Starting phenix.real_space_refine on Mon Apr 6 05:59:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ut7_26757/04_2026/7ut7_26757_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ut7_26757/04_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_26757/04_2026/7ut7_26757_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ut7_26757/04_2026/7ut7_26757_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ut7_26757/04_2026/7ut7_26757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ut7_26757/04_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 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: 5.08, per 1000 atoms: 0.31 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: 1.31 Conformation dependent library (CDL) restraints added in 1.0 seconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 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: 0.53 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: 3.01 Time building geometry restraints manager: 1.63 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 2.260 nonbonded pdb=" OD2 ASP D 357 " pdb="FE FE D 601 " model vdw 2.204 2.260 nonbonded pdb="FE FE B 601 " pdb=" O HOH D 812 " model vdw 2.212 2.260 ... (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: 12.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.450 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 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 covalent geometry : bond 0.04789 (16483) covalent geometry : angle 0.80622 (22243) hydrogen bonds : bond 0.14345 ( 789) hydrogen bonds : angle 6.74059 ( 2247) Misc. bond : bond 0.10353 ( 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 : 0.694 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: 0.8426 time to fit residues: 204.9303 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 : 0.541 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 53 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.146859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.132306 restraints weight = 8591.294| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 0.38 r_work: 0.3308 rms_B_bonded: 0.75 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 1.29 restraints_weight: 0.2500 r_work: 0.3061 rms_B_bonded: 3.69 restraints_weight: 0.1250 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 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 = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.0642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.344 16499 Z= 0.275 Angle : 0.738 30.572 22243 Z= 0.356 Chirality : 0.045 0.143 2336 Planarity : 0.004 0.053 2858 Dihedral : 5.639 55.059 2536 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.45 % Allowed : 11.26 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.18), residues: 1992 helix: 1.12 (0.16), residues: 1028 sheet: -0.73 (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 0.019 0.002 PHE A 431 TRP 0.014 0.002 TRP A 253 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00516 (16483) covalent geometry : angle 0.73751 (22243) hydrogen bonds : bond 0.05904 ( 789) hydrogen bonds : angle 5.76238 ( 2247) Misc. bond : bond 0.16967 ( 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 246 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.6941 (t) cc_final: 0.6727 (m) REVERT: A 18 GLU cc_start: 0.7265 (mt-10) cc_final: 0.7023 (mt-10) REVERT: A 345 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8289 (mtt180) REVERT: A 445 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8022 (m-30) REVERT: B 120 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7269 (mt-10) REVERT: B 299 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8341 (tp30) REVERT: C 18 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7095 (mt-10) REVERT: C 445 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: D 299 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8467 (tp30) outliers start: 25 outliers final: 12 residues processed: 236 average time/residue: 0.8425 time to fit residues: 215.1945 Evaluate side-chains 229 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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: 9.9990 chunk 90 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 171 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN D 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.145344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.129241 restraints weight = 13253.771| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 0.50 r_work: 0.3239 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 1.76 restraints_weight: 0.2500 r_work: 0.2989 rms_B_bonded: 4.76 restraints_weight: 0.1250 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.376 16499 Z= 0.288 Angle : 0.758 30.748 22243 Z= 0.368 Chirality : 0.046 0.148 2336 Planarity : 0.005 0.060 2858 Dihedral : 5.433 52.308 2528 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.33 % Allowed : 11.55 % Favored : 87.12 % 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: -0.71 (0.33), residues: 196 loop : -0.40 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 359 TYR 0.020 0.002 TYR A 229 PHE 0.020 0.002 PHE A 431 TRP 0.013 0.002 TRP A 253 HIS 0.014 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00546 (16483) covalent geometry : angle 0.75848 (22243) hydrogen bonds : bond 0.06218 ( 789) hydrogen bonds : angle 5.75409 ( 2247) Misc. bond : bond 0.17729 ( 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 240 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.6928 (t) cc_final: 0.6724 (m) REVERT: A 18 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7000 (mt-10) REVERT: A 345 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8306 (mtt180) REVERT: A 445 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8105 (m-30) REVERT: B 120 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7344 (mt-10) REVERT: B 299 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8387 (tp30) REVERT: C 18 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7093 (mt-10) REVERT: C 445 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8116 (m-30) outliers start: 23 outliers final: 15 residues processed: 235 average time/residue: 0.8215 time to fit residues: 208.8966 Evaluate side-chains 235 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 92 SER Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain C residue 98 ASN 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 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: 2.9990 chunk 93 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.148676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.132086 restraints weight = 15578.953| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 0.55 r_work: 0.3290 rms_B_bonded: 1.03 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 1.79 restraints_weight: 0.2500 r_work: 0.3040 rms_B_bonded: 4.95 restraints_weight: 0.1250 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.310 16499 Z= 0.247 Angle : 0.716 30.713 22243 Z= 0.340 Chirality : 0.044 0.144 2336 Planarity : 0.004 0.045 2858 Dihedral : 5.185 51.871 2528 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.45 % Allowed : 11.49 % 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: 0.64 (0.18), residues: 1992 helix: 1.28 (0.16), residues: 1028 sheet: -0.72 (0.36), residues: 176 loop : -0.35 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 108 TYR 0.018 0.002 TYR A 229 PHE 0.014 0.002 PHE A 431 TRP 0.012 0.001 TRP A 253 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00469 (16483) covalent geometry : angle 0.71588 (22243) hydrogen bonds : bond 0.05179 ( 789) hydrogen bonds : angle 5.52829 ( 2247) Misc. bond : bond 0.14763 ( 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 251 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6999 (mt-10) REVERT: A 176 LYS cc_start: 0.8320 (tppt) cc_final: 0.8082 (tppt) REVERT: A 345 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8371 (mtt180) REVERT: A 445 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8140 (m-30) REVERT: B 120 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7364 (mt-10) REVERT: B 211 LYS cc_start: 0.8114 (mtpm) cc_final: 0.7803 (mmtt) REVERT: B 238 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8349 (mtt180) REVERT: B 299 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8416 (tp30) REVERT: C 18 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7106 (mt-10) REVERT: C 445 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8131 (m-30) REVERT: D 211 LYS cc_start: 0.8128 (mtpm) cc_final: 0.7840 (mmtt) outliers start: 25 outliers final: 12 residues processed: 243 average time/residue: 0.8399 time to fit residues: 220.4621 Evaluate side-chains 231 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 161 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 100 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 285 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.148469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.132814 restraints weight = 13493.655| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 0.48 r_work: 0.3298 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 1.64 restraints_weight: 0.2500 r_work: 0.3045 rms_B_bonded: 4.76 restraints_weight: 0.1250 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 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 = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.327 16499 Z= 0.249 Angle : 0.718 30.721 22243 Z= 0.340 Chirality : 0.044 0.143 2336 Planarity : 0.004 0.045 2858 Dihedral : 5.117 52.432 2527 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.28 % Allowed : 11.84 % Favored : 86.88 % 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: 0.69 (0.18), residues: 1992 helix: 1.31 (0.16), residues: 1028 sheet: -0.67 (0.36), residues: 176 loop : -0.31 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 359 TYR 0.017 0.002 TYR A 229 PHE 0.017 0.002 PHE C 431 TRP 0.012 0.002 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00473 (16483) covalent geometry : angle 0.71760 (22243) hydrogen bonds : bond 0.05207 ( 789) hydrogen bonds : angle 5.49349 ( 2247) Misc. bond : bond 0.14879 ( 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 237 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6991 (mt-10) REVERT: A 345 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8356 (mtt180) REVERT: A 384 ASN cc_start: 0.7750 (m110) cc_final: 0.7541 (m-40) REVERT: A 392 LYS cc_start: 0.6839 (pttm) cc_final: 0.6620 (ptmt) REVERT: A 445 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: B 211 LYS cc_start: 0.8106 (mtpm) cc_final: 0.7808 (mmtt) REVERT: B 238 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8342 (mtt180) REVERT: B 299 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8402 (tp30) REVERT: C 18 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7103 (mt-10) REVERT: C 386 ASP cc_start: 0.7833 (m-30) cc_final: 0.7550 (m-30) REVERT: C 445 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8081 (m-30) REVERT: D 211 LYS cc_start: 0.8121 (mtpm) cc_final: 0.7849 (mmtt) outliers start: 22 outliers final: 16 residues processed: 232 average time/residue: 0.8524 time to fit residues: 213.6718 Evaluate side-chains 234 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 167 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 92 SER 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: 0.9990 chunk 48 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.145211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.129179 restraints weight = 11805.172| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 0.47 r_work: 0.3269 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work: 0.3015 rms_B_bonded: 4.03 restraints_weight: 0.1250 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.424 16499 Z= 0.292 Angle : 0.770 30.611 22243 Z= 0.373 Chirality : 0.046 0.150 2336 Planarity : 0.005 0.060 2858 Dihedral : 5.326 54.285 2527 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.22 % Allowed : 11.78 % Favored : 87.00 % 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: 0.54 (0.18), residues: 1992 helix: 1.18 (0.16), residues: 1028 sheet: -0.67 (0.33), residues: 196 loop : -0.36 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 108 TYR 0.020 0.002 TYR C 379 PHE 0.019 0.002 PHE A 431 TRP 0.013 0.002 TRP B 296 HIS 0.009 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00560 (16483) covalent geometry : angle 0.76966 (22243) hydrogen bonds : bond 0.06239 ( 789) hydrogen bonds : angle 5.70496 ( 2247) Misc. bond : bond 0.17965 ( 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 237 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6959 (mt-10) REVERT: A 445 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7969 (m-30) REVERT: B 211 LYS cc_start: 0.8076 (mtpm) cc_final: 0.7750 (mmtt) REVERT: B 299 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8381 (tp30) REVERT: C 18 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7027 (mt-10) REVERT: C 445 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7978 (m-30) REVERT: D 211 LYS cc_start: 0.8072 (mtpm) cc_final: 0.7783 (mmtt) REVERT: D 299 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8379 (tp30) outliers start: 21 outliers final: 14 residues processed: 234 average time/residue: 0.8485 time to fit residues: 214.1191 Evaluate side-chains 229 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP 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 299 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: 0.0980 chunk 163 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 180 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 129 GLN C 53 GLN D 268 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.146060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.131619 restraints weight = 13039.310| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 0.44 r_work: 0.3271 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 1.56 restraints_weight: 0.2500 r_work: 0.3020 rms_B_bonded: 4.51 restraints_weight: 0.1250 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 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 = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.409 16499 Z= 0.276 Angle : 0.753 30.619 22243 Z= 0.362 Chirality : 0.045 0.157 2336 Planarity : 0.004 0.054 2858 Dihedral : 5.225 53.867 2524 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.22 % Allowed : 12.07 % 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: 0.54 (0.18), residues: 1992 helix: 1.18 (0.16), residues: 1028 sheet: -0.75 (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 0.019 0.002 TYR C 229 PHE 0.016 0.002 PHE A 431 TRP 0.012 0.002 TRP A 335 HIS 0.009 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00526 (16483) covalent geometry : angle 0.75269 (22243) hydrogen bonds : bond 0.05863 ( 789) hydrogen bonds : angle 5.63836 ( 2247) Misc. bond : bond 0.16960 ( 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 235 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7345 (mt-10) cc_final: 0.7016 (mt-10) REVERT: A 445 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8031 (m-30) REVERT: B 211 LYS cc_start: 0.8139 (mtpm) cc_final: 0.7849 (mmtt) REVERT: B 238 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8385 (mtt180) REVERT: B 299 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8415 (tp30) REVERT: C 18 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7143 (mt-10) REVERT: C 445 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8056 (m-30) REVERT: D 211 LYS cc_start: 0.8101 (mtpm) cc_final: 0.7840 (mmtt) REVERT: D 299 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8405 (tp30) outliers start: 21 outliers final: 14 residues processed: 230 average time/residue: 0.8391 time to fit residues: 208.5762 Evaluate side-chains 230 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP 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 299 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 5 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 188 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3569 r_free = 0.3569 target = 0.145260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.129305 restraints weight = 11726.336| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 0.46 r_work: 0.3269 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.3019 rms_B_bonded: 3.98 restraints_weight: 0.1250 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.447 16499 Z= 0.289 Angle : 0.769 30.660 22243 Z= 0.373 Chirality : 0.046 0.159 2336 Planarity : 0.005 0.058 2858 Dihedral : 5.288 54.414 2524 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: 0.50 (0.18), residues: 1992 helix: 1.14 (0.16), residues: 1028 sheet: -0.67 (0.33), residues: 196 loop : -0.38 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 359 TYR 0.020 0.002 TYR A 379 PHE 0.019 0.002 PHE A 431 TRP 0.012 0.002 TRP B 296 HIS 0.009 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00554 (16483) covalent geometry : angle 0.76945 (22243) hydrogen bonds : bond 0.06180 ( 789) hydrogen bonds : angle 5.70144 ( 2247) Misc. bond : bond 0.17884 ( 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 235 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6947 (mt-10) REVERT: A 23 LYS cc_start: 0.7433 (tttm) cc_final: 0.7231 (ttmm) REVERT: A 176 LYS cc_start: 0.8165 (tppt) cc_final: 0.7963 (tppt) REVERT: A 445 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: B 153 CYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8397 (p) REVERT: B 238 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8353 (mtt180) REVERT: B 299 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8379 (tp30) REVERT: C 18 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7094 (mt-10) REVERT: C 445 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: D 211 LYS cc_start: 0.8093 (mtpm) cc_final: 0.7822 (mmtt) REVERT: D 299 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8380 (tp30) outliers start: 21 outliers final: 14 residues processed: 231 average time/residue: 0.8603 time to fit residues: 214.5041 Evaluate side-chains 230 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 153 CYS 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 299 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: 2.9990 chunk 25 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 142 optimal weight: 0.5980 chunk 147 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3603 r_free = 0.3603 target = 0.148071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.132022 restraints weight = 17675.424| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 0.59 r_work: 0.3263 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work: 0.3043 rms_B_bonded: 4.33 restraints_weight: 0.1250 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 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 = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.350 16499 Z= 0.253 Angle : 0.731 30.694 22243 Z= 0.349 Chirality : 0.045 0.160 2336 Planarity : 0.004 0.048 2858 Dihedral : 5.129 53.285 2524 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.39 % Allowed : 12.01 % Favored : 86.59 % 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: 0.62 (0.18), residues: 1992 helix: 1.25 (0.16), residues: 1026 sheet: -0.68 (0.36), residues: 176 loop : -0.35 (0.21), residues: 790 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 0.014 0.002 PHE A 431 TRP 0.013 0.001 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00480 (16483) covalent geometry : angle 0.73063 (22243) hydrogen bonds : bond 0.05306 ( 789) hydrogen bonds : angle 5.53534 ( 2247) Misc. bond : bond 0.15240 ( 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 239 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6837 (mt-10) REVERT: A 445 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: B 238 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8262 (mtt180) REVERT: C 18 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6966 (mt-10) REVERT: C 445 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8048 (m-30) REVERT: D 171 LYS cc_start: 0.7229 (mttm) cc_final: 0.6861 (mmtt) REVERT: D 211 LYS cc_start: 0.8089 (mtpm) cc_final: 0.7865 (mmtt) outliers start: 24 outliers final: 15 residues processed: 233 average time/residue: 0.8218 time to fit residues: 206.9376 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 : 0.654 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 130 optimal weight: 0.9980 chunk 163 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.147424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.131699 restraints weight = 10871.765| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 0.44 r_work: 0.3304 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 1.36 restraints_weight: 0.2500 r_work: 0.3053 rms_B_bonded: 3.87 restraints_weight: 0.1250 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.378 16499 Z= 0.264 Angle : 0.747 30.659 22243 Z= 0.358 Chirality : 0.045 0.166 2336 Planarity : 0.004 0.050 2858 Dihedral : 5.152 53.967 2524 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.10 % Allowed : 12.30 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.18), residues: 1992 helix: 1.23 (0.16), residues: 1026 sheet: -0.68 (0.36), residues: 176 loop : -0.33 (0.21), residues: 790 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 0.016 0.002 PHE A 431 TRP 0.012 0.002 TRP B 296 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00502 (16483) covalent geometry : angle 0.74702 (22243) hydrogen bonds : bond 0.05563 ( 789) hydrogen bonds : angle 5.57639 ( 2247) Misc. bond : bond 0.16317 ( 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: 19 poor density : 213 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6868 (mt-10) REVERT: A 445 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: B 238 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8300 (mtt180) REVERT: C 18 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6994 (mt-10) REVERT: C 445 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7946 (m-30) REVERT: D 171 LYS cc_start: 0.7184 (mttm) cc_final: 0.6752 (mmtt) outliers start: 19 outliers final: 15 residues processed: 228 average time/residue: 0.8374 time to fit residues: 206.4851 Evaluate side-chains 227 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 139 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 152 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.146005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.130619 restraints weight = 13669.919| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 0.50 r_work: 0.3257 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 1.68 restraints_weight: 0.2500 r_work: 0.3008 rms_B_bonded: 4.60 restraints_weight: 0.1250 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 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 = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.430 16499 Z= 0.284 Angle : 0.769 30.711 22243 Z= 0.373 Chirality : 0.046 0.170 2336 Planarity : 0.005 0.056 2858 Dihedral : 5.248 54.712 2524 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.10 % Allowed : 12.19 % 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: 0.53 (0.18), residues: 1992 helix: 1.16 (0.16), residues: 1026 sheet: -0.63 (0.33), residues: 196 loop : -0.37 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 359 TYR 0.019 0.002 TYR A 379 PHE 0.015 0.002 PHE A 431 TRP 0.013 0.002 TRP B 296 HIS 0.009 0.002 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00543 (16483) covalent geometry : angle 0.76922 (22243) hydrogen bonds : bond 0.06016 ( 789) hydrogen bonds : angle 5.67553 ( 2247) Misc. bond : bond 0.17662 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9980.33 seconds wall clock time: 169 minutes 50.00 seconds (10190.00 seconds total)