Starting phenix.real_space_refine on Mon Apr 6 07:24:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mm1_48384/04_2026/9mm1_48384.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mm1_48384/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mm1_48384/04_2026/9mm1_48384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mm1_48384/04_2026/9mm1_48384.map" model { file = "/net/cci-nas-00/data/ceres_data/9mm1_48384/04_2026/9mm1_48384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mm1_48384/04_2026/9mm1_48384.cif" } resolution = 2.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 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: 5.42, per 1000 atoms: 0.32 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: 1.39 Conformation dependent library (CDL) restraints added in 947.0 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: 0.57 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: 2.64 Time building geometry restraints manager: 1.78 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 2.260 nonbonded pdb=" O ARG D 108 " pdb="FE FE B 601 " model vdw 1.920 2.260 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 2.260 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: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.670 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 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 covalent geometry : bond 0.02417 (16483) covalent geometry : angle 1.15688 (22243) hydrogen bonds : bond 0.16481 ( 805) hydrogen bonds : angle 6.80973 ( 2301) Misc. bond : bond 0.07891 ( 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 : 0.786 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: 0.8683 time to fit residues: 321.8553 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 : 0.639 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3484 r_free = 0.3484 target = 0.129131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112492 restraints weight = 14162.827| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 0.86 r_work: 0.3200 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 1.90 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 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 = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.280 16499 Z= 0.171 Angle : 0.732 28.941 22243 Z= 0.359 Chirality : 0.046 0.156 2336 Planarity : 0.005 0.050 2858 Dihedral : 5.876 58.200 2532 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.80 % Allowed : 8.76 % 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: 0.75 (0.18), residues: 1992 helix: 1.47 (0.16), residues: 1010 sheet: -0.55 (0.35), residues: 190 loop : -0.44 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 277 TYR 0.018 0.002 TYR D 88 PHE 0.016 0.002 PHE C 429 TRP 0.012 0.001 TRP C 479 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00305 (16483) covalent geometry : angle 0.73184 (22243) hydrogen bonds : bond 0.05813 ( 805) hydrogen bonds : angle 5.68840 ( 2301) Misc. bond : bond 0.12883 ( 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 247 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 0.664 Fit side-chains REVERT: A 8 GLU cc_start: 0.6296 (mp0) cc_final: 0.6087 (tm-30) REVERT: A 129 LYS cc_start: 0.7432 (mppt) cc_final: 0.7020 (tptp) REVERT: A 133 LYS cc_start: 0.8394 (tptp) cc_final: 0.8102 (tttm) REVERT: B 6 ASP cc_start: 0.7439 (m-30) cc_final: 0.7092 (p0) REVERT: B 172 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: B 417 LYS cc_start: 0.8242 (pttt) cc_final: 0.7720 (pmtt) REVERT: B 461 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: C 7 GLU cc_start: 0.6361 (mp0) cc_final: 0.5587 (pm20) REVERT: C 22 GLU cc_start: 0.7036 (tp30) cc_final: 0.6806 (tp30) REVERT: C 133 LYS cc_start: 0.8359 (tptp) cc_final: 0.8082 (tttm) REVERT: C 326 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7792 (mt-10) REVERT: D 6 ASP cc_start: 0.7563 (m-30) cc_final: 0.7345 (p0) REVERT: D 243 MET cc_start: 0.8757 (mtm) cc_final: 0.8495 (mtp) REVERT: D 461 GLU cc_start: 0.8219 (pm20) cc_final: 0.7966 (pm20) outliers start: 31 outliers final: 14 residues processed: 239 average time/residue: 0.8509 time to fit residues: 219.9679 Evaluate side-chains 214 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 377 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 172 GLU 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: 8.9990 chunk 102 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3385 r_free = 0.3385 target = 0.121646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102560 restraints weight = 22022.261| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.11 r_work: 0.3046 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.286 16499 Z= 0.235 Angle : 0.807 29.480 22243 Z= 0.405 Chirality : 0.050 0.153 2336 Planarity : 0.006 0.072 2858 Dihedral : 5.692 58.915 2527 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.86 % Allowed : 9.11 % Favored : 89.03 % 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: 0.56 (0.18), residues: 1992 helix: 1.29 (0.16), residues: 1002 sheet: -0.40 (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 0.021 0.003 TYR B 142 PHE 0.028 0.002 PHE C 429 TRP 0.012 0.002 TRP A 472 HIS 0.009 0.002 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00464 (16483) covalent geometry : angle 0.80669 (22243) hydrogen bonds : bond 0.07595 ( 805) hydrogen bonds : angle 5.77032 ( 2301) Misc. bond : bond 0.13418 ( 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 238 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.695 Fit side-chains REVERT: A 22 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6436 (pm20) REVERT: A 129 LYS cc_start: 0.7931 (mppt) cc_final: 0.7475 (tptp) REVERT: A 133 LYS cc_start: 0.8611 (tptp) cc_final: 0.8335 (tttm) REVERT: A 243 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: B 6 ASP cc_start: 0.7682 (m-30) cc_final: 0.7416 (p0) REVERT: B 118 MET cc_start: 0.8930 (mtp) cc_final: 0.8702 (mtp) REVERT: B 121 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7574 (p0) REVERT: B 215 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7465 (p0) REVERT: B 299 GLU cc_start: 0.8007 (mp0) cc_final: 0.7729 (mp0) REVERT: B 417 LYS cc_start: 0.8385 (pttt) cc_final: 0.7869 (pmtt) REVERT: B 461 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8209 (pm20) REVERT: C 7 GLU cc_start: 0.6565 (mp0) cc_final: 0.5932 (pm20) REVERT: C 22 GLU cc_start: 0.7404 (tp30) cc_final: 0.7139 (tp30) REVERT: C 129 LYS cc_start: 0.8226 (mttp) cc_final: 0.7372 (tptp) REVERT: C 133 LYS cc_start: 0.8615 (tptp) cc_final: 0.8336 (tttm) REVERT: C 322 LYS cc_start: 0.7994 (mtpp) cc_final: 0.7788 (mtpp) REVERT: C 326 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7984 (mt-10) REVERT: D 6 ASP cc_start: 0.7709 (m-30) cc_final: 0.7472 (p0) REVERT: D 461 GLU cc_start: 0.8428 (pm20) cc_final: 0.8174 (pm20) outliers start: 32 outliers final: 14 residues processed: 228 average time/residue: 0.8870 time to fit residues: 218.2538 Evaluate side-chains 214 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 18 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 192 optimal weight: 0.0870 chunk 125 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 268 GLN C 31 HIS C 53 GLN C 98 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.128518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109662 restraints weight = 22407.565| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.23 r_work: 0.3121 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 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 = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.204 16499 Z= 0.144 Angle : 0.689 29.141 22243 Z= 0.329 Chirality : 0.044 0.143 2336 Planarity : 0.004 0.043 2858 Dihedral : 5.323 58.382 2524 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.68 % Allowed : 9.81 % Favored : 88.51 % 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: 0.82 (0.19), residues: 1992 helix: 1.54 (0.17), residues: 1014 sheet: -0.36 (0.35), residues: 190 loop : -0.46 (0.21), residues: 788 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 0.014 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 covalent geometry : bond 0.00263 (16483) covalent geometry : angle 0.68901 (22243) hydrogen bonds : bond 0.04993 ( 805) hydrogen bonds : angle 5.43449 ( 2301) Misc. bond : bond 0.09640 ( 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 231 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.608 Fit side-chains REVERT: A 22 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6409 (pm20) REVERT: A 129 LYS cc_start: 0.7726 (mppt) cc_final: 0.7214 (tptp) REVERT: A 133 LYS cc_start: 0.8487 (tptp) cc_final: 0.8248 (tttm) REVERT: A 243 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: B 6 ASP cc_start: 0.7558 (m-30) cc_final: 0.7267 (p0) REVERT: B 121 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7583 (p0) REVERT: B 158 ILE cc_start: 0.8411 (pt) cc_final: 0.8175 (pt) REVERT: B 417 LYS cc_start: 0.8407 (pttt) cc_final: 0.7858 (pmtt) REVERT: C 7 GLU cc_start: 0.6449 (mp0) cc_final: 0.5621 (pm20) REVERT: C 22 GLU cc_start: 0.7384 (tp30) cc_final: 0.7150 (tp30) REVERT: C 133 LYS cc_start: 0.8453 (tptp) cc_final: 0.8222 (tttm) REVERT: C 322 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7496 (mptp) REVERT: D 6 ASP cc_start: 0.7699 (m-30) cc_final: 0.7376 (p0) REVERT: D 50 LYS cc_start: 0.8417 (mttm) cc_final: 0.8129 (mmtt) REVERT: D 243 MET cc_start: 0.8873 (mtm) cc_final: 0.8671 (mtp) REVERT: D 461 GLU cc_start: 0.8439 (pm20) cc_final: 0.8175 (pm20) outliers start: 29 outliers final: 12 residues processed: 220 average time/residue: 0.8737 time to fit residues: 207.3652 Evaluate side-chains 206 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 121 ASP Chi-restraints excluded: chain B residue 212 SER 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 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: 7.9990 chunk 9 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 101 optimal weight: 0.3980 chunk 183 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 98 ASN D 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106297 restraints weight = 22965.735| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.10 r_work: 0.3096 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 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 = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.238 16499 Z= 0.165 Angle : 0.715 29.232 22243 Z= 0.345 Chirality : 0.045 0.147 2336 Planarity : 0.004 0.056 2858 Dihedral : 5.308 58.698 2524 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.86 % Allowed : 9.98 % Favored : 88.16 % 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: 0.84 (0.18), residues: 1992 helix: 1.50 (0.16), residues: 1022 sheet: -0.28 (0.35), residues: 190 loop : -0.43 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 277 TYR 0.016 0.002 TYR D 88 PHE 0.019 0.002 PHE C 429 TRP 0.011 0.002 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00305 (16483) covalent geometry : angle 0.71471 (22243) hydrogen bonds : bond 0.05790 ( 805) hydrogen bonds : angle 5.47037 ( 2301) Misc. bond : bond 0.10992 ( 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 228 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.538 Fit side-chains REVERT: A 4 MET cc_start: 0.2859 (ptm) cc_final: 0.2356 (ppp) REVERT: A 7 GLU cc_start: 0.6731 (mp0) cc_final: 0.6262 (mp0) REVERT: A 22 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6398 (pm20) REVERT: A 129 LYS cc_start: 0.7811 (mppt) cc_final: 0.7307 (tptp) REVERT: A 133 LYS cc_start: 0.8557 (tptp) cc_final: 0.8320 (tttm) REVERT: A 243 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: A 287 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.6816 (tp30) REVERT: B 6 ASP cc_start: 0.7627 (m-30) cc_final: 0.7370 (p0) REVERT: B 121 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7568 (p0) REVERT: B 215 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7425 (p0) REVERT: B 417 LYS cc_start: 0.8449 (pttt) cc_final: 0.7899 (pmtt) REVERT: C 7 GLU cc_start: 0.6539 (mp0) cc_final: 0.5954 (pm20) REVERT: C 47 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8047 (mp) REVERT: C 133 LYS cc_start: 0.8542 (tptp) cc_final: 0.8307 (tttm) REVERT: C 322 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7519 (mptp) REVERT: D 6 ASP cc_start: 0.7690 (m-30) cc_final: 0.7433 (p0) REVERT: D 243 MET cc_start: 0.8888 (mtm) cc_final: 0.8679 (mtp) REVERT: D 461 GLU cc_start: 0.8446 (pm20) cc_final: 0.8189 (pm20) outliers start: 32 outliers final: 15 residues processed: 220 average time/residue: 0.9116 time to fit residues: 217.5366 Evaluate side-chains 211 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 212 SER Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 47 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 72 optimal weight: 0.0270 chunk 177 optimal weight: 7.9990 chunk 193 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 115 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3433 r_free = 0.3433 target = 0.125329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106743 restraints weight = 24870.244| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.14 r_work: 0.3100 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 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 = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.235 16499 Z= 0.156 Angle : 0.701 29.248 22243 Z= 0.335 Chirality : 0.044 0.146 2336 Planarity : 0.004 0.052 2858 Dihedral : 5.264 58.946 2524 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.92 % Allowed : 10.16 % Favored : 87.93 % 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: 0.89 (0.19), residues: 1992 helix: 1.55 (0.16), residues: 1022 sheet: -0.26 (0.35), residues: 190 loop : -0.40 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 277 TYR 0.015 0.002 TYR D 88 PHE 0.016 0.001 PHE C 429 TRP 0.012 0.001 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00286 (16483) covalent geometry : angle 0.70091 (22243) hydrogen bonds : bond 0.05447 ( 805) hydrogen bonds : angle 5.43004 ( 2301) Misc. bond : bond 0.10728 ( 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 227 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.798 Fit side-chains REVERT: A 4 MET cc_start: 0.2881 (ptm) cc_final: 0.2289 (ppp) REVERT: A 7 GLU cc_start: 0.6671 (mp0) cc_final: 0.6213 (mp0) REVERT: A 22 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6404 (pm20) REVERT: A 129 LYS cc_start: 0.7828 (mppt) cc_final: 0.7301 (tptp) REVERT: A 133 LYS cc_start: 0.8537 (tptp) cc_final: 0.8295 (tttm) REVERT: A 243 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: A 287 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.6852 (tp30) REVERT: B 6 ASP cc_start: 0.7640 (m-30) cc_final: 0.7387 (p0) REVERT: B 121 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7548 (p0) REVERT: B 417 LYS cc_start: 0.8447 (pttt) cc_final: 0.7905 (pmtt) REVERT: C 7 GLU cc_start: 0.6426 (mp0) cc_final: 0.5839 (pm20) REVERT: C 47 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8044 (mp) REVERT: C 133 LYS cc_start: 0.8538 (tptp) cc_final: 0.8306 (tttm) REVERT: C 287 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.6880 (tp30) REVERT: C 322 LYS cc_start: 0.7934 (mtpp) cc_final: 0.7529 (mttp) REVERT: D 6 ASP cc_start: 0.7656 (m-30) cc_final: 0.7382 (p0) REVERT: D 243 MET cc_start: 0.8880 (mtm) cc_final: 0.8680 (mtp) REVERT: D 461 GLU cc_start: 0.8448 (pm20) cc_final: 0.8199 (pm20) outliers start: 33 outliers final: 16 residues processed: 216 average time/residue: 0.8890 time to fit residues: 207.7654 Evaluate side-chains 212 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 180 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 171 optimal weight: 0.0070 chunk 62 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3402 r_free = 0.3402 target = 0.122919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.104221 restraints weight = 24611.960| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.12 r_work: 0.3071 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.267 16499 Z= 0.186 Angle : 0.739 29.324 22243 Z= 0.360 Chirality : 0.046 0.150 2336 Planarity : 0.005 0.064 2858 Dihedral : 5.397 59.825 2524 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.80 % Allowed : 10.10 % 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 (0.18), residues: 1992 helix: 1.44 (0.16), residues: 1022 sheet: -0.22 (0.35), residues: 190 loop : -0.40 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 277 TYR 0.017 0.002 TYR D 88 PHE 0.021 0.002 PHE C 429 TRP 0.010 0.002 TRP A 335 HIS 0.009 0.002 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00352 (16483) covalent geometry : angle 0.73863 (22243) hydrogen bonds : bond 0.06363 ( 805) hydrogen bonds : angle 5.54660 ( 2301) Misc. bond : bond 0.12302 ( 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 231 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.770 Fit side-chains REVERT: A 4 MET cc_start: 0.2995 (ptm) cc_final: 0.2212 (ppp) REVERT: A 7 GLU cc_start: 0.6725 (mp0) cc_final: 0.6296 (mp0) REVERT: A 22 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6379 (pm20) REVERT: A 129 LYS cc_start: 0.7947 (mppt) cc_final: 0.7373 (tptp) REVERT: A 133 LYS cc_start: 0.8587 (tptp) cc_final: 0.8330 (tttm) REVERT: A 243 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: A 287 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.6888 (tp30) REVERT: B 6 ASP cc_start: 0.7704 (m-30) cc_final: 0.7444 (p0) REVERT: B 121 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7546 (p0) REVERT: B 299 GLU cc_start: 0.7978 (mp0) cc_final: 0.7688 (mp0) REVERT: B 417 LYS cc_start: 0.8479 (pttt) cc_final: 0.7974 (pmtt) REVERT: C 7 GLU cc_start: 0.6574 (mp0) cc_final: 0.5954 (pm20) REVERT: C 22 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6254 (pm20) REVERT: C 47 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8056 (mp) REVERT: C 133 LYS cc_start: 0.8593 (tptp) cc_final: 0.8351 (tttm) REVERT: C 287 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.6934 (tp30) REVERT: C 322 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7556 (mptp) REVERT: D 6 ASP cc_start: 0.7691 (m-30) cc_final: 0.7407 (p0) REVERT: D 299 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: D 461 GLU cc_start: 0.8468 (pm20) cc_final: 0.8222 (pm20) outliers start: 31 outliers final: 18 residues processed: 219 average time/residue: 0.8802 time to fit residues: 208.1196 Evaluate side-chains 222 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 A residue 473 LYS 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 212 SER Chi-restraints excluded: chain B residue 315 LYS 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 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 Chi-restraints excluded: chain D residue 299 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 20 optimal weight: 0.0980 chunk 18 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 180 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3440 r_free = 0.3440 target = 0.125908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107368 restraints weight = 24961.881| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.14 r_work: 0.3112 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 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 = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.218 16499 Z= 0.146 Angle : 0.690 29.144 22243 Z= 0.328 Chirality : 0.044 0.145 2336 Planarity : 0.004 0.050 2858 Dihedral : 5.241 59.302 2524 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.57 % Allowed : 10.74 % Favored : 87.70 % 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: 1.55 (0.17), residues: 1024 sheet: -0.21 (0.35), residues: 190 loop : -0.37 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 277 TYR 0.013 0.001 TYR A 229 PHE 0.014 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 covalent geometry : bond 0.00265 (16483) covalent geometry : angle 0.69046 (22243) hydrogen bonds : bond 0.05158 ( 805) hydrogen bonds : angle 5.41235 ( 2301) Misc. bond : bond 0.10256 ( 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 224 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.685 Fit side-chains REVERT: A 4 MET cc_start: 0.2976 (ptm) cc_final: 0.2202 (ppp) REVERT: A 7 GLU cc_start: 0.6713 (mp0) cc_final: 0.6286 (mp0) REVERT: A 22 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6447 (pm20) REVERT: A 129 LYS cc_start: 0.7836 (mppt) cc_final: 0.7284 (tptp) REVERT: A 133 LYS cc_start: 0.8523 (tptp) cc_final: 0.8282 (tttm) REVERT: A 243 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: A 287 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.6897 (tp30) REVERT: B 6 ASP cc_start: 0.7657 (m-30) cc_final: 0.7402 (p0) REVERT: B 121 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7520 (p0) REVERT: B 417 LYS cc_start: 0.8463 (pttt) cc_final: 0.7941 (pmtt) REVERT: C 7 GLU cc_start: 0.6447 (mp0) cc_final: 0.5874 (pm20) REVERT: C 133 LYS cc_start: 0.8512 (tptp) cc_final: 0.8275 (tttm) REVERT: C 287 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.6946 (tp30) REVERT: C 322 LYS cc_start: 0.7931 (mtpp) cc_final: 0.7531 (mttp) REVERT: D 6 ASP cc_start: 0.7649 (m-30) cc_final: 0.7361 (p0) REVERT: D 461 GLU cc_start: 0.8443 (pm20) cc_final: 0.8201 (pm20) outliers start: 27 outliers final: 13 residues processed: 215 average time/residue: 0.8930 time to fit residues: 207.3397 Evaluate side-chains 212 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 212 SER 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 467 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 0.4980 chunk 78 optimal weight: 0.4980 chunk 71 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 432 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 = 0.3400 r_free = 0.3400 target = 0.122777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.104114 restraints weight = 20997.198| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.11 r_work: 0.3071 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.268 16499 Z= 0.193 Angle : 0.748 29.380 22243 Z= 0.366 Chirality : 0.047 0.151 2336 Planarity : 0.005 0.066 2858 Dihedral : 5.245 59.372 2520 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.57 % Allowed : 10.85 % 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: 0.81 (0.18), residues: 1992 helix: 1.45 (0.16), residues: 1020 sheet: -0.19 (0.35), residues: 190 loop : -0.41 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 277 TYR 0.018 0.002 TYR D 88 PHE 0.021 0.002 PHE C 429 TRP 0.010 0.002 TRP A 335 HIS 0.009 0.002 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00370 (16483) covalent geometry : angle 0.74776 (22243) hydrogen bonds : bond 0.06541 ( 805) hydrogen bonds : angle 5.56518 ( 2301) Misc. bond : bond 0.12391 ( 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: 27 poor density : 200 time to evaluate : 0.536 Fit side-chains REVERT: A 4 MET cc_start: 0.2697 (OUTLIER) cc_final: 0.1799 (ppp) REVERT: A 7 GLU cc_start: 0.6797 (mp0) cc_final: 0.6386 (mp0) REVERT: A 22 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6399 (pm20) REVERT: A 129 LYS cc_start: 0.7983 (mppt) cc_final: 0.7418 (tptp) REVERT: A 133 LYS cc_start: 0.8594 (tptp) cc_final: 0.8336 (tttm) REVERT: A 243 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: A 287 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.6852 (tp30) REVERT: B 6 ASP cc_start: 0.7706 (m-30) cc_final: 0.7475 (p0) REVERT: B 121 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7519 (p0) REVERT: B 417 LYS cc_start: 0.8464 (pttt) cc_final: 0.7973 (pmtt) REVERT: C 7 GLU cc_start: 0.6563 (mp0) cc_final: 0.5958 (pm20) REVERT: C 47 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8066 (mp) REVERT: C 133 LYS cc_start: 0.8604 (tptp) cc_final: 0.8352 (tttm) REVERT: C 287 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.6923 (tp30) REVERT: C 322 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7582 (mptp) REVERT: D 6 ASP cc_start: 0.7703 (m-30) cc_final: 0.7445 (p0) REVERT: D 461 GLU cc_start: 0.8465 (pm20) cc_final: 0.8220 (pm20) outliers start: 27 outliers final: 13 residues processed: 218 average time/residue: 0.8748 time to fit residues: 206.1286 Evaluate side-chains 218 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET 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 473 LYS 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 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 358 LEU Chi-restraints excluded: chain C residue 362 HIS 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 131 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3408 r_free = 0.3408 target = 0.123109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.104855 restraints weight = 16747.203| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 0.97 r_work: 0.3086 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 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 = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.281 16499 Z= 0.211 Angle : 0.775 29.398 22243 Z= 0.384 Chirality : 0.048 0.153 2336 Planarity : 0.005 0.076 2858 Dihedral : 5.364 58.975 2520 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.45 % Allowed : 11.14 % 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: 0.68 (0.18), residues: 1992 helix: 1.35 (0.16), residues: 1008 sheet: -0.20 (0.35), residues: 190 loop : -0.47 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 277 TYR 0.020 0.002 TYR D 88 PHE 0.022 0.002 PHE C 429 TRP 0.012 0.002 TRP C 294 HIS 0.009 0.002 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00411 (16483) covalent geometry : angle 0.77529 (22243) hydrogen bonds : bond 0.07029 ( 805) hydrogen bonds : angle 5.65853 ( 2301) Misc. bond : bond 0.13103 ( 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 228 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.697 Fit side-chains REVERT: A 4 MET cc_start: 0.2620 (ptm) cc_final: 0.1961 (ppp) REVERT: A 7 GLU cc_start: 0.6600 (mp0) cc_final: 0.6193 (mp0) REVERT: A 22 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6190 (pm20) REVERT: A 129 LYS cc_start: 0.7917 (mppt) cc_final: 0.7193 (tptp) REVERT: A 133 LYS cc_start: 0.8475 (tptp) cc_final: 0.8151 (tttm) REVERT: A 243 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: A 287 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.6761 (tp30) REVERT: B 6 ASP cc_start: 0.7553 (m-30) cc_final: 0.7280 (p0) REVERT: B 121 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7476 (p0) REVERT: B 299 GLU cc_start: 0.7891 (mp0) cc_final: 0.7554 (mp0) REVERT: B 417 LYS cc_start: 0.8334 (pttt) cc_final: 0.7782 (pmtt) REVERT: C 7 GLU cc_start: 0.6394 (mp0) cc_final: 0.5731 (pm20) REVERT: C 47 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7982 (mp) REVERT: C 129 LYS cc_start: 0.8096 (mttp) cc_final: 0.7152 (tptp) REVERT: C 133 LYS cc_start: 0.8469 (tptp) cc_final: 0.8144 (tttm) REVERT: C 287 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.6760 (tp30) REVERT: C 322 LYS cc_start: 0.7784 (mtpp) cc_final: 0.7363 (mptp) REVERT: D 6 ASP cc_start: 0.7529 (m-30) cc_final: 0.7226 (p0) REVERT: D 171 LYS cc_start: 0.8497 (tttt) cc_final: 0.8140 (ttmt) REVERT: D 461 GLU cc_start: 0.8315 (pm20) cc_final: 0.8058 (pm20) outliers start: 25 outliers final: 13 residues processed: 219 average time/residue: 0.8908 time to fit residues: 210.3342 Evaluate side-chains 217 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 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 358 LEU Chi-restraints excluded: chain C residue 362 HIS 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: 0.0980 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3442 r_free = 0.3442 target = 0.125804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.106934 restraints weight = 19948.136| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.07 r_work: 0.3114 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.237 16499 Z= 0.161 Angle : 0.714 29.224 22243 Z= 0.344 Chirality : 0.045 0.146 2336 Planarity : 0.004 0.058 2858 Dihedral : 5.196 59.920 2520 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.33 % Allowed : 11.38 % Favored : 87.29 % 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: 0.82 (0.18), residues: 1992 helix: 1.47 (0.16), residues: 1022 sheet: -0.21 (0.35), residues: 190 loop : -0.43 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 277 TYR 0.014 0.002 TYR D 88 PHE 0.017 0.001 PHE C 429 TRP 0.012 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00295 (16483) covalent geometry : angle 0.71359 (22243) hydrogen bonds : bond 0.05676 ( 805) hydrogen bonds : angle 5.49921 ( 2301) Misc. bond : bond 0.11223 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7876.55 seconds wall clock time: 134 minutes 34.64 seconds (8074.64 seconds total)