Starting phenix.real_space_refine on Fri Jul 3 21:58:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ut7_26757/07_2026/7ut7_26757_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ut7_26757/07_2026/7ut7_26757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ut7_26757/07_2026/7ut7_26757_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ut7_26757/07_2026/7ut7_26757_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ut7_26757/07_2026/7ut7_26757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ut7_26757/07_2026/7ut7_26757.map" } resolution = 1.91 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= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 32 7.16 5 S 139 5.16 5 C 10170 2.51 5 N 2702 2.21 5 O 3397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16442 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} bond proxies already assigned to first conformer: 3874 Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 3790 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 3871 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Classifications: {'water': 126} Link IDs: {None: 125} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "D" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 28.964 56.061 35.742 1.00 23.62 S ATOM 4552 SG CYS B 95 38.305 71.094 51.086 1.00 19.10 S ATOM 1170 SG CYS A 154 35.131 74.245 48.043 1.00 18.14 S ATOM 465 SG CYS A 62 35.486 68.260 45.626 1.00 15.85 S ATOM 652 SG CYS A 88 41.010 72.533 45.467 1.00 17.18 S ATOM 652 SG CYS A 88 41.010 72.533 45.467 1.00 17.18 S ATOM 5005 SG CYS B 153 39.570 76.343 49.466 1.00 19.41 S ATOM 4372 SG CYS B 70 44.948 72.141 51.043 1.00 16.63 S ATOM 4552 SG CYS B 95 38.305 71.094 51.086 1.00 19.10 S ATOM 10056 SG CYS C 275 106.321 44.990 35.735 1.00 24.05 S ATOM 12516 SG CYS D 95 96.985 29.963 51.085 1.00 19.28 S ATOM 9134 SG CYS C 154 100.140 26.797 48.017 1.00 17.76 S ATOM 8429 SG CYS C 62 99.848 32.839 45.574 1.00 13.97 S ATOM 8616 SG CYS C 88 94.297 28.530 45.477 1.00 13.41 S ATOM 8616 SG CYS C 88 94.297 28.530 45.477 1.00 13.41 S ATOM 12969 SG CYS D 153 95.719 24.718 49.472 1.00 19.66 S ATOM 12336 SG CYS D 70 90.344 28.918 51.049 1.00 16.19 S ATOM 12516 SG CYS D 95 96.985 29.963 51.085 1.00 19.28 S Time building chain proxies: 4.23, per 1000 atoms: 0.26 Number of scatterers: 16442 At special positions: 0 Unit cell: (136.105, 101.06, 94.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mo 2 41.97 Fe 32 26.01 S 139 16.00 O 3397 8.00 N 2702 7.00 C 10170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 861.7 milliseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 59.6% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.954A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.505A pdb=" N GLN A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.947A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.637A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.240A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.147A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 5.793A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 383 through 394 removed outlier: 3.930A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 434 removed outlier: 4.477A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.627A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 32 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 81 removed outlier: 4.070A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.073A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 211 through 216 removed outlier: 5.477A pdb=" N ASP B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP B 215 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.832A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 320 through 337 removed outlier: 4.093A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.461A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 30 removed outlier: 3.955A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 92 removed outlier: 3.507A pdb=" N GLN C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 removed outlier: 3.977A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.224A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 245 removed outlier: 4.114A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 275 through 291 removed outlier: 5.786A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 314 Processing helix chain 'C' and resid 317 through 347 Proline residue: C 333 - end of helix Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 363 through 370 removed outlier: 3.571A pdb=" N LEU C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.268A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 434 removed outlier: 4.505A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.621A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.518A pdb=" N GLU D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 70 through 81 removed outlier: 4.069A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.022A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 211 through 216 removed outlier: 5.475A pdb=" N ASP D 214 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP D 215 " --> pdb=" O SER D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.829A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.318A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 445 through 447 No H-bonds generated for 'chain 'D' and resid 445 through 447' Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.384A pdb=" N LEU A 353 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR A 377 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 6.888A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 6.992A pdb=" N VAL A 223 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N TRP A 253 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A 225 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.332A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.580A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N MET B 442 " --> pdb=" O ILE B 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.372A pdb=" N LEU C 353 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR C 377 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 6.881A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254 removed outlier: 6.935A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE C 225 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.330A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.559A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET D 442 " --> pdb=" O ILE D 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 789 hydrogen bonds defined for protein. 2247 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: 2.79 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.85: 16347 1.85 - 2.48: 102 2.48 - 3.11: 20 3.11 - 3.74: 10 3.74 - 4.38: 4 Bond restraints: 16483 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 4.375 -2.175 2.00e-02 2.50e+03 1.18e+04 bond pdb="FE2 CLF B 602 " pdb="FE8 CLF B 602 " ideal model delta sigma weight residual 2.200 4.369 -2.169 2.00e-02 2.50e+03 1.18e+04 bond pdb="FE5 CLF D 602 " pdb="FE6 CLF D 602 " ideal model delta sigma weight residual 2.200 3.929 -1.729 2.00e-02 2.50e+03 7.47e+03 bond pdb="FE5 CLF B 602 " pdb="FE6 CLF B 602 " ideal model delta sigma weight residual 2.200 3.923 -1.723 2.00e-02 2.50e+03 7.42e+03 bond pdb=" S1 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 3.688 -1.488 2.00e-02 2.50e+03 5.53e+03 ... (remaining 16478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.87: 22237 6.87 - 13.75: 0 13.75 - 20.62: 2 20.62 - 27.50: 0 27.50 - 34.37: 4 Bond angle restraints: 22243 Sorted by residual: angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE4 CLF B 602 " ideal model delta sigma weight residual 90.00 55.63 34.37 3.00e+00 1.11e-01 1.31e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.63 34.37 3.00e+00 1.11e-01 1.31e+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 60.63 29.37 3.00e+00 1.11e-01 9.59e+01 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE1 CLF D 602 " ideal model delta sigma weight residual 90.00 60.75 29.25 3.00e+00 1.11e-01 9.50e+01 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE3 CLF D 602 " ideal model delta sigma weight residual 90.00 108.24 -18.24 3.00e+00 1.11e-01 3.70e+01 ... (remaining 22238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 9029 18.00 - 36.00: 784 36.00 - 54.01: 201 54.01 - 72.01: 51 72.01 - 90.01: 36 Dihedral angle restraints: 10101 sinusoidal: 4359 harmonic: 5742 Sorted by residual: dihedral pdb=" CA ILE C 75 " pdb=" C ILE C 75 " pdb=" N LYS C 76 " pdb=" CA LYS C 76 " ideal model delta harmonic sigma weight residual 180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA SER D 11 " pdb=" C SER D 11 " pdb=" N TYR D 12 " pdb=" CA TYR D 12 " ideal model delta harmonic sigma weight residual 180.00 161.00 19.00 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA SER B 11 " pdb=" C SER B 11 " pdb=" N TYR B 12 " pdb=" CA TYR B 12 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1573 0.042 - 0.085: 564 0.085 - 0.127: 182 0.127 - 0.170: 16 0.170 - 0.212: 1 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA GLU D 109 " pdb=" N GLU D 109 " pdb=" C GLU D 109 " pdb=" CB GLU D 109 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA PHE C 431 " pdb=" N PHE C 431 " pdb=" C PHE C 431 " pdb=" CB PHE C 431 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA PHE A 431 " pdb=" N PHE A 431 " pdb=" C PHE A 431 " pdb=" CB PHE A 431 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 2333 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 359 " 0.030 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO A 360 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 73 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO A 74 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 73 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO C 74 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " -0.022 5.00e-02 4.00e+02 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 531 2.69 - 3.24: 17096 3.24 - 3.80: 30869 3.80 - 4.35: 41735 4.35 - 4.90: 65109 Nonbonded interactions: 155340 Sorted by model distance: nonbonded pdb=" O1 HCA C 501 " pdb=" O7 HCA C 501 " model vdw 2.140 3.040 nonbonded pdb=" O1 HCA A 501 " pdb=" O7 HCA A 501 " model vdw 2.155 3.040 nonbonded pdb=" OD2 ASP D 353 " pdb="FE FE D 601 " model vdw 2.204 3.000 nonbonded pdb=" OD2 ASP D 357 " pdb="FE FE D 601 " model vdw 2.204 3.000 nonbonded pdb="FE FE B 601 " pdb=" O HOH D 812 " model vdw 2.212 3.000 ... (remaining 155335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 248 or resid 250 through 502)) selection = (chain 'C' and (resid 4 through 248 or resid 250 through 502)) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.160 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.048 2.175 16499 Z= 2.413 Angle : 0.806 34.373 22243 Z= 0.400 Chirality : 0.047 0.212 2336 Planarity : 0.005 0.061 2858 Dihedral : 15.928 90.009 6433 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.87 % Allowed : 12.42 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.18), residues: 1992 helix: 0.98 (0.16), residues: 992 sheet: -0.89 (0.32), residues: 202 loop : -0.44 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 359 TYR 0.024 0.003 TYR A 229 PHE 0.023 0.003 PHE A 431 TRP 0.015 0.002 TRP C 444 HIS 0.009 0.002 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.04789 / 2.40 (16483) covalent geometry : angle 0.80622 / 0.40 (22243) hydrogen bonds : bond 0.14345 / 9.80 ( 789) hydrogen bonds : angle 6.74059 / 4.85 ( 2247) Misc. bond : bond 0.10353 / 7.76 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 211 LYS cc_start: 0.7652 (mtpm) cc_final: 0.7444 (mttt) REVERT: D 211 LYS cc_start: 0.7650 (mtpm) cc_final: 0.7439 (mttt) REVERT: D 299 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7790 (tp30) outliers start: 15 outliers final: 12 residues processed: 225 average time/residue: 0.7226 time to fit residues: 176.0454 Evaluate side-chains 223 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 211 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 53 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.146867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.132724 restraints weight = 8442.072| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 0.36 r_work: 0.3305 rms_B_bonded: 0.74 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 1.29 restraints_weight: 0.2500 r_work: 0.3058 rms_B_bonded: 3.70 restraints_weight: 0.1250 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.342 16499 Z= 0.280 Angle : 0.743 30.802 22243 Z= 0.359 Chirality : 0.045 0.145 2336 Planarity : 0.004 0.053 2858 Dihedral : 5.657 56.200 2536 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.39 % Allowed : 11.26 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.18), residues: 1992 helix: 1.12 (0.16), residues: 1028 sheet: -0.74 (0.33), residues: 196 loop : -0.39 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 108 TYR 0.019 0.002 TYR C 229 PHE 0.020 0.002 PHE A 431 TRP 0.013 0.002 TRP A 253 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.26 (16483) covalent geometry : angle 0.74346 / 0.36 (22243) hydrogen bonds : bond 0.05987 / 4.15 ( 789) hydrogen bonds : angle 5.81270 / 4.16 ( 2247) Misc. bond : bond 0.17020 / 10.62 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.6942 (t) cc_final: 0.6725 (m) REVERT: A 18 GLU cc_start: 0.7258 (mt-10) cc_final: 0.7021 (mt-10) REVERT: A 345 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8288 (mtt180) REVERT: A 445 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8032 (m-30) REVERT: B 299 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8339 (tp30) REVERT: C 18 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7100 (mt-10) REVERT: C 445 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: D 299 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8464 (tp30) outliers start: 24 outliers final: 12 residues processed: 234 average time/residue: 0.7214 time to fit residues: 183.5659 Evaluate side-chains 227 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 120 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 79 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 chunk 90 optimal weight: 0.5980 chunk 113 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 362 HIS B 129 GLN D 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.147416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.131481 restraints weight = 13040.569| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 0.48 r_work: 0.3279 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 1.65 restraints_weight: 0.2500 r_work: 0.3027 rms_B_bonded: 4.72 restraints_weight: 0.1250 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.342 16499 Z= 0.265 Angle : 0.731 30.777 22243 Z= 0.350 Chirality : 0.045 0.145 2336 Planarity : 0.004 0.051 2858 Dihedral : 5.277 51.320 2528 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.33 % Allowed : 11.90 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 1992 helix: 1.23 (0.16), residues: 1028 sheet: -0.76 (0.36), residues: 176 loop : -0.36 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 108 TYR 0.019 0.002 TYR C 229 PHE 0.017 0.002 PHE A 431 TRP 0.013 0.002 TRP A 253 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.24 (16483) covalent geometry : angle 0.73063 / 0.35 (22243) hydrogen bonds : bond 0.05625 / 3.89 ( 789) hydrogen bonds : angle 5.65823 / 4.05 ( 2247) Misc. bond : bond 0.16275 / 10.09 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7039 (mt-10) REVERT: A 345 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8351 (mtt180) REVERT: A 445 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: B 120 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7370 (mt-10) REVERT: B 238 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8373 (mtt180) REVERT: B 299 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8386 (tp30) REVERT: C 18 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7136 (mt-10) REVERT: C 445 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8097 (m-30) REVERT: C 476 GLN cc_start: 0.8180 (tp-100) cc_final: 0.7878 (tt0) REVERT: D 299 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8473 (tp30) outliers start: 23 outliers final: 12 residues processed: 235 average time/residue: 0.7442 time to fit residues: 189.9719 Evaluate side-chains 230 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 120 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 195 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN A 285 HIS ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.147948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.131366 restraints weight = 15392.350| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 0.56 r_work: 0.3268 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.3030 rms_B_bonded: 4.71 restraints_weight: 0.1250 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.332 16499 Z= 0.258 Angle : 0.726 30.751 22243 Z= 0.346 Chirality : 0.044 0.147 2336 Planarity : 0.004 0.048 2858 Dihedral : 5.203 52.041 2527 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.33 % Allowed : 11.61 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 1992 helix: 1.28 (0.16), residues: 1028 sheet: -0.74 (0.36), residues: 176 loop : -0.36 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 108 TYR 0.018 0.002 TYR C 229 PHE 0.019 0.002 PHE A 431 TRP 0.012 0.002 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.24 (16483) covalent geometry : angle 0.72607 / 0.35 (22243) hydrogen bonds : bond 0.05436 / 3.77 ( 789) hydrogen bonds : angle 5.59769 / 4.00 ( 2247) Misc. bond : bond 0.15547 / 9.60 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6982 (mt-10) REVERT: A 345 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8337 (mtt180) REVERT: A 445 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8120 (m-30) REVERT: B 120 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7372 (mt-10) REVERT: B 211 LYS cc_start: 0.8141 (mtpm) cc_final: 0.7861 (mmtt) REVERT: B 238 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8326 (mtt180) REVERT: B 299 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8380 (tp30) REVERT: C 18 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7088 (mt-10) REVERT: C 445 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: C 476 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7888 (tt0) REVERT: D 211 LYS cc_start: 0.8123 (mtpm) cc_final: 0.7853 (mmtt) outliers start: 23 outliers final: 16 residues processed: 232 average time/residue: 0.7570 time to fit residues: 190.2739 Evaluate side-chains 232 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 120 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 161 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN A 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.146486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.130401 restraints weight = 13461.894| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 0.53 r_work: 0.3245 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work: 0.3021 rms_B_bonded: 4.37 restraints_weight: 0.1250 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.381 16499 Z= 0.276 Angle : 0.748 30.662 22243 Z= 0.360 Chirality : 0.045 0.154 2336 Planarity : 0.004 0.054 2858 Dihedral : 5.271 53.567 2527 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.33 % Allowed : 11.61 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 1992 helix: 1.22 (0.16), residues: 1028 sheet: -0.76 (0.36), residues: 176 loop : -0.37 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.018 0.002 TYR D 88 PHE 0.019 0.002 PHE C 431 TRP 0.012 0.002 TRP B 296 HIS 0.009 0.002 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.26 (16483) covalent geometry : angle 0.74797 / 0.36 (22243) hydrogen bonds : bond 0.05876 / 4.06 ( 789) hydrogen bonds : angle 5.67027 / 4.06 ( 2247) Misc. bond : bond 0.16674 / 10.13 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6930 (mt-10) REVERT: A 345 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8292 (mtt180) REVERT: A 445 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8087 (m-30) REVERT: B 211 LYS cc_start: 0.8121 (mtpm) cc_final: 0.7856 (mmtt) REVERT: C 18 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7010 (mt-10) REVERT: C 445 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8097 (m-30) REVERT: D 211 LYS cc_start: 0.8100 (mtpm) cc_final: 0.7867 (mmtt) outliers start: 23 outliers final: 15 residues processed: 235 average time/residue: 0.7408 time to fit residues: 188.2871 Evaluate side-chains 230 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 120 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 185 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 146 optimal weight: 0.0010 chunk 52 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN B 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.146691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.130718 restraints weight = 11604.512| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 0.46 r_work: 0.3293 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.3043 rms_B_bonded: 3.92 restraints_weight: 0.1250 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.390 16499 Z= 0.273 Angle : 0.746 30.660 22243 Z= 0.359 Chirality : 0.045 0.154 2336 Planarity : 0.004 0.053 2858 Dihedral : 5.256 53.767 2527 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.28 % Allowed : 11.90 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 1992 helix: 1.22 (0.16), residues: 1028 sheet: -0.74 (0.36), residues: 176 loop : -0.37 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.018 0.002 TYR C 229 PHE 0.015 0.002 PHE C 431 TRP 0.012 0.002 TRP A 335 HIS 0.008 0.002 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.25 (16483) covalent geometry : angle 0.74642 / 0.36 (22243) hydrogen bonds : bond 0.05805 / 4.01 ( 789) hydrogen bonds : angle 5.65294 / 4.04 ( 2247) Misc. bond : bond 0.16500 / 9.96 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 217 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6891 (mt-10) REVERT: A 345 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8302 (mtt180) REVERT: A 445 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: B 211 LYS cc_start: 0.8110 (mtpm) cc_final: 0.7799 (mmtt) REVERT: B 238 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8340 (mtt180) REVERT: C 18 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6987 (mt-10) REVERT: C 386 ASP cc_start: 0.7759 (m-30) cc_final: 0.7539 (m-30) REVERT: C 445 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7968 (m-30) REVERT: D 211 LYS cc_start: 0.8067 (mtpm) cc_final: 0.7787 (mmtt) outliers start: 22 outliers final: 16 residues processed: 233 average time/residue: 0.7435 time to fit residues: 187.9600 Evaluate side-chains 234 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 120 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 163 optimal weight: 0.0010 chunk 31 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 176 optimal weight: 0.1980 chunk 155 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN C 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.147762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.132770 restraints weight = 12790.343| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 0.46 r_work: 0.3285 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 1.65 restraints_weight: 0.2500 r_work: 0.3037 rms_B_bonded: 4.53 restraints_weight: 0.1250 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.360 16499 Z= 0.259 Angle : 0.733 30.689 22243 Z= 0.350 Chirality : 0.045 0.153 2336 Planarity : 0.004 0.049 2858 Dihedral : 5.137 53.642 2524 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.39 % Allowed : 12.19 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 1992 helix: 1.27 (0.16), residues: 1028 sheet: -0.70 (0.36), residues: 176 loop : -0.35 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.018 0.002 TYR A 229 PHE 0.019 0.002 PHE C 431 TRP 0.012 0.002 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.24 (16483) covalent geometry : angle 0.73317 / 0.35 (22243) hydrogen bonds : bond 0.05471 / 3.78 ( 789) hydrogen bonds : angle 5.58567 / 3.99 ( 2247) Misc. bond : bond 0.15613 / 9.46 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6920 (mt-10) REVERT: A 345 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8337 (mtt180) REVERT: A 384 ASN cc_start: 0.7782 (m110) cc_final: 0.7578 (m-40) REVERT: A 445 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8048 (m-30) REVERT: B 211 LYS cc_start: 0.8138 (mtpm) cc_final: 0.7873 (mmtt) REVERT: B 238 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8312 (mtt180) REVERT: C 18 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7027 (mt-10) REVERT: C 445 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8078 (m-30) REVERT: D 211 LYS cc_start: 0.8119 (mtpm) cc_final: 0.7883 (mmtt) outliers start: 24 outliers final: 17 residues processed: 237 average time/residue: 0.7818 time to fit residues: 201.0691 Evaluate side-chains 232 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 120 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 5 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.145280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.129504 restraints weight = 11603.509| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 0.50 r_work: 0.3240 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 1.72 restraints_weight: 0.2500 r_work: 0.2994 rms_B_bonded: 4.56 restraints_weight: 0.1250 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.452 16499 Z= 0.297 Angle : 0.778 30.678 22243 Z= 0.378 Chirality : 0.046 0.165 2336 Planarity : 0.005 0.060 2858 Dihedral : 5.306 54.656 2524 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.39 % Allowed : 12.19 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.18), residues: 1992 helix: 1.16 (0.16), residues: 1028 sheet: -0.69 (0.33), residues: 196 loop : -0.39 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 359 TYR 0.021 0.002 TYR A 379 PHE 0.017 0.002 PHE C 431 TRP 0.012 0.002 TRP B 296 HIS 0.009 0.002 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.27 (16483) covalent geometry : angle 0.77787 / 0.38 (22243) hydrogen bonds : bond 0.06311 / 4.36 ( 789) hydrogen bonds : angle 5.75266 / 4.12 ( 2247) Misc. bond : bond 0.18434 / 10.89 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6973 (mt-10) REVERT: A 345 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8274 (mtt180) REVERT: A 445 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8062 (m-30) REVERT: B 238 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8360 (mtt180) REVERT: B 299 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8340 (mm-30) REVERT: C 18 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7107 (mt-10) REVERT: C 445 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8091 (m-30) REVERT: D 171 LYS cc_start: 0.7294 (mttm) cc_final: 0.6881 (mmtt) outliers start: 24 outliers final: 16 residues processed: 230 average time/residue: 0.7522 time to fit residues: 187.1903 Evaluate side-chains 229 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 120 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 162 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 147 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN C 53 GLN D 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.147691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.131392 restraints weight = 17439.594| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 0.56 r_work: 0.3244 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work: 0.3040 rms_B_bonded: 4.27 restraints_weight: 0.1250 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.369 16499 Z= 0.261 Angle : 0.737 30.618 22243 Z= 0.353 Chirality : 0.045 0.160 2336 Planarity : 0.004 0.050 2858 Dihedral : 5.165 53.677 2524 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.33 % Allowed : 12.13 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 1992 helix: 1.24 (0.16), residues: 1028 sheet: -0.71 (0.36), residues: 176 loop : -0.34 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.019 0.002 TYR C 229 PHE 0.014 0.002 PHE A 431 TRP 0.013 0.002 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.24 (16483) covalent geometry : angle 0.73666 / 0.35 (22243) hydrogen bonds : bond 0.05483 / 3.79 ( 789) hydrogen bonds : angle 5.59734 / 4.00 ( 2247) Misc. bond : bond 0.15972 / 9.61 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6817 (mt-10) REVERT: A 345 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8323 (mtt180) REVERT: A 445 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: B 238 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8276 (mtt180) REVERT: C 18 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6933 (mt-10) REVERT: C 445 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8039 (m-30) REVERT: D 171 LYS cc_start: 0.7298 (mttm) cc_final: 0.6880 (mmtt) REVERT: D 299 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8030 (tp30) outliers start: 23 outliers final: 16 residues processed: 230 average time/residue: 0.7681 time to fit residues: 191.1384 Evaluate side-chains 230 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 299 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 130 optimal weight: 0.8980 chunk 163 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN B 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.147682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.132202 restraints weight = 10760.235| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 0.47 r_work: 0.3281 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 1.76 restraints_weight: 0.2500 r_work: 0.3040 rms_B_bonded: 4.55 restraints_weight: 0.1250 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.379 16499 Z= 0.263 Angle : 0.744 30.658 22243 Z= 0.356 Chirality : 0.045 0.166 2336 Planarity : 0.004 0.050 2858 Dihedral : 5.156 54.007 2524 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.33 % Allowed : 12.19 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 1992 helix: 1.25 (0.16), residues: 1028 sheet: -0.70 (0.36), residues: 176 loop : -0.31 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.018 0.002 TYR C 229 PHE 0.014 0.002 PHE C 431 TRP 0.012 0.002 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.24 (16483) covalent geometry : angle 0.74446 / 0.36 (22243) hydrogen bonds : bond 0.05532 / 3.83 ( 789) hydrogen bonds : angle 5.59525 / 4.00 ( 2247) Misc. bond : bond 0.16099 / 9.63 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6905 (mt-10) REVERT: A 345 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8313 (mtt180) REVERT: A 384 ASN cc_start: 0.7769 (m110) cc_final: 0.7530 (m-40) REVERT: A 445 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: B 238 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8302 (mtt180) REVERT: C 18 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7039 (mt-10) REVERT: C 445 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: D 171 LYS cc_start: 0.7318 (mttm) cc_final: 0.6901 (mmtt) outliers start: 23 outliers final: 16 residues processed: 225 average time/residue: 0.7716 time to fit residues: 188.3531 Evaluate side-chains 229 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 120 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 139 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 184 optimal weight: 0.9990 chunk 152 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN C 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.149679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.133905 restraints weight = 13295.532| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 0.48 r_work: 0.3303 rms_B_bonded: 1.03 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 1.79 restraints_weight: 0.2500 r_work: 0.3062 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.318 16499 Z= 0.245 Angle : 0.724 30.672 22243 Z= 0.344 Chirality : 0.044 0.160 2336 Planarity : 0.004 0.044 2858 Dihedral : 5.055 52.587 2524 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.22 % Allowed : 12.13 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.19), residues: 1992 helix: 1.30 (0.16), residues: 1028 sheet: -0.66 (0.37), residues: 176 loop : -0.28 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 359 TYR 0.019 0.002 TYR A 229 PHE 0.013 0.002 PHE C 431 TRP 0.013 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.23 (16483) covalent geometry : angle 0.72380 / 0.34 (22243) hydrogen bonds : bond 0.05034 / 3.49 ( 789) hydrogen bonds : angle 5.51137 / 3.93 ( 2247) Misc. bond : bond 0.14851 / 9.07 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8782.02 seconds wall clock time: 149 minutes 52.30 seconds (8992.30 seconds total)