Starting phenix.real_space_refine on Mon Apr 6 09:35:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cr0_45829/04_2026/9cr0_45829.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cr0_45829/04_2026/9cr0_45829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cr0_45829/04_2026/9cr0_45829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cr0_45829/04_2026/9cr0_45829.map" model { file = "/net/cci-nas-00/data/ceres_data/9cr0_45829/04_2026/9cr0_45829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cr0_45829/04_2026/9cr0_45829.cif" } resolution = 2.08 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= 0.014 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 4718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 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: 17763 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: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {' FE': 2, 'CLF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 360 Classifications: {'water': 360} Link IDs: {None: 359} Chain: "B" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 507 Classifications: {'water': 507} Link IDs: {None: 506} Chain: "C" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 365 Classifications: {'water': 365} Link IDs: {None: 364} Chain: "D" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 504 Classifications: {'water': 504} Link IDs: {None: 503} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 26.563 38.260 35.755 1.00 19.21 S ATOM 4552 SG CYS B 95 31.310 55.159 51.295 1.00 13.76 S ATOM 1170 SG CYS A 154 27.527 57.621 48.117 1.00 19.97 S ATOM 465 SG CYS A 62 29.399 51.786 45.699 1.00 19.02 S ATOM 652 SG CYS A 88 33.623 57.604 45.706 1.00 24.40 S ATOM 652 SG CYS A 88 33.623 57.604 45.706 1.00 24.40 S ATOM 5005 SG CYS B 153 31.011 60.602 49.766 1.00 20.22 S ATOM 4372 SG CYS B 70 37.486 58.152 51.173 1.00 14.70 S ATOM 4552 SG CYS B 95 31.310 55.159 51.295 1.00 13.76 S ATOM 10056 SG CYS C 275 104.311 48.453 35.780 1.00 18.74 S ATOM 12516 SG CYS D 95 99.450 31.509 51.295 1.00 12.73 S ATOM 9134 SG CYS C 154 103.334 29.084 48.041 1.00 20.77 S ATOM 8429 SG CYS C 62 101.429 34.934 45.681 1.00 19.51 S ATOM 8616 SG CYS C 88 97.200 29.121 45.693 1.00 24.11 S ATOM 8616 SG CYS C 88 97.200 29.121 45.693 1.00 24.11 S ATOM 12969 SG CYS D 153 99.826 26.147 49.765 1.00 20.16 S ATOM 12336 SG CYS D 70 93.346 28.578 51.167 1.00 15.13 S ATOM 12516 SG CYS D 95 99.450 31.509 51.295 1.00 12.73 S Time building chain proxies: 5.58, per 1000 atoms: 0.31 Number of scatterers: 17763 At special positions: 0 Unit cell: (132.3, 87.465, 95.55, 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 4718 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: 1.27 Conformation dependent library (CDL) restraints added in 806.3 milliseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 59.8% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.073A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.724A pdb=" N LYS A 44 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.751A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.788A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.210A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 4.496A pdb=" N ARG A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP A 211 " --> pdb=" O GLY A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 211' 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: 4.163A 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: 5.851A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.693A pdb=" N LYS A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) 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: 3.953A 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: 4.666A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.665A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.805A 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 removed outlier: 3.551A pdb=" N GLU B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) 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: 4.020A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.065A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.501A pdb=" N PHE B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.834A 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: 4.144A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.221A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.956A 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 447 through 459 removed outlier: 4.316A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 30 removed outlier: 4.027A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.564A pdb=" N LYS C 44 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.761A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.570A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.216A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 4.492A pdb=" N ARG C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 211' 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: 4.163A 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: 5.839A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 5.784A 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 Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.181A 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: 4.662A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET C 434 " --> pdb=" O ILE C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.624A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.774A 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: 3.592A 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: 4.032A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.036A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.839A 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: 5.219A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.957A 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 447 through 459 removed outlier: 4.328A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.147A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.472A 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: 6.999A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 7.190A pdb=" N VAL A 223 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N TRP A 253 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.893A 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: 6.329A pdb=" N ILE B 224 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.766A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE B 367 " --> pdb=" O HIS B 392 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU B 394 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU B 369 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.167A pdb=" N VAL C 351 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY C 376 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.402A 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: 6.914A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254 removed outlier: 7.251A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 225 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 270 " --> pdb=" O ASP C 222 " (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: 6.244A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.795A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE D 367 " --> pdb=" O HIS D 392 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU D 394 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU D 369 " --> pdb=" O LEU D 394 " (cutoff:3.500A) 792 hydrogen bonds defined for protein. 2265 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: 3.39 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.86: 16347 1.86 - 2.49: 104 2.49 - 3.12: 18 3.12 - 3.75: 10 3.75 - 4.38: 4 Bond restraints: 16483 Sorted by residual: bond pdb="FE2 CLF D 601 " pdb="FE8 CLF D 601 " ideal model delta sigma weight residual 2.200 4.385 -2.185 2.00e-02 2.50e+03 1.19e+04 bond pdb="FE2 CLF B 602 " pdb="FE8 CLF B 602 " ideal model delta sigma weight residual 2.200 4.381 -2.181 2.00e-02 2.50e+03 1.19e+04 bond pdb="FE5 CLF B 602 " pdb="FE6 CLF B 602 " ideal model delta sigma weight residual 2.200 3.928 -1.728 2.00e-02 2.50e+03 7.47e+03 bond pdb="FE5 CLF D 601 " pdb="FE6 CLF D 601 " ideal model delta sigma weight residual 2.200 3.927 -1.727 2.00e-02 2.50e+03 7.46e+03 bond pdb=" S1 CLF B 602 " pdb="FE6 CLF B 602 " ideal model delta sigma weight residual 2.200 3.616 -1.416 2.00e-02 2.50e+03 5.01e+03 ... (remaining 16478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.88: 22236 6.88 - 13.76: 1 13.76 - 20.63: 2 20.63 - 27.51: 0 27.51 - 34.39: 4 Bond angle restraints: 22243 Sorted by residual: angle pdb=" S1 CLF D 601 " pdb="FE2 CLF D 601 " pdb="FE4 CLF D 601 " ideal model delta sigma weight residual 90.00 55.61 34.39 3.00e+00 1.11e-01 1.31e+02 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE4 CLF B 602 " ideal model delta sigma weight residual 90.00 55.64 34.36 3.00e+00 1.11e-01 1.31e+02 angle pdb=" S1 CLF D 601 " pdb="FE2 CLF D 601 " pdb="FE1 CLF D 601 " ideal model delta sigma weight residual 90.00 60.74 29.26 3.00e+00 1.11e-01 9.51e+01 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE1 CLF B 602 " ideal model delta sigma weight residual 90.00 60.79 29.21 3.00e+00 1.11e-01 9.48e+01 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE3 CLF B 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 - 17.99: 8839 17.99 - 35.98: 917 35.98 - 53.97: 237 53.97 - 71.96: 69 71.96 - 89.95: 39 Dihedral angle restraints: 10101 sinusoidal: 4359 harmonic: 5742 Sorted by residual: dihedral pdb=" CA PHE B 367 " pdb=" C PHE B 367 " pdb=" N ALA B 368 " pdb=" CA ALA B 368 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA PHE D 367 " pdb=" C PHE D 367 " pdb=" N ALA D 368 " pdb=" CA ALA D 368 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ASP D 177 " pdb=" CB ASP D 177 " pdb=" CG ASP D 177 " pdb=" OD1 ASP D 177 " ideal model delta sinusoidal sigma weight residual -30.00 -86.83 56.83 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1556 0.039 - 0.078: 575 0.078 - 0.117: 169 0.117 - 0.155: 31 0.155 - 0.194: 5 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CG LEU D 485 " pdb=" CB LEU D 485 " pdb=" CD1 LEU D 485 " pdb=" CD2 LEU D 485 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CG LEU D 14 " pdb=" CB LEU D 14 " pdb=" CD1 LEU D 14 " pdb=" CD2 LEU D 14 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CB ILE A 240 " pdb=" CA ILE A 240 " pdb=" CG1 ILE A 240 " pdb=" CG2 ILE A 240 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.48e-01 ... (remaining 2333 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 359 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 360 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 294 " -0.014 2.00e-02 2.50e+03 1.09e-02 2.98e+00 pdb=" CG TRP A 294 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 294 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 294 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 294 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 294 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 294 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 294 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 294 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 294 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 73 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.94e+00 pdb=" N PRO A 74 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.024 5.00e-02 4.00e+02 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 1185 2.58 - 3.16: 16713 3.16 - 3.74: 36280 3.74 - 4.32: 50853 4.32 - 4.90: 74698 Nonbonded interactions: 179729 Sorted by model distance: nonbonded pdb=" OG1 THR B 455 " pdb=" O HOH B 701 " model vdw 2.003 3.040 nonbonded pdb=" O HIS A 383 " pdb=" O HOH A 601 " model vdw 2.004 3.040 nonbonded pdb=" O LEU A 17 " pdb=" O HOH A 602 " model vdw 2.008 3.040 nonbonded pdb=" OG1 THR D 455 " pdb=" O HOH D 701 " model vdw 2.010 3.040 nonbonded pdb=" O LEU B 362 " pdb=" O HOH B 702 " model vdw 2.015 3.040 ... (remaining 179724 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' and resid 2 through 523) selection = (chain 'D' and resid 2 through 523) } 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=0.39 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: 3.630 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.340 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 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 2.185 16499 Z= 2.418 Angle : 0.737 34.388 22243 Z= 0.349 Chirality : 0.045 0.194 2336 Planarity : 0.004 0.047 2858 Dihedral : 16.853 89.955 6433 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.81 % Allowed : 16.19 % Favored : 82.99 % 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: 1.43 (0.17), residues: 972 sheet: -0.56 (0.36), residues: 174 loop : -0.56 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.014 0.002 TYR D 88 PHE 0.014 0.001 PHE A 429 TRP 0.028 0.002 TRP A 294 HIS 0.006 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.04736 (16483) covalent geometry : angle 0.73689 (22243) hydrogen bonds : bond 0.15073 ( 792) hydrogen bonds : angle 6.66466 ( 2265) Misc. bond : bond 0.16167 ( 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 201 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.3889 (pp-130) cc_final: 0.3580 (pmm) REVERT: A 11 SER cc_start: 0.8134 (m) cc_final: 0.7604 (p) REVERT: B 171 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7252 (mtpt) REVERT: B 213 MET cc_start: 0.8635 (mmm) cc_final: 0.8408 (mmm) REVERT: C 8 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6709 (pt0) REVERT: C 11 SER cc_start: 0.8112 (m) cc_final: 0.7577 (p) REVERT: C 22 GLU cc_start: 0.7401 (tp30) cc_final: 0.6958 (mp0) REVERT: C 26 LYS cc_start: 0.7800 (mptt) cc_final: 0.7514 (ptpp) REVERT: D 7 LYS cc_start: 0.8181 (tptm) cc_final: 0.7595 (ttmm) REVERT: D 171 LYS cc_start: 0.8026 (ttpp) cc_final: 0.7366 (mppt) outliers start: 14 outliers final: 8 residues processed: 198 average time/residue: 0.8518 time to fit residues: 183.5517 Evaluate side-chains 190 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 181 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 432 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 98 ASN B 518 ASN C 29 ASN C 468 ASN D 18 GLN D 418 ASN D 518 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.137527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119200 restraints weight = 14254.580| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 0.89 r_work: 0.3291 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.397 16499 Z= 0.292 Angle : 0.786 31.241 22243 Z= 0.377 Chirality : 0.047 0.160 2336 Planarity : 0.005 0.055 2858 Dihedral : 6.050 71.876 2535 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.32 % Allowed : 14.45 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 1992 helix: 1.31 (0.16), residues: 1002 sheet: -0.70 (0.36), residues: 174 loop : -0.46 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 25 TYR 0.017 0.002 TYR B 88 PHE 0.015 0.002 PHE B 208 TRP 0.022 0.002 TRP C 294 HIS 0.008 0.001 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.00556 (16483) covalent geometry : angle 0.78589 (22243) hydrogen bonds : bond 0.06075 ( 792) hydrogen bonds : angle 5.66780 ( 2265) Misc. bond : bond 0.19061 ( 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 236 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.3690 (pp-130) cc_final: 0.3443 (pmm) REVERT: A 11 SER cc_start: 0.8071 (m) cc_final: 0.7517 (p) REVERT: A 15 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6857 (tm-30) REVERT: A 18 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7175 (mt-10) REVERT: A 25 ARG cc_start: 0.7841 (ttp-110) cc_final: 0.7496 (ttp-110) REVERT: A 391 MET cc_start: 0.7943 (mmt) cc_final: 0.7705 (mmt) REVERT: B 54 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: B 171 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7278 (mtpt) REVERT: C 8 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6805 (pt0) REVERT: C 11 SER cc_start: 0.8035 (m) cc_final: 0.7472 (p) REVERT: C 15 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6924 (tm-30) REVERT: C 22 GLU cc_start: 0.7275 (tp30) cc_final: 0.6981 (mp0) REVERT: C 318 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6463 (tm-30) REVERT: C 394 MET cc_start: 0.8453 (mmm) cc_final: 0.8030 (mmm) REVERT: D 7 LYS cc_start: 0.8125 (tptm) cc_final: 0.7528 (ttmm) REVERT: D 54 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: D 171 LYS cc_start: 0.7998 (ttpp) cc_final: 0.7392 (mppt) outliers start: 40 outliers final: 13 residues processed: 225 average time/residue: 0.8176 time to fit residues: 200.6072 Evaluate side-chains 202 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 165 SER 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 B residue 54 GLU Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 318 GLU 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 D residue 54 GLU Chi-restraints excluded: chain D residue 258 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 4 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 104 optimal weight: 0.0770 chunk 61 optimal weight: 0.0270 chunk 5 optimal weight: 0.0770 chunk 168 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 18 GLN C 83 HIS C 98 ASN D 418 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.144049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121773 restraints weight = 23622.718| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.30 r_work: 0.3303 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.323 16499 Z= 0.237 Angle : 0.736 30.683 22243 Z= 0.346 Chirality : 0.046 0.226 2336 Planarity : 0.005 0.044 2858 Dihedral : 5.898 76.867 2533 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.09 % Allowed : 14.92 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.19), residues: 1992 helix: 1.38 (0.17), residues: 1004 sheet: -0.85 (0.35), residues: 174 loop : -0.46 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 242 TYR 0.016 0.002 TYR D 88 PHE 0.015 0.002 PHE B 208 TRP 0.021 0.002 TRP A 294 HIS 0.006 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00456 (16483) covalent geometry : angle 0.73633 (22243) hydrogen bonds : bond 0.04707 ( 792) hydrogen bonds : angle 5.41991 ( 2265) Misc. bond : bond 0.14485 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 11 SER cc_start: 0.7990 (m) cc_final: 0.7575 (p) REVERT: A 15 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: A 18 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7243 (mt-10) REVERT: B 54 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: B 171 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7282 (mtpt) REVERT: B 389 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7011 (mt-10) REVERT: C 8 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6832 (pt0) REVERT: C 11 SER cc_start: 0.8008 (m) cc_final: 0.7429 (p) REVERT: C 18 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7358 (mt-10) REVERT: C 25 ARG cc_start: 0.7916 (ttp-110) cc_final: 0.7601 (ttm-80) REVERT: C 36 ASP cc_start: 0.6844 (t0) cc_final: 0.6519 (t0) REVERT: C 394 MET cc_start: 0.8428 (mmm) cc_final: 0.8026 (mmm) REVERT: D 7 LYS cc_start: 0.8055 (tptm) cc_final: 0.7428 (ttmm) REVERT: D 54 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: D 171 LYS cc_start: 0.8052 (ttpp) cc_final: 0.7399 (mppt) outliers start: 36 outliers final: 10 residues processed: 230 average time/residue: 0.7880 time to fit residues: 198.0154 Evaluate side-chains 201 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 165 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 D residue 54 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 33 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 160 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 252 GLN A 274 HIS B 104 ASN C 98 ASN C 468 ASN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.141476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120559 restraints weight = 20807.546| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.20 r_work: 0.3292 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.312 16499 Z= 0.246 Angle : 0.737 30.731 22243 Z= 0.348 Chirality : 0.045 0.149 2336 Planarity : 0.005 0.069 2858 Dihedral : 5.827 79.486 2533 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.86 % Allowed : 15.15 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 1992 helix: 1.43 (0.17), residues: 1006 sheet: -0.82 (0.35), residues: 174 loop : -0.47 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 182 TYR 0.017 0.002 TYR B 88 PHE 0.013 0.001 PHE A 429 TRP 0.022 0.002 TRP C 294 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00480 (16483) covalent geometry : angle 0.73750 (22243) hydrogen bonds : bond 0.04978 ( 792) hydrogen bonds : angle 5.39446 ( 2265) Misc. bond : bond 0.14186 ( 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 227 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 11 SER cc_start: 0.7976 (m) cc_final: 0.7562 (p) REVERT: A 15 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: A 25 ARG cc_start: 0.7513 (ttp-110) cc_final: 0.7261 (ttp-110) REVERT: A 391 MET cc_start: 0.7970 (mmt) cc_final: 0.7751 (mmt) REVERT: B 54 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: B 171 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7298 (mtpt) REVERT: B 330 MET cc_start: 0.8942 (mtp) cc_final: 0.8690 (mtm) REVERT: C 8 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6855 (pt0) REVERT: C 11 SER cc_start: 0.8034 (m) cc_final: 0.7464 (p) REVERT: C 15 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6938 (tm-30) REVERT: C 18 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7397 (mt-10) REVERT: C 25 ARG cc_start: 0.8015 (ttp-110) cc_final: 0.7808 (ttp-110) REVERT: C 36 ASP cc_start: 0.6830 (t0) cc_final: 0.6504 (t0) REVERT: C 394 MET cc_start: 0.8401 (mmm) cc_final: 0.7985 (mmm) REVERT: D 7 LYS cc_start: 0.8135 (tptm) cc_final: 0.7506 (ttmm) REVERT: D 54 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: D 171 LYS cc_start: 0.8061 (ttpp) cc_final: 0.7443 (mppt) REVERT: D 463 GLU cc_start: 0.8215 (tt0) cc_final: 0.7999 (tt0) outliers start: 32 outliers final: 12 residues processed: 218 average time/residue: 0.7915 time to fit residues: 189.1314 Evaluate side-chains 206 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 165 SER 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 B residue 54 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 15 GLU 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 D residue 54 GLU Chi-restraints excluded: chain D residue 258 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 14 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.134168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113930 restraints weight = 17669.767| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.06 r_work: 0.3206 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.396 16499 Z= 0.304 Angle : 0.801 30.799 22243 Z= 0.387 Chirality : 0.048 0.235 2336 Planarity : 0.006 0.062 2858 Dihedral : 5.999 75.709 2533 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.03 % Allowed : 15.21 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 1992 helix: 1.32 (0.16), residues: 1008 sheet: -0.77 (0.36), residues: 174 loop : -0.52 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 25 TYR 0.020 0.002 TYR D 88 PHE 0.015 0.002 PHE A 429 TRP 0.031 0.002 TRP C 294 HIS 0.008 0.002 HIS D 392 Details of bonding type rmsd covalent geometry : bond 0.00602 (16483) covalent geometry : angle 0.80079 (22243) hydrogen bonds : bond 0.06396 ( 792) hydrogen bonds : angle 5.58657 ( 2265) Misc. bond : bond 0.18289 ( 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 221 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 11 SER cc_start: 0.8031 (m) cc_final: 0.7463 (p) REVERT: A 18 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7300 (mt-10) REVERT: A 26 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7039 (tptt) REVERT: A 287 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: B 54 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: B 171 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7439 (mtpt) REVERT: B 330 MET cc_start: 0.8966 (mtp) cc_final: 0.8676 (mtm) REVERT: B 463 GLU cc_start: 0.8382 (tt0) cc_final: 0.8094 (tt0) REVERT: C 8 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6934 (pt0) REVERT: C 11 SER cc_start: 0.8136 (m) cc_final: 0.7528 (p) REVERT: C 15 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: C 25 ARG cc_start: 0.7986 (ttp-110) cc_final: 0.7605 (ttp-110) REVERT: C 36 ASP cc_start: 0.6859 (t0) cc_final: 0.6520 (t0) REVERT: C 287 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: D 54 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: D 171 LYS cc_start: 0.8080 (ttpp) cc_final: 0.7499 (mppt) REVERT: D 330 MET cc_start: 0.8958 (mtp) cc_final: 0.8635 (mtm) outliers start: 35 outliers final: 16 residues processed: 208 average time/residue: 0.7871 time to fit residues: 179.0980 Evaluate side-chains 205 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 287 GLU 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 D residue 54 GLU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 484 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 136 optimal weight: 6.9990 chunk 196 optimal weight: 0.7980 chunk 64 optimal weight: 0.0050 chunk 183 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118990 restraints weight = 19700.714| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.19 r_work: 0.3279 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 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 = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.324 16499 Z= 0.247 Angle : 0.738 30.741 22243 Z= 0.350 Chirality : 0.046 0.144 2336 Planarity : 0.005 0.070 2858 Dihedral : 5.896 79.050 2533 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.97 % Allowed : 15.38 % Favored : 82.65 % 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: 0.60 (0.18), residues: 1992 helix: 1.42 (0.16), residues: 1002 sheet: -0.88 (0.35), residues: 174 loop : -0.53 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 25 TYR 0.017 0.002 TYR D 88 PHE 0.014 0.002 PHE D 208 TRP 0.027 0.002 TRP C 294 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00478 (16483) covalent geometry : angle 0.73836 (22243) hydrogen bonds : bond 0.05023 ( 792) hydrogen bonds : angle 5.41639 ( 2265) Misc. bond : bond 0.14530 ( 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 226 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 11 SER cc_start: 0.8064 (m) cc_final: 0.7585 (p) REVERT: A 18 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: A 287 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: B 54 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: B 171 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7392 (mtpt) REVERT: B 330 MET cc_start: 0.8958 (mtp) cc_final: 0.8635 (mtm) REVERT: C 8 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6810 (pt0) REVERT: C 11 SER cc_start: 0.8031 (m) cc_final: 0.7451 (p) REVERT: C 15 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6932 (tm-30) REVERT: C 25 ARG cc_start: 0.8000 (ttp-110) cc_final: 0.7775 (ttp-110) REVERT: C 36 ASP cc_start: 0.6820 (t0) cc_final: 0.6487 (t0) REVERT: C 287 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: C 394 MET cc_start: 0.8401 (mmm) cc_final: 0.7993 (mmm) REVERT: D 54 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: D 171 LYS cc_start: 0.8086 (ttpp) cc_final: 0.7481 (mppt) REVERT: D 330 MET cc_start: 0.8962 (mtp) cc_final: 0.8686 (mtm) outliers start: 34 outliers final: 16 residues processed: 212 average time/residue: 0.7906 time to fit residues: 183.2767 Evaluate side-chains 210 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 287 GLU 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 434 MET Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 258 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 191 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.140307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119603 restraints weight = 19754.911| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.18 r_work: 0.3283 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 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 = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.303 16499 Z= 0.244 Angle : 0.734 30.720 22243 Z= 0.347 Chirality : 0.046 0.141 2336 Planarity : 0.005 0.049 2858 Dihedral : 5.826 78.264 2533 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.68 % Allowed : 15.61 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.19), residues: 1992 helix: 1.45 (0.17), residues: 1002 sheet: -0.89 (0.35), residues: 174 loop : -0.51 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 182 TYR 0.017 0.002 TYR D 88 PHE 0.014 0.002 PHE C 429 TRP 0.028 0.002 TRP C 294 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00476 (16483) covalent geometry : angle 0.73352 (22243) hydrogen bonds : bond 0.05004 ( 792) hydrogen bonds : angle 5.38410 ( 2265) Misc. bond : bond 0.13983 ( 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 225 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.4595 (pmm) cc_final: 0.4028 (pmm) REVERT: A 11 SER cc_start: 0.8059 (m) cc_final: 0.7580 (p) REVERT: A 25 ARG cc_start: 0.7448 (ttm110) cc_final: 0.7128 (ttm-80) REVERT: A 287 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: B 54 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: B 171 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7400 (mtpt) REVERT: B 330 MET cc_start: 0.8948 (mtp) cc_final: 0.8613 (mtm) REVERT: C 8 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6778 (pt0) REVERT: C 11 SER cc_start: 0.8028 (m) cc_final: 0.7446 (p) REVERT: C 15 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: C 25 ARG cc_start: 0.7962 (ttp-110) cc_final: 0.7720 (ttp-110) REVERT: C 36 ASP cc_start: 0.6780 (t0) cc_final: 0.6470 (t0) REVERT: C 287 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: D 54 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: D 171 LYS cc_start: 0.8078 (ttpp) cc_final: 0.7475 (mppt) REVERT: D 330 MET cc_start: 0.8960 (mtp) cc_final: 0.8659 (mtm) outliers start: 29 outliers final: 14 residues processed: 214 average time/residue: 0.8036 time to fit residues: 187.7413 Evaluate side-chains 209 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 287 GLU 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 D residue 54 GLU Chi-restraints excluded: chain D residue 258 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 14 optimal weight: 6.9990 chunk 10 optimal weight: 0.0970 chunk 59 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116253 restraints weight = 21596.792| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.25 r_work: 0.3247 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.332 16499 Z= 0.262 Angle : 0.754 30.781 22243 Z= 0.360 Chirality : 0.046 0.144 2336 Planarity : 0.005 0.051 2858 Dihedral : 5.870 74.584 2533 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.74 % Allowed : 16.08 % Favored : 82.18 % 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: 1.42 (0.16), residues: 1002 sheet: -0.87 (0.35), residues: 174 loop : -0.53 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.018 0.002 TYR D 88 PHE 0.015 0.002 PHE C 429 TRP 0.034 0.002 TRP C 294 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00511 (16483) covalent geometry : angle 0.75440 (22243) hydrogen bonds : bond 0.05457 ( 792) hydrogen bonds : angle 5.44241 ( 2265) Misc. bond : bond 0.15453 ( 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 219 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.4466 (pmm) cc_final: 0.4041 (pmm) REVERT: A 11 SER cc_start: 0.7998 (m) cc_final: 0.7416 (p) REVERT: A 25 ARG cc_start: 0.7379 (ttm110) cc_final: 0.7091 (ttm-80) REVERT: A 287 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: B 54 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: B 171 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7444 (mtpt) REVERT: B 330 MET cc_start: 0.8969 (mtp) cc_final: 0.8629 (mtm) REVERT: C 11 SER cc_start: 0.8037 (m) cc_final: 0.7459 (p) REVERT: C 15 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6958 (tm-30) REVERT: C 25 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7665 (ttp-110) REVERT: C 36 ASP cc_start: 0.6809 (t0) cc_final: 0.6484 (t0) REVERT: C 287 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: D 54 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: D 171 LYS cc_start: 0.8071 (ttpp) cc_final: 0.7479 (mppt) REVERT: D 330 MET cc_start: 0.8965 (mtp) cc_final: 0.8660 (mtm) REVERT: D 463 GLU cc_start: 0.8181 (tt0) cc_final: 0.7979 (tt0) outliers start: 30 outliers final: 17 residues processed: 207 average time/residue: 0.7979 time to fit residues: 180.8353 Evaluate side-chains 211 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 287 GLU 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 D residue 54 GLU Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 123 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 194 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 156 optimal weight: 0.0470 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.142495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123479 restraints weight = 16707.410| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.01 r_work: 0.3335 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.294 16499 Z= 0.231 Angle : 0.726 30.631 22243 Z= 0.342 Chirality : 0.045 0.176 2336 Planarity : 0.005 0.048 2858 Dihedral : 5.816 75.167 2533 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.57 % Allowed : 16.37 % Favored : 82.07 % 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 (0.19), residues: 1992 helix: 1.45 (0.17), residues: 1002 sheet: -0.93 (0.35), residues: 174 loop : -0.53 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 182 TYR 0.018 0.002 TYR A 401 PHE 0.015 0.001 PHE D 450 TRP 0.033 0.002 TRP C 294 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00448 (16483) covalent geometry : angle 0.72558 (22243) hydrogen bonds : bond 0.04644 ( 792) hydrogen bonds : angle 5.34892 ( 2265) Misc. bond : bond 0.12977 ( 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 225 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.4328 (pmm) cc_final: 0.3752 (pmm) REVERT: A 11 SER cc_start: 0.7983 (m) cc_final: 0.7544 (p) REVERT: A 22 GLU cc_start: 0.7324 (tp30) cc_final: 0.7073 (mp0) REVERT: A 25 ARG cc_start: 0.7146 (ttm110) cc_final: 0.6833 (ttp-170) REVERT: A 26 LYS cc_start: 0.7905 (mtmt) cc_final: 0.7548 (mttp) REVERT: A 287 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: B 171 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7380 (mtpt) REVERT: B 330 MET cc_start: 0.8924 (mtp) cc_final: 0.8671 (mtm) REVERT: C 11 SER cc_start: 0.8002 (m) cc_final: 0.7444 (p) REVERT: C 25 ARG cc_start: 0.7896 (ttp-110) cc_final: 0.7656 (ttp-110) REVERT: C 36 ASP cc_start: 0.6791 (t0) cc_final: 0.6489 (t0) REVERT: C 287 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: D 54 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: D 171 LYS cc_start: 0.8065 (ttpp) cc_final: 0.7485 (mppt) REVERT: D 330 MET cc_start: 0.8936 (mtp) cc_final: 0.8623 (mtm) outliers start: 27 outliers final: 15 residues processed: 215 average time/residue: 0.7869 time to fit residues: 185.2809 Evaluate side-chains 200 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 287 GLU 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 D residue 54 GLU 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 34 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 104 optimal weight: 0.0870 chunk 100 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 167 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.138657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.117382 restraints weight = 20863.689| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.20 r_work: 0.3253 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.324 16499 Z= 0.258 Angle : 0.758 30.749 22243 Z= 0.360 Chirality : 0.047 0.244 2336 Planarity : 0.005 0.049 2858 Dihedral : 5.844 71.614 2533 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.39 % Allowed : 17.01 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.19), residues: 1992 helix: 1.43 (0.17), residues: 1002 sheet: -0.90 (0.35), residues: 174 loop : -0.51 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 345 TYR 0.018 0.002 TYR D 88 PHE 0.015 0.002 PHE A 429 TRP 0.043 0.002 TRP C 294 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00505 (16483) covalent geometry : angle 0.75791 (22243) hydrogen bonds : bond 0.05309 ( 792) hydrogen bonds : angle 5.39820 ( 2265) Misc. bond : bond 0.14924 ( 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 211 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.4327 (pmm) cc_final: 0.3763 (pmm) REVERT: A 11 SER cc_start: 0.8015 (m) cc_final: 0.7474 (p) REVERT: A 25 ARG cc_start: 0.7191 (ttm110) cc_final: 0.6899 (ttp-110) REVERT: A 26 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7605 (mttp) REVERT: A 287 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: B 171 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7418 (mtpt) REVERT: B 330 MET cc_start: 0.8971 (mtp) cc_final: 0.8627 (mtm) REVERT: C 8 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6084 (mm-30) REVERT: C 11 SER cc_start: 0.8024 (m) cc_final: 0.7433 (p) REVERT: C 25 ARG cc_start: 0.7936 (ttp-110) cc_final: 0.7680 (ttm-80) REVERT: C 36 ASP cc_start: 0.6815 (t0) cc_final: 0.6494 (t0) REVERT: C 287 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: D 54 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: D 171 LYS cc_start: 0.8091 (ttpp) cc_final: 0.7483 (mppt) REVERT: D 330 MET cc_start: 0.8976 (mtp) cc_final: 0.8667 (mtm) outliers start: 24 outliers final: 14 residues processed: 205 average time/residue: 0.8062 time to fit residues: 180.5284 Evaluate side-chains 206 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 287 GLU 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 D residue 54 GLU 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 97 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.118364 restraints weight = 23397.809| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.28 r_work: 0.3264 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.307 16499 Z= 0.244 Angle : 0.742 30.707 22243 Z= 0.350 Chirality : 0.046 0.197 2336 Planarity : 0.005 0.049 2858 Dihedral : 5.820 70.232 2533 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.22 % Allowed : 17.01 % Favored : 81.78 % 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 (0.19), residues: 1992 helix: 1.45 (0.17), residues: 1000 sheet: -0.95 (0.35), residues: 174 loop : -0.52 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 182 TYR 0.018 0.002 TYR D 88 PHE 0.015 0.002 PHE A 429 TRP 0.038 0.002 TRP A 294 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00475 (16483) covalent geometry : angle 0.74184 (22243) hydrogen bonds : bond 0.04938 ( 792) hydrogen bonds : angle 5.35219 ( 2265) Misc. bond : bond 0.13869 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7712.44 seconds wall clock time: 132 minutes 2.40 seconds (7922.40 seconds total)