogen bonds : angle 5.62578 / 4.15 ( 2169) Misc. bond : bond 0.10315 / 5.96 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.506 Fit side-chains REVERT: B 7 LYS cc_start: 0.7753 (tttp) cc_final: 0.7188 (ttpt) REVERT: B 32 ASN cc_start: 0.8181 (t0) cc_final: 0.7403 (m110) REVERT: B 211 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7016 (mtm-85) REVERT: B 307 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8298 (mtmm) REVERT: B 433 LYS cc_start: 0.8545 (ttpp) cc_final: 0.8221 (mppt) REVERT: B 447 GLU cc_start: 0.8168 (tt0) cc_final: 0.7967 (tt0) REVERT: B 480 ARG cc_start: 0.8042 (mtt90) cc_final: 0.7797 (tmt90) REVERT: D 32 ASN cc_start: 0.8152 (t0) cc_final: 0.7455 (m-40) REVERT: D 209 LYS cc_start: 0.8503 (tttp) cc_final: 0.7798 (ptpp) REVERT: D 338 GLU cc_start: 0.8076 (mp0) cc_final: 0.7799 (pm20) REVERT: D 425 MET cc_start: 0.9253 (tpp) cc_final: 0.9024 (tpp) REVERT: D 447 GLU cc_start: 0.8274 (tt0) cc_final: 0.8007 (tt0) REVERT: A 16 ARG cc_start: 0.7661 (ttp-110) cc_final: 0.7309 (mtm110) REVERT: A 145 LYS cc_start: 0.8471 (mttm) cc_final: 0.8246 (mttm) REVERT: A 283 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8614 (mttm) REVERT: A 361 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.6736 (mtp180) REVERT: A 411 ARG cc_start: 0.7463 (mmt180) cc_final: 0.6845 (ptt-90) REVERT: A 430 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7490 (tt0) REVERT: C 67 LYS cc_start: 0.8101 (ptpt) cc_final: 0.7869 (pttm) REVERT: C 303 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.6819 (tp30) REVERT: C 411 ARG cc_start: 0.7666 (mmt180) cc_final: 0.6889 (ptt-90) REVERT: C 490 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7993 (mmt) REVERT: C 492 LYS cc_start: 0.8453 (ttmm) cc_final: 0.8235 (ttpt) REVERT: C 496 LYS cc_start: 0.7751 (mtpp) cc_final: 0.7471 (mmtt) outliers start: 28 outliers final: 14 residues processed: 224 average time/residue: 0.7349 time to fit residues: 178.2830 Evaluate side-chains 218 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 490 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 88 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN A 381 ASN A 404 GLN C 114 ASN C 381 ASN C 404 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.129108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111991 restraints weight = 12280.298| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 0.87 r_work: 0.3192 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.232 16235 Z= 0.177 Angle : 0.724 29.392 21913 Z= 0.343 Chirality : 0.044 0.140 2283 Planarity : 0.005 0.072 2839 Dihedral : 4.999 56.440 2520 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.75 % Allowed : 8.56 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.19), residues: 1973 helix: 1.62 (0.16), residues: 967 sheet: -0.25 (0.38), residues: 186 loop : -0.72 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 16 TYR 0.019 0.002 TYR A 462 PHE 0.027 0.002 PHE A 125 TRP 0.010 0.002 TRP C 460 HIS 0.009 0.002 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (16219) covalent geometry : angle 0.72398 / 0.34 (21913) hydrogen bonds : bond 0.05103 / 3.46 ( 747) hydrogen bonds : angle 5.63605 / 4.16 ( 2169) Misc. bond : bond 0.10459 / 6.04 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.579 Fit side-chains REVERT: B 7 LYS cc_start: 0.7760 (tttp) cc_final: 0.7187 (ttpt) REVERT: B 32 ASN cc_start: 0.8158 (t0) cc_final: 0.7371 (m110) REVERT: B 211 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7014 (mtm-85) REVERT: B 307 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8289 (mtmm) REVERT: B 433 LYS cc_start: 0.8527 (ttpp) cc_final: 0.8216 (mppt) REVERT: B 480 ARG cc_start: 0.8027 (mtt90) cc_final: 0.7812 (tmt90) REVERT: D 32 ASN cc_start: 0.8187 (t0) cc_final: 0.7453 (m-40) REVERT: D 209 LYS cc_start: 0.8524 (tttp) cc_final: 0.7805 (ptpp) REVERT: D 338 GLU cc_start: 0.8069 (mp0) cc_final: 0.7788 (pm20) REVERT: D 447 GLU cc_start: 0.8281 (tt0) cc_final: 0.8032 (tt0) REVERT: A 16 ARG cc_start: 0.7667 (ttp-110) cc_final: 0.7311 (mtm110) REVERT: A 283 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8608 (mttm) REVERT: A 361 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.6758 (mtp180) REVERT: A 411 ARG cc_start: 0.7477 (mmt180) cc_final: 0.6827 (ptt-90) REVERT: A 430 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: C 67 LYS cc_start: 0.8103 (ptpt) cc_final: 0.7865 (pttm) REVERT: C 283 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8354 (mttm) REVERT: C 303 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.6835 (tp30) REVERT: C 411 ARG cc_start: 0.7675 (mmt180) cc_final: 0.6853 (ptt-90) REVERT: C 490 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7924 (mmt) REVERT: C 496 LYS cc_start: 0.7758 (mtpp) cc_final: 0.7543 (mmtt) outliers start: 29 outliers final: 13 residues processed: 222 average time/residue: 0.7347 time to fit residues: 176.3721 Evaluate side-chains 220 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 490 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 180 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 0.4980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 184 HIS A 114 ASN A 381 ASN A 404 GLN C 36 HIS C 114 ASN C 381 ASN C 404 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.128339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111204 restraints weight = 12250.732| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 0.87 r_work: 0.3179 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.2909 rms_B_bonded: 4.98 restraints_weight: 0.1250 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.241 16235 Z= 0.188 Angle : 0.739 29.425 21913 Z= 0.353 Chirality : 0.045 0.145 2283 Planarity : 0.005 0.063 2839 Dihedral : 5.055 56.178 2520 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.69 % Allowed : 8.81 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.18), residues: 1973 helix: 1.63 (0.16), residues: 958 sheet: -0.31 (0.35), residues: 215 loop : -0.77 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 16 TYR 0.021 0.002 TYR A 462 PHE 0.027 0.002 PHE A 125 TRP 0.010 0.002 TRP C 460 HIS 0.009 0.002 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (16219) covalent geometry : angle 0.73878 / 0.35 (21913) hydrogen bonds : bond 0.05346 / 3.62 ( 747) hydrogen bonds : angle 5.68796 / 4.20 ( 2169) Misc. bond : bond 0.10782 / 6.22 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.582 Fit side-chains REVERT: B 7 LYS cc_start: 0.7804 (tttp) cc_final: 0.7080 (ttpp) REVERT: B 32 ASN cc_start: 0.8371 (t0) cc_final: 0.7555 (m110) REVERT: B 211 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7019 (mtm-85) REVERT: B 307 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8417 (mtmm) REVERT: B 433 LYS cc_start: 0.8805 (ttpp) cc_final: 0.8301 (mppt) REVERT: B 480 ARG cc_start: 0.8538 (mtt90) cc_final: 0.7930 (tmt90) REVERT: D 10 ASP cc_start: 0.7863 (p0) cc_final: 0.7640 (p0) REVERT: D 32 ASN cc_start: 0.8408 (t0) cc_final: 0.7548 (m-40) REVERT: D 209 LYS cc_start: 0.8734 (tttp) cc_final: 0.7877 (ptpp) REVERT: D 338 GLU cc_start: 0.8363 (mp0) cc_final: 0.8009 (pm20) REVERT: D 447 GLU cc_start: 0.8603 (tt0) cc_final: 0.8351 (tt0) REVERT: A 16 ARG cc_start: 0.7966 (ttp-110) cc_final: 0.7601 (mtm110) REVERT: A 283 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8637 (mttm) REVERT: A 361 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.6928 (mtp180) REVERT: A 411 ARG cc_start: 0.7771 (mmt180) cc_final: 0.6802 (ptt-90) REVERT: A 430 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: C 67 LYS cc_start: 0.8141 (ptpt) cc_final: 0.7793 (pttm) REVERT: C 303 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7205 (tp30) REVERT: C 411 ARG cc_start: 0.7937 (mmt180) cc_final: 0.6882 (ptt-90) REVERT: C 490 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8283 (mmt) REVERT: C 496 LYS cc_start: 0.7825 (mtpp) cc_final: 0.7442 (mttt) outliers start: 28 outliers final: 14 residues processed: 219 average time/residue: 0.7687 time to fit residues: 182.2463 Evaluate side-chains 211 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 490 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 76 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN A 381 ASN A 404 GLN C 114 ASN C 301 HIS C 381 ASN C 404 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.127022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109828 restraints weight = 12315.061| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 0.86 r_work: 0.3160 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 1.86 restraints_weight: 0.2500 r_work: 0.2890 rms_B_bonded: 4.93 restraints_weight: 0.1250 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.266 16235 Z= 0.233 Angle : 0.786 29.542 21913 Z= 0.382 Chirality : 0.047 0.160 2283 Planarity : 0.006 0.087 2839 Dihedral : 5.192 55.713 2520 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.69 % Allowed : 8.87 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.11 % 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: 0.49 (0.18), residues: 1973 helix: 1.47 (0.16), residues: 970 sheet: -0.28 (0.34), residues: 220 loop : -0.92 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 16 TYR 0.024 0.003 TYR A 462 PHE 0.032 0.003 PHE A 125 TRP 0.011 0.002 TRP A 269 HIS 0.009 0.002 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (16219) covalent geometry : angle 0.78646 / 0.38 (21913) hydrogen bonds : bond 0.05965 / 4.04 ( 747) hydrogen bonds : angle 5.80404 / 4.28 ( 2169) Misc. bond : bond 0.11882 / 6.84 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: B 7 LYS cc_start: 0.7817 (tttp) cc_final: 0.7086 (ttpp) REVERT: B 10 ASP cc_start: 0.8035 (p0) cc_final: 0.7824 (p0) REVERT: B 211 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.6978 (mtm-85) REVERT: B 307 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8432 (mtmm) REVERT: B 433 LYS cc_start: 0.8790 (ttpp) cc_final: 0.8284 (mppt) REVERT: B 480 ARG cc_start: 0.8549 (mtt90) cc_final: 0.7943 (tmt90) REVERT: D 32 ASN cc_start: 0.8445 (t0) cc_final: 0.7579 (m-40) REVERT: D 209 LYS cc_start: 0.8739 (tttp) cc_final: 0.7904 (ptpp) REVERT: D 338 GLU cc_start: 0.8382 (mp0) cc_final: 0.8024 (pm20) REVERT: D 447 GLU cc_start: 0.8609 (tt0) cc_final: 0.8344 (tt0) REVERT: A 16 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7609 (mtm110) REVERT: A 283 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8652 (mttm) REVERT: A 361 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.6984 (mtp180) REVERT: A 411 ARG cc_start: 0.7793 (mmt180) cc_final: 0.6767 (ptt-90) REVERT: A 430 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: C 67 LYS cc_start: 0.8137 (ptpt) cc_final: 0.7775 (pttm) REVERT: C 283 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8435 (mttm) REVERT: C 303 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7258 (tp30) REVERT: C 411 ARG cc_start: 0.7956 (mmt180) cc_final: 0.6877 (ptt-90) REVERT: C 490 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8196 (mmt) REVERT: C 496 LYS cc_start: 0.7852 (mtpp) cc_final: 0.7460 (mttt) outliers start: 28 outliers final: 15 residues processed: 215 average time/residue: 0.6560 time to fit residues: 152.8097 Evaluate side-chains 214 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 361 ARG Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 490 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 174 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN A 381 ASN A 404 GLN C 114 ASN C 381 ASN C 404 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110342 restraints weight = 12232.193| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 0.86 r_work: 0.3157 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 1.86 restraints_weight: 0.2500 r_work: 0.2887 rms_B_bonded: 4.94 restraints_weight: 0.1250 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.254 16235 Z= 0.206 Angle : 0.764 29.474 21913 Z= 0.368 Chirality : 0.045 0.154 2283 Planarity : 0.005 0.079 2839 Dihedral : 5.178 55.848 2520 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.93 % Allowed : 8.93 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.11 % 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: 0.48 (0.18), residues: 1973 helix: 1.47 (0.16), residues: 970 sheet: -0.28 (0.34), residues: 220 loop : -0.94 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 16 TYR 0.022 0.002 TYR A 462 PHE 0.028 0.002 PHE A 125 TRP 0.010 0.002 TRP C 460 HIS 0.009 0.002 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (16219) covalent geometry : angle 0.76361 / 0.37 (21913) hydrogen bonds : bond 0.05649 / 3.83 ( 747) hydrogen bonds : angle 5.76314 / 4.25 ( 2169) Misc. bond : bond 0.11339 / 6.54 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: B 7 LYS cc_start: 0.7805 (tttp) cc_final: 0.7066 (ttpp) REVERT: B 211 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.6945 (mtm-85) REVERT: B 307 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8422 (mtmm) REVERT: B 433 LYS cc_start: 0.8784 (ttpp) cc_final: 0.8268 (mppt) REVERT: B 480 ARG cc_start: 0.8548 (mtt90) cc_final: 0.7938 (tmt90) REVERT: D 10 ASP cc_start: 0.7924 (p0) cc_final: 0.7690 (p0) REVERT: D 32 ASN cc_start: 0.8436 (t0) cc_final: 0.7577 (m-40) REVERT: D 209 LYS cc_start: 0.8734 (tttp) cc_final: 0.7901 (ptpp) REVERT: D 338 GLU cc_start: 0.8385 (mp0) cc_final: 0.8028 (pm20) REVERT: D 447 GLU cc_start: 0.8604 (tt0) cc_final: 0.8337 (tt0) REVERT: A 16 ARG cc_start: 0.7974 (ttp-110) cc_final: 0.7602 (mtm110) REVERT: A 283 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8626 (mttm) REVERT: A 361 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.6975 (mtp180) REVERT: A 411 ARG cc_start: 0.7803 (mmt180) cc_final: 0.7095 (mtp85) REVERT: A 430 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: C 67 LYS cc_start: 0.8111 (ptpt) cc_final: 0.7760 (pttm) REVERT: C 233 GLU cc_start: 0.7360 (tp30) cc_final: 0.6432 (tm-30) REVERT: C 283 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8417 (mttm) REVERT: C 303 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7241 (tp30) REVERT: C 411 ARG cc_start: 0.7960 (mmt180) cc_final: 0.6875 (ptt-90) REVERT: C 490 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8164 (mmt) REVERT: C 496 LYS cc_start: 0.7856 (mtpp) cc_final: 0.7423 (mmtt) outliers start: 32 outliers final: 16 residues processed: 215 average time/residue: 0.7408 time to fit residues: 172.4801 Evaluate side-chains 217 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 361 ARG Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 490 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 194 optimal weight: 0.9990 chunk 57 optimal weight: 0.0770 chunk 143 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 165 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN A 381 ASN A 404 GLN C 114 ASN C 381 ASN C 404 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.130389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113462 restraints weight = 12338.260| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 0.86 r_work: 0.3213 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.198 16235 Z= 0.144 Angle : 0.695 29.257 21913 Z= 0.326 Chirality : 0.042 0.133 2283 Planarity : 0.004 0.072 2839 Dihedral : 4.967 56.750 2520 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.57 % Allowed : 9.65 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.11 % 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: 0.74 (0.19), residues: 1973 helix: 1.72 (0.16), residues: 964 sheet: -0.25 (0.38), residues: 186 loop : -0.79 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 16 TYR 0.016 0.002 TYR A 462 PHE 0.017 0.001 PHE A 125 TRP 0.010 0.001 TRP A 460 HIS 0.005 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (16219) covalent geometry : angle 0.69511 / 0.33 (21913) hydrogen bonds : bond 0.04479 / 3.04 ( 747) hydrogen bonds : angle 5.53478 / 4.09 ( 2169) Misc. bond : bond 0.09123 / 5.25 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3946 Ramachandran restraints generated. 1973 Oldfield, 0 Emsley, 1973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: B 7 LYS cc_start: 0.7640 (tttp) cc_final: 0.7019 (ttpp) REVERT: B 211 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7014 (mtm-85) REVERT: B 307 LYS cc_start: 0.8673 (mtmt) cc_final: 0.8262 (mtmm) REVERT: B 433 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8196 (mppt) REVERT: B 480 ARG cc_start: 0.8100 (mtt90) cc_final: 0.7884 (tmt90) REVERT: D 32 ASN cc_start: 0.8175 (t0) cc_final: 0.7440 (m-40) REVERT: D 209 LYS cc_start: 0.8539 (tttp) cc_final: 0.7823 (ptpp) REVERT: D 338 GLU cc_start: 0.8039 (mp0) cc_final: 0.7769 (pm20) REVERT: D 447 GLU cc_start: 0.8253 (tt0) cc_final: 0.7979 (tt0) REVERT: A 16 ARG cc_start: 0.7626 (ttp-110) cc_final: 0.7250 (mtm110) REVERT: A 283 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8577 (mttm) REVERT: A 361 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.6752 (mtp180) REVERT: A 411 ARG cc_start: 0.7541 (mmt180) cc_final: 0.6833 (ptt-90) REVERT: A 430 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7491 (tt0) REVERT: C 67 LYS cc_start: 0.8018 (ptpt) cc_final: 0.7782 (pttm) REVERT: C 233 GLU cc_start: 0.7091 (tp30) cc_final: 0.6593 (tm-30) REVERT: C 283 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8305 (mttm) REVERT: C 303 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.6819 (tp30) REVERT: C 411 ARG cc_start: 0.7674 (mmt180) cc_final: 0.6874 (ptt-90) REVERT: C 490 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7743 (mmt) REVERT: C 496 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7566 (mmtt) outliers start: 26 outliers final: 15 residues processed: 216 average time/residue: 0.7359 time to fit residues: 172.1013 Evaluate side-chains 216 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 361 ARG Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 490 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 66 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 162 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 181 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN A 381 ASN A 404 GLN C 114 ASN C 381 ASN C 404 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.129622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112650 restraints weight = 12282.370| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 0.86 r_work: 0.3201 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.213 16235 Z= 0.159 Angle : 0.710 29.321 21913 Z= 0.334 Chirality : 0.043 0.137 2283 Planarity : 0.005 0.072 2839 Dihedral : 4.960 56.677 2520 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.69 % Allowed : 9.47 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 1973 helix: 1.72 (0.16), residues: 964 sheet: -0.21 (0.38), residues: 186 loop : -0.77 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 16 TYR 0.017 0.002 TYR A 462 PHE 0.021 0.002 PHE A 125 TRP 0.009 0.001 TRP C 460 HIS 0.006 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (16219) covalent geometry : angle 0.71003 / 0.33 (21913) hydrogen bonds : bond 0.04761 / 3.23 ( 747) hydrogen bonds : angle 5.55072 / 4.10 ( 2169) Misc. bond : bond 0.09789 / 5.63 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6450.98 seconds wall clock time: 110 minutes 21.34 seconds (6621.34 seconds total)