Starting phenix.real_space_refine on Sat Jul 4 02:28:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cr0_45829/07_2026/9cr0_45829.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cr0_45829/07_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_45829/07_2026/9cr0_45829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cr0_45829/07_2026/9cr0_45829.map" model { file = "/net/cci-nas-00/data/ceres_data/9cr0_45829/07_2026/9cr0_45829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cr0_45829/07_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-dev-6108/lib/python3.11/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, 15 Ad-hoc single atom residues: {' FE': 2} Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 5.50, 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: 1.57 Conformation dependent library (CDL) restraints added in 754.6 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: 0.54 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: 3.10 Time building geometry restraints manager: 2.02 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: 3.780 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.490 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 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/Z covalent geometry : bond 0.04736 / 2.37 (16483) covalent geometry : angle 0.73689 / 0.35 (22243) hydrogen bonds : bond 0.15073 / 9.94 ( 792) hydrogen bonds : angle 6.66466 / 4.66 ( 2265) Misc. bond : bond 0.16167 / 12.19 ( 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 : 0.727 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: 0.8174 time to fit residues: 177.2014 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 : 1.048 ------------------------------------------------------------------------------- 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... 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 = 0.3578 r_free = 0.3578 target = 0.137809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119543 restraints weight = 14281.681| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 0.89 r_work: 0.3296 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.381 16499 Z= 0.285 Angle : 0.791 30.550 22243 Z= 0.380 Chirality : 0.047 0.169 2336 Planarity : 0.005 0.057 2858 Dihedral : 6.063 71.139 2535 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.32 % Allowed : 14.39 % Favored : 83.28 % 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: 0.56 (0.18), residues: 1992 helix: 1.29 (0.16), residues: 1002 sheet: -0.71 (0.36), residues: 174 loop : -0.47 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 25 TYR 0.018 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/Z covalent geometry : bond 0.00549 / 0.26 (16483) covalent geometry : angle 0.79083 / 0.38 (22243) hydrogen bonds : bond 0.05939 / 4.06 ( 792) hydrogen bonds : angle 5.67274 / 3.94 ( 2265) Misc. bond : bond 0.17838 / 11.04 ( 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 237 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.3684 (pp-130) cc_final: 0.3434 (pmm) REVERT: A 11 SER cc_start: 0.8052 (m) cc_final: 0.7494 (p) REVERT: A 15 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6887 (tm-30) REVERT: A 18 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7181 (mt-10) REVERT: A 25 ARG cc_start: 0.7825 (ttp-110) cc_final: 0.7610 (ttp-110) REVERT: A 391 MET cc_start: 0.7947 (mmt) cc_final: 0.7706 (mmt) REVERT: B 54 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: B 171 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7280 (mtpt) REVERT: C 8 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6802 (pt0) REVERT: C 11 SER cc_start: 0.8032 (m) cc_final: 0.7466 (p) REVERT: C 15 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6916 (tm-30) REVERT: C 318 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6452 (tm-30) REVERT: D 7 LYS cc_start: 0.8117 (tptm) cc_final: 0.7511 (ttmm) REVERT: D 54 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: D 171 LYS cc_start: 0.7994 (ttpp) cc_final: 0.7385 (mppt) outliers start: 40 outliers final: 13 residues processed: 226 average time/residue: 0.7631 time to fit residues: 188.6273 Evaluate side-chains 203 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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: 6.9990 chunk 126 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 104 optimal weight: 0.0980 chunk 61 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 274 HIS B 18 GLN D 418 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.110376 restraints weight = 23077.260| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.18 r_work: 0.3154 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.451 16499 Z= 0.331 Angle : 0.840 30.484 22243 Z= 0.410 Chirality : 0.051 0.255 2336 Planarity : 0.006 0.068 2858 Dihedral : 6.143 73.744 2533 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.50 % Allowed : 14.57 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.18), residues: 1992 helix: 1.30 (0.16), residues: 994 sheet: -0.70 (0.36), residues: 174 loop : -0.57 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 242 TYR 0.021 0.003 TYR D 88 PHE 0.016 0.002 PHE A 186 TRP 0.025 0.002 TRP C 294 HIS 0.008 0.002 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.31 (16483) covalent geometry : angle 0.84027 / 0.41 (22243) hydrogen bonds : bond 0.07065 / 4.83 ( 792) hydrogen bonds : angle 5.76897 / 4.02 ( 2265) Misc. bond : bond 0.20441 / 12.65 ( 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 223 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 11 SER cc_start: 0.8084 (m) cc_final: 0.7482 (p) REVERT: A 18 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7276 (mt-10) REVERT: A 26 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7137 (tptt) REVERT: B 54 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: B 171 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7494 (mtpt) REVERT: C 8 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7094 (pt0) REVERT: C 11 SER cc_start: 0.8081 (m) cc_final: 0.7650 (t) REVERT: C 26 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7208 (mptt) REVERT: C 36 ASP cc_start: 0.6818 (t0) cc_final: 0.6456 (t0) REVERT: D 54 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: D 171 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7417 (mppt) outliers start: 43 outliers final: 14 residues processed: 207 average time/residue: 0.7758 time to fit residues: 176.2770 Evaluate side-chains 194 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 467 LEU 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 26 LYS Chi-restraints excluded: chain C residue 98 ASN 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 D residue 54 GLU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 484 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 33 optimal weight: 0.5980 chunk 186 optimal weight: 0.9980 chunk 43 optimal weight: 0.0370 chunk 160 optimal weight: 0.0870 chunk 99 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 104 optimal weight: 0.0980 chunk 11 optimal weight: 4.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 252 GLN C 83 HIS C 468 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.142657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.122067 restraints weight = 20838.218| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.14 r_work: 0.3312 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.327 16499 Z= 0.237 Angle : 0.742 30.577 22243 Z= 0.349 Chirality : 0.046 0.137 2336 Planarity : 0.005 0.082 2858 Dihedral : 6.003 80.073 2533 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.92 % Allowed : 15.09 % 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: 0.53 (0.18), residues: 1992 helix: 1.34 (0.17), residues: 1000 sheet: -0.91 (0.35), residues: 174 loop : -0.54 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 25 TYR 0.017 0.002 TYR A 401 PHE 0.016 0.002 PHE B 208 TRP 0.022 0.002 TRP C 294 HIS 0.006 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 (16483) covalent geometry : angle 0.74158 / 0.35 (22243) hydrogen bonds : bond 0.04727 / 3.25 ( 792) hydrogen bonds : angle 5.46748 / 3.79 ( 2265) Misc. bond : bond 0.14053 / 9.04 ( 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 223 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.4640 (ppp) cc_final: 0.4327 (pmm) REVERT: A 11 SER cc_start: 0.8043 (m) cc_final: 0.7599 (p) REVERT: A 25 ARG cc_start: 0.7476 (ttm-80) cc_final: 0.7235 (ttm110) REVERT: B 54 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: B 171 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7400 (mtpt) REVERT: B 389 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7185 (mt-10) REVERT: C 8 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6789 (pt0) REVERT: C 11 SER cc_start: 0.7993 (m) cc_final: 0.7408 (p) REVERT: C 22 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7502 (tp30) REVERT: C 36 ASP cc_start: 0.6789 (t0) cc_final: 0.6454 (t0) REVERT: C 394 MET cc_start: 0.8413 (mmm) cc_final: 0.7963 (mmm) REVERT: D 54 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: D 171 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7397 (mppt) outliers start: 33 outliers final: 13 residues processed: 213 average time/residue: 0.7180 time to fit residues: 168.2872 Evaluate side-chains 203 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 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 98 ASN 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: 7.9990 chunk 166 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.139518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119183 restraints weight = 17855.091| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.10 r_work: 0.3280 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- 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 = 0.37 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.321 16499 Z= 0.252 Angle : 0.745 30.711 22243 Z= 0.353 Chirality : 0.046 0.140 2336 Planarity : 0.005 0.054 2858 Dihedral : 5.879 79.203 2533 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.45 % Allowed : 16.08 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 1992 helix: 1.42 (0.17), residues: 1002 sheet: -0.84 (0.35), residues: 174 loop : -0.52 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 25 TYR 0.017 0.002 TYR D 88 PHE 0.013 0.002 PHE A 429 TRP 0.023 0.002 TRP A 294 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.23 (16483) covalent geometry : angle 0.74530 / 0.35 (22243) hydrogen bonds : bond 0.05177 / 3.55 ( 792) hydrogen bonds : angle 5.44767 / 3.78 ( 2265) Misc. bond : bond 0.14783 / 9.19 ( 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 215 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.4439 (ppp) cc_final: 0.3456 (ptp) REVERT: A 11 SER cc_start: 0.8022 (m) cc_final: 0.7548 (p) REVERT: A 25 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.7244 (ttm110) REVERT: B 54 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: B 171 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7421 (mtpt) REVERT: B 330 MET cc_start: 0.8951 (mtp) cc_final: 0.8664 (mtm) REVERT: C 8 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6965 (pt0) REVERT: C 11 SER cc_start: 0.8038 (m) cc_final: 0.7597 (t) REVERT: C 18 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7271 (mt-10) REVERT: C 22 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7615 (tp30) REVERT: C 36 ASP cc_start: 0.6829 (t0) cc_final: 0.6499 (t0) REVERT: C 394 MET cc_start: 0.8402 (mmm) cc_final: 0.8014 (mmm) REVERT: D 54 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: D 171 LYS cc_start: 0.8058 (ttpp) cc_final: 0.7455 (mppt) outliers start: 25 outliers final: 13 residues processed: 207 average time/residue: 0.7551 time to fit residues: 171.6108 Evaluate side-chains 202 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 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 446 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 98 ASN 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 258 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 136 optimal weight: 8.9990 chunk 196 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 180 optimal weight: 0.2980 chunk 139 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN ** B 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 = 0.3577 r_free = 0.3577 target = 0.137589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116696 restraints weight = 19518.439| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.14 r_work: 0.3245 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.338 16499 Z= 0.268 Angle : 0.764 30.772 22243 Z= 0.364 Chirality : 0.046 0.145 2336 Planarity : 0.005 0.058 2858 Dihedral : 5.931 77.367 2533 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.68 % Allowed : 15.96 % Favored : 82.36 % 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: 0.59 (0.18), residues: 1992 helix: 1.40 (0.16), residues: 1002 sheet: -0.83 (0.35), residues: 174 loop : -0.53 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 25 TYR 0.019 0.002 TYR D 88 PHE 0.014 0.002 PHE A 429 TRP 0.029 0.002 TRP A 294 HIS 0.011 0.001 HIS D 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.25 (16483) covalent geometry : angle 0.76373 / 0.36 (22243) hydrogen bonds : bond 0.05561 / 3.81 ( 792) hydrogen bonds : angle 5.49512 / 3.81 ( 2265) Misc. bond : bond 0.15810 / 9.84 ( 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 216 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.4350 (ppp) cc_final: 0.3284 (ptp) REVERT: A 11 SER cc_start: 0.8004 (m) cc_final: 0.7524 (p) REVERT: B 54 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: B 171 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7416 (mtpt) REVERT: B 330 MET cc_start: 0.8966 (mtp) cc_final: 0.8638 (mtm) REVERT: C 11 SER cc_start: 0.8068 (m) cc_final: 0.7629 (t) REVERT: C 36 ASP cc_start: 0.6797 (t0) cc_final: 0.6458 (t0) REVERT: C 394 MET cc_start: 0.8394 (mmm) cc_final: 0.8008 (mmm) REVERT: D 54 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: D 171 LYS cc_start: 0.8074 (ttpp) cc_final: 0.7448 (mppt) REVERT: D 463 GLU cc_start: 0.8279 (tt0) cc_final: 0.8072 (tt0) outliers start: 29 outliers final: 13 residues processed: 206 average time/residue: 0.8320 time to fit residues: 187.5045 Evaluate side-chains 197 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 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 446 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 98 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 191 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 120 optimal weight: 0.0020 chunk 175 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN B 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.141835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121214 restraints weight = 19785.213| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.14 r_work: 0.3306 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.300 16499 Z= 0.237 Angle : 0.729 30.670 22243 Z= 0.344 Chirality : 0.046 0.164 2336 Planarity : 0.005 0.047 2858 Dihedral : 5.865 79.610 2533 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.80 % Allowed : 15.73 % Favored : 82.47 % 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 (0.19), residues: 1992 helix: 1.40 (0.17), residues: 1004 sheet: -0.88 (0.35), residues: 174 loop : -0.51 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 25 TYR 0.016 0.002 TYR D 88 PHE 0.014 0.001 PHE D 450 TRP 0.027 0.002 TRP A 294 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 (16483) covalent geometry : angle 0.72895 / 0.34 (22243) hydrogen bonds : bond 0.04796 / 3.29 ( 792) hydrogen bonds : angle 5.39539 / 3.74 ( 2265) Misc. bond : bond 0.13407 / 8.44 ( 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 232 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.4298 (ppp) cc_final: 0.3708 (pmm) REVERT: A 11 SER cc_start: 0.7915 (m) cc_final: 0.7501 (p) REVERT: A 15 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: A 391 MET cc_start: 0.8013 (mmt) cc_final: 0.7799 (mmt) REVERT: B 54 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: B 171 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7406 (mtpt) REVERT: B 330 MET cc_start: 0.8947 (mtp) cc_final: 0.8603 (mtm) REVERT: C 8 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6070 (mm-30) REVERT: C 11 SER cc_start: 0.8007 (m) cc_final: 0.7430 (p) REVERT: C 22 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7475 (tp30) REVERT: C 25 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7319 (ttm110) REVERT: C 36 ASP cc_start: 0.6743 (t0) cc_final: 0.6411 (t0) REVERT: C 394 MET cc_start: 0.8362 (mmm) cc_final: 0.7990 (mmm) REVERT: D 54 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: D 171 LYS cc_start: 0.8073 (ttpp) cc_final: 0.7468 (mppt) outliers start: 31 outliers final: 18 residues processed: 220 average time/residue: 0.8522 time to fit residues: 205.3513 Evaluate side-chains 211 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 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 446 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 98 ASN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 167 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3617 r_free = 0.3617 target = 0.140963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.119846 restraints weight = 21772.670| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.19 r_work: 0.3286 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.299 16499 Z= 0.241 Angle : 0.733 30.709 22243 Z= 0.346 Chirality : 0.046 0.147 2336 Planarity : 0.005 0.052 2858 Dihedral : 5.818 78.539 2533 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.92 % Allowed : 15.96 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.19), residues: 1992 helix: 1.44 (0.17), residues: 1002 sheet: -0.90 (0.35), residues: 174 loop : -0.48 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.017 0.002 TYR D 88 PHE 0.012 0.001 PHE A 429 TRP 0.031 0.002 TRP C 294 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.23 (16483) covalent geometry : angle 0.73317 / 0.35 (22243) hydrogen bonds : bond 0.04914 / 3.37 ( 792) hydrogen bonds : angle 5.40193 / 3.74 ( 2265) Misc. bond : bond 0.13647 / 8.51 ( 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 226 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.4175 (ppp) cc_final: 0.3703 (pmm) REVERT: A 11 SER cc_start: 0.7937 (m) cc_final: 0.7532 (p) REVERT: A 15 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6920 (tm-30) REVERT: B 54 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: B 171 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7423 (mtpt) REVERT: C 11 SER cc_start: 0.8020 (m) cc_final: 0.7585 (t) REVERT: C 22 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7552 (tp30) REVERT: C 25 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7437 (ttm110) REVERT: C 36 ASP cc_start: 0.6745 (t0) cc_final: 0.6441 (t0) REVERT: C 394 MET cc_start: 0.8355 (mmm) cc_final: 0.7996 (mmm) REVERT: D 54 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: D 171 LYS cc_start: 0.8099 (ttpp) cc_final: 0.7472 (mppt) REVERT: D 330 MET cc_start: 0.8930 (mtp) cc_final: 0.8651 (mtm) outliers start: 33 outliers final: 17 residues processed: 216 average time/residue: 0.8084 time to fit residues: 192.2530 Evaluate side-chains 210 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 446 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 98 ASN 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 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 158 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 123 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 164 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3624 r_free = 0.3624 target = 0.141477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122666 restraints weight = 16645.731| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 0.97 r_work: 0.3322 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.295 16499 Z= 0.238 Angle : 0.734 30.682 22243 Z= 0.346 Chirality : 0.045 0.140 2336 Planarity : 0.005 0.096 2858 Dihedral : 5.812 78.387 2533 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.51 % Allowed : 16.66 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.19), residues: 1992 helix: 1.46 (0.17), residues: 1002 sheet: -0.91 (0.35), residues: 174 loop : -0.50 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 25 TYR 0.018 0.002 TYR A 401 PHE 0.013 0.001 PHE D 450 TRP 0.035 0.002 TRP C 294 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.22 (16483) covalent geometry : angle 0.73366 / 0.35 (22243) hydrogen bonds : bond 0.04848 / 3.32 ( 792) hydrogen bonds : angle 5.38530 / 3.73 ( 2265) Misc. bond : bond 0.13380 / 8.36 ( 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 224 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.744 Fit side-chains REVERT: A 4 MET cc_start: 0.4138 (ppp) cc_final: 0.3670 (pmm) REVERT: A 11 SER cc_start: 0.7986 (m) cc_final: 0.7575 (p) REVERT: A 15 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6930 (tm-30) REVERT: B 54 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: B 171 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7445 (mtpt) REVERT: C 11 SER cc_start: 0.7985 (m) cc_final: 0.7398 (p) REVERT: C 22 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7491 (tp30) REVERT: C 25 ARG cc_start: 0.7819 (ttm110) cc_final: 0.7387 (ttm110) REVERT: C 36 ASP cc_start: 0.6774 (t0) cc_final: 0.6451 (t0) REVERT: C 394 MET cc_start: 0.8349 (mmm) cc_final: 0.7988 (mmm) REVERT: D 54 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: D 171 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7488 (mppt) REVERT: D 330 MET cc_start: 0.8914 (mtp) cc_final: 0.8629 (mtm) outliers start: 26 outliers final: 15 residues processed: 216 average time/residue: 0.8466 time to fit residues: 200.5732 Evaluate side-chains 210 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 446 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 98 ASN 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 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: 2.9990 chunk 67 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 167 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3589 r_free = 0.3589 target = 0.138450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117703 restraints weight = 20880.171| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.14 r_work: 0.3256 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.327 16499 Z= 0.261 Angle : 0.760 30.769 22243 Z= 0.362 Chirality : 0.046 0.143 2336 Planarity : 0.005 0.050 2858 Dihedral : 5.856 75.604 2533 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.33 % Allowed : 17.01 % Favored : 81.66 % 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: 1.43 (0.17), residues: 998 sheet: -0.88 (0.35), residues: 174 loop : -0.58 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 182 TYR 0.018 0.002 TYR D 88 PHE 0.014 0.002 PHE A 429 TRP 0.038 0.002 TRP A 294 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.24 (16483) covalent geometry : angle 0.76025 / 0.36 (22243) hydrogen bonds : bond 0.05377 / 3.68 ( 792) hydrogen bonds : angle 5.43934 / 3.78 ( 2265) Misc. bond : bond 0.15305 / 9.47 ( 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 216 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.733 Fit side-chains REVERT: A 4 MET cc_start: 0.4150 (ppp) cc_final: 0.3701 (pmm) REVERT: A 11 SER cc_start: 0.7984 (m) cc_final: 0.7564 (p) REVERT: A 36 ASP cc_start: 0.6820 (t0) cc_final: 0.6450 (t0) REVERT: B 171 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7433 (mtpt) REVERT: B 330 MET cc_start: 0.8956 (mtp) cc_final: 0.8604 (mtm) REVERT: C 11 SER cc_start: 0.8045 (m) cc_final: 0.7602 (t) REVERT: C 22 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7575 (tp30) REVERT: C 36 ASP cc_start: 0.6779 (t0) cc_final: 0.6471 (t0) REVERT: C 394 MET cc_start: 0.8363 (mmm) cc_final: 0.8005 (mmm) REVERT: D 54 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: D 171 LYS cc_start: 0.8081 (ttpp) cc_final: 0.7480 (mppt) REVERT: D 330 MET cc_start: 0.8947 (mtp) cc_final: 0.8662 (mtm) outliers start: 23 outliers final: 16 residues processed: 209 average time/residue: 0.8459 time to fit residues: 193.8271 Evaluate side-chains 207 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 355 ILE Chi-restraints excluded: chain A residue 362 HIS 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 98 ASN 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 C residue 434 MET 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: 1.9990 chunk 122 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 104 optimal weight: 0.0570 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3550 r_free = 0.3550 target = 0.135210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112876 restraints weight = 22968.556| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.27 r_work: 0.3192 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.358 16499 Z= 0.288 Angle : 0.795 30.703 22243 Z= 0.383 Chirality : 0.048 0.183 2336 Planarity : 0.005 0.057 2858 Dihedral : 5.990 71.167 2533 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.45 % Allowed : 16.95 % 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: 0.49 (0.18), residues: 1992 helix: 1.35 (0.16), residues: 998 sheet: -0.88 (0.35), residues: 174 loop : -0.62 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 25 TYR 0.020 0.002 TYR D 88 PHE 0.014 0.002 PHE A 429 TRP 0.047 0.002 TRP C 294 HIS 0.008 0.002 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.27 (16483) covalent geometry : angle 0.79509 / 0.38 (22243) hydrogen bonds : bond 0.06024 / 4.12 ( 792) hydrogen bonds : angle 5.54648 / 3.85 ( 2265) Misc. bond : bond 0.17230 / 10.59 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7667.54 seconds wall clock time: 131 minutes 48.76 seconds (7908.76 seconds total)