Starting phenix.real_space_refine on Fri Jul 3 23:44:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mm1_48384/07_2026/9mm1_48384.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mm1_48384/07_2026/9mm1_48384.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 { model { file = "/net/cci-nas-00/data/ceres_data/9mm1_48384/07_2026/9mm1_48384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mm1_48384/07_2026/9mm1_48384.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mm1_48384/07_2026/9mm1_48384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mm1_48384/07_2026/9mm1_48384.map" } 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= 0.013 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 3995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 17040 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, 'PTRANS': 20, '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, 'PTRANS': 20, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 3871 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "A" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 191 Classifications: {'water': 191} Link IDs: {None: 190} Chain: "B" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 308 Classifications: {'water': 308} Link IDs: {None: 307} Chain: "C" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 205 Classifications: {'water': 205} Link IDs: {None: 204} Chain: "D" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 309 Classifications: {'water': 309} Link IDs: {None: 308} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 27.149 37.262 35.791 1.00 17.24 S ATOM 1170 SG CYS A 154 28.063 56.786 48.094 1.00 14.01 S ATOM 4552 SG CYS B 95 32.113 54.608 51.249 1.00 12.52 S ATOM 465 SG CYS A 62 30.134 51.132 45.774 1.00 8.61 S ATOM 652 SG CYS A 88 34.194 56.702 45.566 1.00 14.92 S ATOM 652 SG CYS A 88 34.194 56.702 45.566 1.00 14.92 S ATOM 5005 SG CYS B 153 31.701 59.830 49.833 1.00 15.28 S ATOM 4372 SG CYS B 70 38.198 57.658 51.133 1.00 14.37 S ATOM 4552 SG CYS B 95 32.113 54.608 51.249 1.00 12.52 S ATOM 10056 SG CYS C 275 105.071 47.677 35.769 1.00 19.42 S ATOM 9134 SG CYS C 154 104.184 28.293 48.055 1.00 14.24 S ATOM 12516 SG CYS D 95 100.132 30.645 51.302 1.00 13.19 S ATOM 8429 SG CYS C 62 101.743 34.277 45.688 1.00 11.00 S ATOM 8616 SG CYS C 88 98.107 28.547 45.570 1.00 16.52 S ATOM 8616 SG CYS C 88 98.107 28.547 45.570 1.00 16.52 S ATOM 12969 SG CYS D 153 100.545 25.628 49.893 1.00 15.67 S ATOM 12336 SG CYS D 70 94.092 27.603 51.110 1.00 14.93 S ATOM 12516 SG CYS D 95 100.132 30.645 51.302 1.00 13.19 S Time building chain proxies: 4.16, per 1000 atoms: 0.24 Number of scatterers: 17040 At special positions: 0 Unit cell: (133.035, 85.995, 94.815, 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 3995 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: 1.21 Conformation dependent library (CDL) restraints added in 914.8 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: 105 helices and 12 sheets defined 59.5% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.142A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.682A 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: 4.016A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.803A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 206 Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.051A 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: 5.648A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.156A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 434 removed outlier: 4.695A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.614A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.693A pdb=" N TRP A 472 " --> pdb=" O ASN A 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 8 removed outlier: 4.237A pdb=" N ILE B 8 " --> pdb=" O VAL B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 32 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 81 removed outlier: 4.081A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.104A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.985A pdb=" N VAL B 124 " --> pdb=" O GLU B 120 " (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: 3.958A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 4.046A pdb=" N THR B 263 " --> pdb=" O VAL B 260 " (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: 4.216A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.245A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 6.090A 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 removed outlier: 3.772A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 447 through 459 removed outlier: 4.374A 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: 3.883A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 92 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: 3.868A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.683A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.142A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 4.036A 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 275 through 291 removed outlier: 5.858A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 314 Processing helix chain 'C' and resid 317 through 347 Proline residue: C 333 - end of helix Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 363 through 370 removed outlier: 3.524A pdb=" N LEU C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.375A 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: 4.042A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 469 removed outlier: 3.567A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 474 Processing helix chain 'D' and resid 4 through 8 removed outlier: 4.297A pdb=" N ILE D 8 " --> pdb=" O VAL D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.554A 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: 4.080A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.314A 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 216 removed outlier: 5.741A pdb=" N ASP D 214 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP D 215 " --> pdb=" O SER D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.929A 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: 5.304A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 6.135A 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 removed outlier: 3.788A pdb=" N LYS D 417 " --> pdb=" O PRO D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 447 through 459 removed outlier: 4.380A 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: 6.167A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 6.359A 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: 7.002A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 6.634A pdb=" N VAL A 223 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 251 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN A 271 " --> pdb=" O MET A 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 removed outlier: 8.498A pdb=" N VAL B 114 " --> pdb=" O THR B 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.561A pdb=" N ILE B 224 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.425A 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: 8.623A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.505A pdb=" N LEU C 353 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR C 377 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE C 355 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR C 379 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 6.266A 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: 7.011A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.190A 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: 7.274A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE C 225 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.555A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.417A 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: 8.609A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2301 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.55: 16159 1.55 - 1.90: 188 1.90 - 2.25: 36 2.25 - 2.61: 82 2.61 - 2.96: 18 Bond restraints: 16483 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 2.957 -0.757 2.00e-02 2.50e+03 1.43e+03 bond pdb="FE2 CLF B 602 " pdb="FE8 CLF B 602 " ideal model delta sigma weight residual 2.200 2.926 -0.726 2.00e-02 2.50e+03 1.32e+03 bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 2.871 -0.671 2.00e-02 2.50e+03 1.13e+03 bond pdb="FE4 CLF B 602 " pdb="FE5 CLF B 602 " ideal model delta sigma weight residual 2.200 2.859 -0.659 2.00e-02 2.50e+03 1.09e+03 bond pdb="FE6 CLF D 602 " pdb="FE7 CLF D 602 " ideal model delta sigma weight residual 2.200 2.846 -0.646 2.00e-02 2.50e+03 1.04e+03 ... (remaining 16478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.90: 22229 6.90 - 13.80: 8 13.80 - 20.70: 2 20.70 - 27.60: 0 27.60 - 34.50: 4 Bond angle restraints: 22243 Sorted by residual: angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE4 CLF B 602 " ideal model delta sigma weight residual 90.00 55.50 34.50 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.67 34.33 3.00e+00 1.11e-01 1.31e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE1 CLF D 602 " ideal model delta sigma weight residual 90.00 56.84 33.16 3.00e+00 1.11e-01 1.22e+02 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE1 CLF B 602 " ideal model delta sigma weight residual 90.00 56.89 33.11 3.00e+00 1.11e-01 1.22e+02 angle pdb=" C PHE C 429 " pdb=" CA PHE C 429 " pdb=" CB PHE C 429 " ideal model delta sigma weight residual 110.79 121.27 -10.48 1.66e+00 3.63e-01 3.99e+01 ... (remaining 22238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 9119 17.78 - 35.57: 728 35.57 - 53.35: 161 53.35 - 71.14: 56 71.14 - 88.92: 37 Dihedral angle restraints: 10101 sinusoidal: 4359 harmonic: 5742 Sorted by residual: dihedral pdb=" CA GLY C 448 " pdb=" C GLY C 448 " pdb=" N PRO C 449 " pdb=" CA PRO C 449 " ideal model delta harmonic sigma weight residual 180.00 -139.65 -40.35 0 5.00e+00 4.00e-02 6.51e+01 dihedral pdb=" CA GLY A 448 " pdb=" C GLY A 448 " pdb=" N PRO A 449 " pdb=" CA PRO A 449 " ideal model delta harmonic sigma weight residual 0.00 -24.64 24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" C PHE B 15 " pdb=" N PHE B 15 " pdb=" CA PHE B 15 " pdb=" CB PHE B 15 " ideal model delta harmonic sigma weight residual -122.60 -134.46 11.86 0 2.50e+00 1.60e-01 2.25e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1754 0.069 - 0.137: 452 0.137 - 0.206: 105 0.206 - 0.274: 22 0.274 - 0.343: 3 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA ILE C 75 " pdb=" N ILE C 75 " pdb=" C ILE C 75 " pdb=" CB ILE C 75 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB VAL C 404 " pdb=" CA VAL C 404 " pdb=" CG1 VAL C 404 " pdb=" CG2 VAL C 404 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA PHE D 15 " pdb=" N PHE D 15 " pdb=" C PHE D 15 " pdb=" CB PHE D 15 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 2333 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 357 " -0.025 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C GLY A 357 " 0.087 2.00e-02 2.50e+03 pdb=" O GLY A 357 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU A 358 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 356 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C GLY A 356 " -0.060 2.00e-02 2.50e+03 pdb=" O GLY A 356 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY A 357 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 153 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C GLU A 153 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU A 153 " 0.017 2.00e-02 2.50e+03 pdb=" N CYS A 154 " 0.016 2.00e-02 2.50e+03 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 108 2.51 - 3.10: 13082 3.10 - 3.70: 30399 3.70 - 4.30: 47151 4.30 - 4.90: 70775 Nonbonded interactions: 161515 Sorted by model distance: nonbonded pdb=" O ARG B 108 " pdb="FE FE D 601 " model vdw 1.907 3.000 nonbonded pdb=" O ARG D 108 " pdb="FE FE B 601 " model vdw 1.920 3.000 nonbonded pdb=" OD1 ASP B 326 " pdb=" OH TYR B 487 " model vdw 2.226 3.040 nonbonded pdb=" OE1 GLU D 109 " pdb="FE FE B 601 " model vdw 2.256 3.000 nonbonded pdb=" OD1 ASP D 326 " pdb=" OH TYR D 487 " model vdw 2.286 3.040 ... (remaining 161510 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 248 or resid 250 through 502)) selection = (chain 'C' and (resid 4 through 248 or resid 250 through 502)) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.44 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.430 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 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 : 0.024 0.757 16499 Z= 1.270 Angle : 1.157 34.503 22243 Z= 0.754 Chirality : 0.068 0.343 2336 Planarity : 0.006 0.063 2858 Dihedral : 15.192 88.923 6433 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.37 % Allowed : 3.48 % Favored : 93.15 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.10 % Twisted Proline : 1.09 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.18), residues: 1992 helix: 1.44 (0.16), residues: 966 sheet: -0.48 (0.34), residues: 204 loop : -0.45 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 277 TYR 0.034 0.003 TYR D 88 PHE 0.047 0.003 PHE C 118 TRP 0.018 0.003 TRP C 444 HIS 0.024 0.003 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.02417 / 1.27 (16483) covalent geometry : angle 1.15688 / 0.75 (22243) hydrogen bonds : bond 0.16481 / 10.98 ( 805) hydrogen bonds : angle 6.80973 / 4.99 ( 2301) Misc. bond : bond 0.07891 / 5.36 ( 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 366 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 308 time to evaluate : 0.616 Fit side-chains REVERT: A 8 GLU cc_start: 0.6478 (mp0) cc_final: 0.6037 (tm-30) REVERT: A 11 SER cc_start: 0.8131 (t) cc_final: 0.7920 (p) REVERT: A 15 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7494 (mt-10) REVERT: A 129 LYS cc_start: 0.7502 (mppt) cc_final: 0.7206 (tptp) REVERT: A 133 LYS cc_start: 0.8513 (tptp) cc_final: 0.8219 (tttp) REVERT: A 322 LYS cc_start: 0.7661 (ttpp) cc_final: 0.7363 (mtmt) REVERT: A 326 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7982 (mt-10) REVERT: B 6 ASP cc_start: 0.7547 (m-30) cc_final: 0.7145 (p0) REVERT: B 417 LYS cc_start: 0.8331 (pttt) cc_final: 0.7955 (pmtt) REVERT: C 7 GLU cc_start: 0.6373 (mp0) cc_final: 0.5569 (pm20) REVERT: C 15 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7459 (tt0) REVERT: C 22 GLU cc_start: 0.7338 (tp30) cc_final: 0.7055 (tp30) REVERT: C 133 LYS cc_start: 0.8450 (tptp) cc_final: 0.8157 (tttp) REVERT: C 322 LYS cc_start: 0.7852 (tttm) cc_final: 0.7612 (mptp) REVERT: C 326 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7980 (mt-10) REVERT: D 6 ASP cc_start: 0.7611 (m-30) cc_final: 0.7332 (p0) REVERT: D 21 LYS cc_start: 0.8346 (mttt) cc_final: 0.8076 (ttmm) REVERT: D 50 LYS cc_start: 0.8337 (mttp) cc_final: 0.8134 (mmtt) REVERT: D 461 GLU cc_start: 0.8368 (pm20) cc_final: 0.8154 (pm20) outliers start: 58 outliers final: 9 residues processed: 344 average time/residue: 0.7517 time to fit residues: 279.8526 Evaluate side-chains 215 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 206 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN A 252 GLN A 469 ASN B 18 GLN B 104 ASN B 268 GLN C 53 GLN C 98 ASN C 199 ASN C 274 HIS C 280 ASN C 451 HIS D 18 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.130092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.113203 restraints weight = 14008.663| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 0.87 r_work: 0.3203 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.250 16499 Z= 0.167 Angle : 0.726 29.171 22243 Z= 0.355 Chirality : 0.046 0.160 2336 Planarity : 0.005 0.049 2858 Dihedral : 5.842 59.462 2532 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.86 % Allowed : 8.71 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % 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: 0.77 (0.18), residues: 1992 helix: 1.49 (0.16), residues: 1010 sheet: -0.54 (0.35), residues: 190 loop : -0.43 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 277 TYR 0.017 0.002 TYR D 88 PHE 0.015 0.002 PHE C 429 TRP 0.013 0.001 TRP A 472 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (16483) covalent geometry : angle 0.72625 / 0.35 (22243) hydrogen bonds : bond 0.05655 / 3.80 ( 805) hydrogen bonds : angle 5.67482 / 4.06 ( 2301) Misc. bond : bond 0.11719 / 7.51 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 0.548 Fit side-chains REVERT: A 22 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6345 (pm20) REVERT: A 129 LYS cc_start: 0.7434 (mppt) cc_final: 0.7014 (tptp) REVERT: A 133 LYS cc_start: 0.8392 (tptp) cc_final: 0.8097 (tttm) REVERT: A 287 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6614 (tp30) REVERT: B 6 ASP cc_start: 0.7442 (m-30) cc_final: 0.7089 (p0) REVERT: B 417 LYS cc_start: 0.8235 (pttt) cc_final: 0.7712 (pmtt) REVERT: B 461 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8000 (pm20) REVERT: C 7 GLU cc_start: 0.6347 (mp0) cc_final: 0.5570 (pm20) REVERT: C 22 GLU cc_start: 0.7027 (tp30) cc_final: 0.6798 (tp30) REVERT: C 133 LYS cc_start: 0.8320 (tptp) cc_final: 0.8039 (tttm) REVERT: C 326 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7766 (mt-10) REVERT: D 243 MET cc_start: 0.8744 (mtm) cc_final: 0.8496 (mtp) REVERT: D 461 GLU cc_start: 0.8209 (pm20) cc_final: 0.7960 (pm20) outliers start: 32 outliers final: 13 residues processed: 238 average time/residue: 0.7744 time to fit residues: 200.0714 Evaluate side-chains 215 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 189 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 163 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 180 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 53 GLN C 98 ASN C 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.101658 restraints weight = 21789.237| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.12 r_work: 0.3028 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.292 16499 Z= 0.258 Angle : 0.835 29.517 22243 Z= 0.422 Chirality : 0.052 0.164 2336 Planarity : 0.006 0.081 2858 Dihedral : 5.751 59.106 2527 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.92 % Allowed : 8.94 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.18), residues: 1992 helix: 1.24 (0.16), residues: 1002 sheet: -0.41 (0.35), residues: 190 loop : -0.55 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 277 TYR 0.023 0.003 TYR A 450 PHE 0.029 0.003 PHE C 429 TRP 0.013 0.003 TRP D 296 HIS 0.010 0.002 HIS D 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.24 (16483) covalent geometry : angle 0.83464 / 0.42 (22243) hydrogen bonds : bond 0.08036 / 5.40 ( 805) hydrogen bonds : angle 5.83695 / 4.19 ( 2301) Misc. bond : bond 0.13887 / 8.90 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.605 Fit side-chains REVERT: A 7 GLU cc_start: 0.6769 (mp0) cc_final: 0.6347 (mp0) REVERT: A 22 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6423 (pm20) REVERT: A 129 LYS cc_start: 0.7994 (mppt) cc_final: 0.7487 (tptp) REVERT: A 243 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: B 6 ASP cc_start: 0.7659 (m-30) cc_final: 0.7419 (p0) REVERT: B 121 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7571 (p0) REVERT: B 172 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: B 215 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7471 (p0) REVERT: B 299 GLU cc_start: 0.8008 (mp0) cc_final: 0.7725 (mp0) REVERT: B 417 LYS cc_start: 0.8388 (pttt) cc_final: 0.7890 (pmtt) REVERT: B 461 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8209 (pm20) REVERT: C 7 GLU cc_start: 0.6594 (mp0) cc_final: 0.5937 (pm20) REVERT: C 22 GLU cc_start: 0.7412 (tp30) cc_final: 0.7146 (tp30) REVERT: C 129 LYS cc_start: 0.8237 (mttp) cc_final: 0.7470 (tptp) REVERT: C 322 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7796 (mtpp) REVERT: C 326 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7945 (mt-10) REVERT: D 299 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: D 461 GLU cc_start: 0.8437 (pm20) cc_final: 0.8191 (pm20) outliers start: 33 outliers final: 16 residues processed: 229 average time/residue: 0.8262 time to fit residues: 204.3781 Evaluate side-chains 215 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 299 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 18 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103450 restraints weight = 21838.261| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.08 r_work: 0.3059 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.274 16499 Z= 0.200 Angle : 0.761 29.363 22243 Z= 0.376 Chirality : 0.047 0.148 2336 Planarity : 0.005 0.073 2858 Dihedral : 5.576 59.445 2524 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.15 % Allowed : 9.52 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % 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: 1.30 (0.16), residues: 1014 sheet: -0.34 (0.35), residues: 190 loop : -0.51 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 277 TYR 0.017 0.002 TYR D 88 PHE 0.023 0.002 PHE C 429 TRP 0.012 0.002 TRP A 253 HIS 0.009 0.002 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (16483) covalent geometry : angle 0.76085 / 0.38 (22243) hydrogen bonds : bond 0.06740 / 4.52 ( 805) hydrogen bonds : angle 5.67828 / 4.07 ( 2301) Misc. bond : bond 0.12885 / 8.25 ( 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 236 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.526 Fit side-chains REVERT: A 7 GLU cc_start: 0.6743 (mp0) cc_final: 0.6330 (mp0) REVERT: A 22 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6457 (pm20) REVERT: A 129 LYS cc_start: 0.7964 (mppt) cc_final: 0.7378 (tptp) REVERT: A 133 LYS cc_start: 0.8626 (tptm) cc_final: 0.8200 (tttp) REVERT: A 243 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: A 287 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.6830 (tp30) REVERT: B 6 ASP cc_start: 0.7708 (m-30) cc_final: 0.7460 (p0) REVERT: B 121 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7578 (p0) REVERT: B 215 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7415 (p0) REVERT: B 299 GLU cc_start: 0.7949 (mp0) cc_final: 0.7697 (mp0) REVERT: B 417 LYS cc_start: 0.8415 (pttt) cc_final: 0.7864 (pmtt) REVERT: C 7 GLU cc_start: 0.6553 (mp0) cc_final: 0.5940 (pm20) REVERT: C 22 GLU cc_start: 0.7436 (tp30) cc_final: 0.7158 (pm20) REVERT: C 47 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8038 (mp) REVERT: C 129 LYS cc_start: 0.8155 (mttp) cc_final: 0.7330 (tptp) REVERT: C 133 LYS cc_start: 0.8628 (tptm) cc_final: 0.8297 (tttm) REVERT: C 287 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.6926 (tp30) REVERT: C 322 LYS cc_start: 0.7935 (mtpp) cc_final: 0.7493 (mptp) REVERT: C 326 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7958 (mt-10) REVERT: D 461 GLU cc_start: 0.8445 (pm20) cc_final: 0.8197 (pm20) outliers start: 37 outliers final: 16 residues processed: 224 average time/residue: 0.7804 time to fit residues: 189.2345 Evaluate side-chains 213 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 197 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN B 268 GLN C 98 ASN D 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106875 restraints weight = 22787.796| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.09 r_work: 0.3108 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.224 16499 Z= 0.153 Angle : 0.701 29.157 22243 Z= 0.336 Chirality : 0.044 0.145 2336 Planarity : 0.004 0.053 2858 Dihedral : 5.350 59.001 2524 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.86 % Allowed : 10.04 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % 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: 0.81 (0.19), residues: 1992 helix: 1.50 (0.17), residues: 1012 sheet: -0.30 (0.35), residues: 190 loop : -0.45 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 277 TYR 0.014 0.001 TYR A 387 PHE 0.017 0.001 PHE C 429 TRP 0.013 0.001 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (16483) covalent geometry : angle 0.70076 / 0.34 (22243) hydrogen bonds : bond 0.05417 / 3.65 ( 805) hydrogen bonds : angle 5.48874 / 3.92 ( 2301) Misc. bond : bond 0.10491 / 6.73 ( 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 231 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.508 Fit side-chains REVERT: A 4 MET cc_start: 0.3292 (ptm) cc_final: 0.2622 (ppp) REVERT: A 7 GLU cc_start: 0.6658 (mp0) cc_final: 0.6252 (mp0) REVERT: A 22 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6400 (pm20) REVERT: A 129 LYS cc_start: 0.7808 (mppt) cc_final: 0.7300 (tptp) REVERT: A 133 LYS cc_start: 0.8537 (tptm) cc_final: 0.8247 (tttm) REVERT: A 243 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: A 287 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.6846 (tp30) REVERT: B 6 ASP cc_start: 0.7643 (m-30) cc_final: 0.7419 (p0) REVERT: B 121 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7533 (p0) REVERT: B 417 LYS cc_start: 0.8443 (pttt) cc_final: 0.7891 (pmtt) REVERT: C 7 GLU cc_start: 0.6479 (mp0) cc_final: 0.5894 (pm20) REVERT: C 22 GLU cc_start: 0.7394 (tp30) cc_final: 0.7173 (pm20) REVERT: C 133 LYS cc_start: 0.8505 (tptm) cc_final: 0.8216 (tttm) REVERT: C 287 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.6894 (tp30) REVERT: C 322 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7487 (mptp) REVERT: C 326 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7955 (mt-10) REVERT: D 4 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7231 (mp-120) REVERT: D 461 GLU cc_start: 0.8424 (pm20) cc_final: 0.8181 (pm20) outliers start: 32 outliers final: 15 residues processed: 219 average time/residue: 0.8012 time to fit residues: 190.1974 Evaluate side-chains 218 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 177 optimal weight: 7.9990 chunk 193 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 160 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN B 268 GLN C 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107894 restraints weight = 24389.858| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.11 r_work: 0.3119 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.216 16499 Z= 0.146 Angle : 0.690 29.168 22243 Z= 0.328 Chirality : 0.044 0.144 2336 Planarity : 0.004 0.049 2858 Dihedral : 5.218 58.781 2524 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.97 % Allowed : 10.04 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % 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: 0.92 (0.19), residues: 1992 helix: 1.56 (0.17), residues: 1024 sheet: -0.24 (0.35), residues: 190 loop : -0.38 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 277 TYR 0.014 0.001 TYR D 88 PHE 0.015 0.001 PHE C 429 TRP 0.013 0.001 TRP C 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (16483) covalent geometry : angle 0.69017 / 0.33 (22243) hydrogen bonds : bond 0.05151 / 3.47 ( 805) hydrogen bonds : angle 5.40801 / 3.86 ( 2301) Misc. bond : bond 0.09963 / 6.43 ( 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 233 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.535 Fit side-chains REVERT: A 4 MET cc_start: 0.3599 (ptm) cc_final: 0.2664 (ppp) REVERT: A 7 GLU cc_start: 0.6609 (mp0) cc_final: 0.6222 (mp0) REVERT: A 22 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6416 (pm20) REVERT: A 129 LYS cc_start: 0.7809 (mppt) cc_final: 0.7279 (tptp) REVERT: A 133 LYS cc_start: 0.8513 (tptm) cc_final: 0.8242 (tttm) REVERT: A 243 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.6859 (mp0) REVERT: B 6 ASP cc_start: 0.7610 (m-30) cc_final: 0.7405 (p0) REVERT: B 121 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7497 (p0) REVERT: B 417 LYS cc_start: 0.8443 (pttt) cc_final: 0.7915 (pmtt) REVERT: C 7 GLU cc_start: 0.6456 (mp0) cc_final: 0.5880 (pm20) REVERT: C 133 LYS cc_start: 0.8492 (tptm) cc_final: 0.8236 (tttm) REVERT: C 322 LYS cc_start: 0.7902 (mtpp) cc_final: 0.7465 (mttp) REVERT: D 4 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7352 (mp-120) REVERT: D 50 LYS cc_start: 0.8373 (mttm) cc_final: 0.8110 (mmtt) REVERT: D 461 GLU cc_start: 0.8413 (pm20) cc_final: 0.8173 (pm20) outliers start: 34 outliers final: 13 residues processed: 222 average time/residue: 0.7673 time to fit residues: 184.3404 Evaluate side-chains 212 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 180 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 186 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 432 GLN C 31 HIS C 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102914 restraints weight = 24125.476| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.11 r_work: 0.3041 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.283 16499 Z= 0.210 Angle : 0.771 29.346 22243 Z= 0.380 Chirality : 0.048 0.155 2336 Planarity : 0.005 0.074 2858 Dihedral : 5.411 59.355 2522 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.51 % Allowed : 10.62 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % 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: 0.74 (0.18), residues: 1992 helix: 1.36 (0.16), residues: 1022 sheet: -0.21 (0.35), residues: 190 loop : -0.42 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 277 TYR 0.018 0.002 TYR D 88 PHE 0.022 0.002 PHE C 429 TRP 0.010 0.002 TRP A 444 HIS 0.009 0.002 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (16483) covalent geometry : angle 0.77074 / 0.38 (22243) hydrogen bonds : bond 0.06985 / 4.68 ( 805) hydrogen bonds : angle 5.63972 / 4.04 ( 2301) Misc. bond : bond 0.13106 / 8.42 ( 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 228 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.466 Fit side-chains REVERT: A 4 MET cc_start: 0.3311 (ptm) cc_final: 0.2342 (pp-130) REVERT: A 7 GLU cc_start: 0.6738 (mp0) cc_final: 0.6387 (mp0) REVERT: A 22 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6422 (pm20) REVERT: A 129 LYS cc_start: 0.8055 (mppt) cc_final: 0.7402 (tptp) REVERT: A 133 LYS cc_start: 0.8625 (tptm) cc_final: 0.8294 (tttm) REVERT: A 243 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: A 287 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.6955 (tp30) REVERT: B 6 ASP cc_start: 0.7714 (m-30) cc_final: 0.7455 (p0) REVERT: B 121 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7562 (p0) REVERT: B 417 LYS cc_start: 0.8461 (pttt) cc_final: 0.7933 (pmtt) REVERT: C 7 GLU cc_start: 0.6601 (mp0) cc_final: 0.5978 (pm20) REVERT: C 47 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8049 (mp) REVERT: C 129 LYS cc_start: 0.8194 (mttp) cc_final: 0.7355 (tptp) REVERT: C 133 LYS cc_start: 0.8641 (tptm) cc_final: 0.8305 (tttm) REVERT: C 287 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.6955 (tp30) REVERT: C 322 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7513 (mptp) REVERT: D 4 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7502 (mp-120) REVERT: D 50 LYS cc_start: 0.8485 (mttm) cc_final: 0.8153 (mmtt) REVERT: D 461 GLU cc_start: 0.8467 (pm20) cc_final: 0.8229 (pm20) outliers start: 26 outliers final: 15 residues processed: 220 average time/residue: 0.7756 time to fit residues: 184.6859 Evaluate side-chains 220 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 20 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.107042 restraints weight = 24264.530| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.22 r_work: 0.3084 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.237 16499 Z= 0.155 Angle : 0.703 29.231 22243 Z= 0.337 Chirality : 0.044 0.145 2336 Planarity : 0.004 0.056 2858 Dihedral : 5.234 59.978 2522 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.63 % Allowed : 10.80 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % 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: 0.85 (0.19), residues: 1992 helix: 1.50 (0.16), residues: 1022 sheet: -0.22 (0.35), residues: 190 loop : -0.41 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 277 TYR 0.014 0.001 TYR A 229 PHE 0.016 0.001 PHE C 429 TRP 0.013 0.001 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (16483) covalent geometry : angle 0.70324 / 0.34 (22243) hydrogen bonds : bond 0.05448 / 3.66 ( 805) hydrogen bonds : angle 5.46273 / 3.90 ( 2301) Misc. bond : bond 0.11142 / 7.11 ( 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 222 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.696 Fit side-chains REVERT: A 4 MET cc_start: 0.3029 (ptm) cc_final: 0.2623 (pmm) REVERT: A 7 GLU cc_start: 0.6548 (mp0) cc_final: 0.6190 (mp0) REVERT: A 22 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6413 (pm20) REVERT: A 129 LYS cc_start: 0.7935 (mppt) cc_final: 0.7314 (tptp) REVERT: A 133 LYS cc_start: 0.8525 (tptm) cc_final: 0.8236 (tttm) REVERT: A 243 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: A 287 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.6878 (tp30) REVERT: B 6 ASP cc_start: 0.7637 (m-30) cc_final: 0.7351 (p0) REVERT: B 121 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7546 (p0) REVERT: B 417 LYS cc_start: 0.8467 (pttt) cc_final: 0.7944 (pmtt) REVERT: C 7 GLU cc_start: 0.6509 (mp0) cc_final: 0.5876 (pm20) REVERT: C 47 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8043 (mp) REVERT: C 129 LYS cc_start: 0.8078 (mttp) cc_final: 0.7216 (tptp) REVERT: C 133 LYS cc_start: 0.8522 (tptm) cc_final: 0.8226 (tttm) REVERT: C 287 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.6901 (tp30) REVERT: C 322 LYS cc_start: 0.7922 (mtpp) cc_final: 0.7546 (mttp) REVERT: D 4 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7374 (mp-120) REVERT: D 7 LYS cc_start: 0.8310 (tptp) cc_final: 0.7803 (ttmt) REVERT: D 461 GLU cc_start: 0.8481 (pm20) cc_final: 0.8249 (pm20) outliers start: 28 outliers final: 16 residues processed: 213 average time/residue: 0.8245 time to fit residues: 189.6231 Evaluate side-chains 215 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.102415 restraints weight = 20229.340| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.08 r_work: 0.3047 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.304 16499 Z= 0.253 Angle : 0.822 29.528 22243 Z= 0.413 Chirality : 0.051 0.177 2336 Planarity : 0.006 0.088 2858 Dihedral : 5.553 59.085 2522 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.74 % Allowed : 10.80 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 1992 helix: 1.25 (0.16), residues: 1002 sheet: -0.21 (0.35), residues: 190 loop : -0.48 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 277 TYR 0.020 0.003 TYR D 88 PHE 0.025 0.003 PHE C 429 TRP 0.012 0.003 TRP A 444 HIS 0.008 0.002 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.24 (16483) covalent geometry : angle 0.82240 / 0.41 (22243) hydrogen bonds : bond 0.07901 / 5.29 ( 805) hydrogen bonds : angle 5.76268 / 4.14 ( 2301) Misc. bond : bond 0.14210 / 9.09 ( 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 227 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.471 Fit side-chains REVERT: A 4 MET cc_start: 0.2680 (ptm) cc_final: 0.1510 (pp-130) REVERT: A 7 GLU cc_start: 0.6626 (mp0) cc_final: 0.6361 (mp0) REVERT: A 22 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6324 (pm20) REVERT: A 129 LYS cc_start: 0.7993 (mppt) cc_final: 0.7242 (tptp) REVERT: A 243 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: A 287 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.6741 (tp30) REVERT: B 6 ASP cc_start: 0.7558 (m-30) cc_final: 0.7273 (p0) REVERT: B 121 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7500 (p0) REVERT: B 417 LYS cc_start: 0.8347 (pttt) cc_final: 0.7793 (pmtt) REVERT: C 7 GLU cc_start: 0.6516 (mp0) cc_final: 0.5813 (pm20) REVERT: C 22 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6221 (pm20) REVERT: C 47 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8045 (mp) REVERT: C 129 LYS cc_start: 0.8095 (mttp) cc_final: 0.7223 (tptp) REVERT: C 133 LYS cc_start: 0.8539 (tptm) cc_final: 0.8270 (tttm) REVERT: C 287 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.6810 (tp30) REVERT: D 4 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7414 (mp-120) REVERT: D 50 LYS cc_start: 0.8376 (mttm) cc_final: 0.7973 (mmtt) outliers start: 30 outliers final: 17 residues processed: 216 average time/residue: 0.8037 time to fit residues: 188.2288 Evaluate side-chains 219 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 131 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 187 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.104148 restraints weight = 16255.807| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 0.95 r_work: 0.3074 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.294 16499 Z= 0.233 Angle : 0.802 29.476 22243 Z= 0.400 Chirality : 0.050 0.171 2336 Planarity : 0.005 0.086 2858 Dihedral : 5.560 59.674 2522 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.63 % Allowed : 11.03 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 1992 helix: 1.23 (0.16), residues: 1002 sheet: -0.23 (0.35), residues: 190 loop : -0.51 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 277 TYR 0.019 0.003 TYR D 88 PHE 0.024 0.002 PHE C 429 TRP 0.013 0.002 TRP A 294 HIS 0.008 0.002 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.22 (16483) covalent geometry : angle 0.80163 / 0.40 (22243) hydrogen bonds : bond 0.07462 / 5.00 ( 805) hydrogen bonds : angle 5.73040 / 4.11 ( 2301) Misc. bond : bond 0.13839 / 8.83 ( 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 224 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.455 Fit side-chains REVERT: A 4 MET cc_start: 0.3008 (ptm) cc_final: 0.2094 (pp-130) REVERT: A 7 GLU cc_start: 0.6613 (mp0) cc_final: 0.6275 (mp0) REVERT: A 22 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6310 (pm20) REVERT: A 121 LYS cc_start: 0.8233 (ptpp) cc_final: 0.8025 (ptmm) REVERT: A 129 LYS cc_start: 0.7976 (mppt) cc_final: 0.7239 (tptp) REVERT: A 243 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: A 287 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.6746 (tp30) REVERT: B 6 ASP cc_start: 0.7537 (m-30) cc_final: 0.7298 (p0) REVERT: B 121 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7464 (p0) REVERT: B 172 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: B 299 GLU cc_start: 0.7864 (mp0) cc_final: 0.7536 (mp0) REVERT: B 417 LYS cc_start: 0.8334 (pttt) cc_final: 0.7793 (pmtt) REVERT: C 7 GLU cc_start: 0.6449 (mp0) cc_final: 0.5782 (pm20) REVERT: C 22 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6212 (pm20) REVERT: C 47 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8047 (mp) REVERT: C 129 LYS cc_start: 0.8050 (mttp) cc_final: 0.7200 (tptp) REVERT: C 287 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.6757 (tp30) REVERT: D 4 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7156 (mp-120) REVERT: D 50 LYS cc_start: 0.8357 (mttm) cc_final: 0.7968 (mmtt) outliers start: 28 outliers final: 15 residues processed: 213 average time/residue: 0.8186 time to fit residues: 188.8618 Evaluate side-chains 220 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 144 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 140 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 182 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104848 restraints weight = 19279.046| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.05 r_work: 0.3083 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.270 16499 Z= 0.194 Angle : 0.758 29.353 22243 Z= 0.372 Chirality : 0.047 0.154 2336 Planarity : 0.005 0.073 2858 Dihedral : 5.453 59.446 2522 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.51 % Allowed : 11.09 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 1992 helix: 1.35 (0.16), residues: 1002 sheet: -0.25 (0.35), residues: 190 loop : -0.51 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 277 TYR 0.016 0.002 TYR D 88 PHE 0.020 0.002 PHE C 429 TRP 0.013 0.002 TRP A 294 HIS 0.008 0.002 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (16483) covalent geometry : angle 0.75817 / 0.37 (22243) hydrogen bonds : bond 0.06594 / 4.42 ( 805) hydrogen bonds : angle 5.62630 / 4.03 ( 2301) Misc. bond : bond 0.12731 / 8.12 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7001.72 seconds wall clock time: 119 minutes 53.83 seconds (7193.83 seconds total)