Starting phenix.real_space_refine on Mon Jun 16 23:51:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9btg_44889/06_2025/9btg_44889_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9btg_44889/06_2025/9btg_44889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9btg_44889/06_2025/9btg_44889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9btg_44889/06_2025/9btg_44889.map" model { file = "/net/cci-nas-00/data/ceres_data/9btg_44889/06_2025/9btg_44889_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9btg_44889/06_2025/9btg_44889_trim.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.009 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: 5 Type Number sf(0) Gaussians S 94 5.16 5 C 6251 2.51 5 N 1613 2.21 5 O 1880 1.98 5 H 9273 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19111 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 6435 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 387} Chain breaks: 3 Chain: "B" Number of atoms: 6498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 6498 Classifications: {'peptide': 413} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 391} Chain breaks: 3 Chain: "C" Number of atoms: 6010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6010 Classifications: {'peptide': 381} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 363} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.75, per 1000 atoms: 0.56 Number of scatterers: 19111 At special positions: 0 Unit cell: (104.195, 107.401, 94.577, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 O 1880 8.00 N 1613 7.00 C 6251 6.00 H 9273 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 272 " distance=2.04 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 189 " distance=2.04 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 203 " distance=2.03 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 444 " distance=2.03 Simple disulfide: pdb=" SG CYS A 390 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS A 399 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 401 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 272 " distance=2.03 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 203 " distance=2.04 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 444 " distance=2.03 Simple disulfide: pdb=" SG CYS B 390 " - pdb=" SG CYS B 440 " distance=2.04 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 401 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 267 " distance=2.03 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 457 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 453 " distance=2.03 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 449 " distance=2.03 Simple disulfide: pdb=" SG CYS C 407 " - pdb=" SG CYS C 434 " distance=2.03 Simple disulfide: pdb=" SG CYS C 409 " - pdb=" SG CYS C 423 " distance=2.03 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=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 701 " - " ASN A 141 " " NAG A 703 " - " ASN A 449 " " NAG B 701 " - " ASN B 141 " " NAG B 703 " - " ASN B 449 " " NAG D 1 " - " ASN A 260 " " NAG E 1 " - " ASN B 207 " " NAG F 1 " - " ASN C 271 " Time building additional restraints: 5.21 Conformation dependent library (CDL) restraints added in 1.5 seconds 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2300 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 12 sheets defined 34.2% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 104 through 128 removed outlier: 6.068A pdb=" N HIS A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASP A 114 " --> pdb=" O HIS A 110 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.523A pdb=" N TRP A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 228 removed outlier: 3.532A pdb=" N ILE A 226 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 290 through 293 Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.559A pdb=" N GLU A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 4.116A pdb=" N GLU A 367 " --> pdb=" O ASN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 399 removed outlier: 3.590A pdb=" N GLN A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 433 removed outlier: 3.583A pdb=" N SER A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 Processing helix chain 'A' and resid 467 through 478 Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'B' and resid 104 through 128 removed outlier: 6.130A pdb=" N HIS B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP B 114 " --> pdb=" O HIS B 110 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.742A pdb=" N TRP B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 228 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 241 through 245 Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 290 through 293 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.564A pdb=" N TYR B 306 " --> pdb=" O GLN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 382 through 399 Processing helix chain 'B' and resid 422 through 433 Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 468 through 476 Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'C' and resid 106 through 111 Processing helix chain 'C' and resid 114 through 130 Processing helix chain 'C' and resid 221 through 239 Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.614A pdb=" N ASN C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 301 through 304 Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.853A pdb=" N TYR C 317 " --> pdb=" O GLU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 removed outlier: 4.504A pdb=" N ASP C 378 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL C 379 " --> pdb=" O GLY C 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 375 through 379' Processing helix chain 'C' and resid 390 through 407 Processing helix chain 'C' and resid 430 through 444 removed outlier: 3.652A pdb=" N CYS C 434 " --> pdb=" O ASN C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 453 Processing helix chain 'C' and resid 476 through 489 removed outlier: 3.721A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Proline residue: C 482 - end of helix Processing helix chain 'C' and resid 497 through 499 No H-bonds generated for 'chain 'C' and resid 497 through 499' Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 86 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 80 through 86 current: chain 'A' and resid 254 through 256 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 254 through 256 current: chain 'A' and resid 449 through 461 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 266 removed outlier: 6.872A pdb=" N ASN A 271 " --> pdb=" O ASN A 99 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN A 99 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 165 Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 86 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 79 through 86 current: chain 'B' and resid 254 through 256 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 254 through 256 current: chain 'B' and resid 449 through 461 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.514A pdb=" N MET B 90 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 261 through 266 removed outlier: 7.068A pdb=" N ASN B 271 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN B 99 " --> pdb=" O ASN B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 162 through 165 removed outlier: 3.841A pdb=" N SER B 197 " --> pdb=" O GLN B 202 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN B 202 " --> pdb=" O SER B 197 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 81 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 81 through 85 current: chain 'C' and resid 265 through 267 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 265 through 267 current: chain 'C' and resid 458 through 465 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AB2, first strand: chain 'C' and resid 272 through 277 removed outlier: 7.177A pdb=" N ASN C 282 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN C 101 " --> pdb=" O ASN C 282 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.748A pdb=" N VAL C 201 " --> pdb=" O PHE C 163 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 879 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: 6.91 Time building geometry restraints manager: 6.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 9269 1.04 - 1.24: 1271 1.24 - 1.44: 3176 1.44 - 1.64: 5500 1.64 - 1.84: 136 Bond restraints: 19352 Sorted by residual: bond pdb=" C VAL A 368 " pdb=" N PRO A 369 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.89e+00 bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.05e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.78e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.50e+00 ... (remaining 19347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 33609 1.59 - 3.17: 1069 3.17 - 4.76: 72 4.76 - 6.34: 7 6.34 - 7.93: 1 Bond angle restraints: 34758 Sorted by residual: angle pdb=" N ILE C 355 " pdb=" CA ILE C 355 " pdb=" C ILE C 355 " ideal model delta sigma weight residual 106.21 110.95 -4.74 1.07e+00 8.73e-01 1.97e+01 angle pdb=" C ILE C 355 " pdb=" CA ILE C 355 " pdb=" CB ILE C 355 " ideal model delta sigma weight residual 113.22 108.64 4.58 1.12e+00 7.97e-01 1.67e+01 angle pdb=" CA CYS B 203 " pdb=" CB CYS B 203 " pdb=" SG CYS B 203 " ideal model delta sigma weight residual 114.40 122.33 -7.93 2.30e+00 1.89e-01 1.19e+01 angle pdb=" CA ILE C 355 " pdb=" C ILE C 355 " pdb=" N GLY C 356 " ideal model delta sigma weight residual 115.25 118.15 -2.90 9.50e-01 1.11e+00 9.35e+00 angle pdb=" CA ILE C 355 " pdb=" C ILE C 355 " pdb=" O ILE C 355 " ideal model delta sigma weight residual 122.63 120.12 2.51 8.70e-01 1.32e+00 8.30e+00 ... (remaining 34753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8803 17.99 - 35.98: 465 35.98 - 53.97: 155 53.97 - 71.96: 57 71.96 - 89.95: 7 Dihedral angle restraints: 9487 sinusoidal: 5161 harmonic: 4326 Sorted by residual: dihedral pdb=" CB CYS C 372 " pdb=" SG CYS C 372 " pdb=" SG CYS C 457 " pdb=" CB CYS C 457 " ideal model delta sinusoidal sigma weight residual -86.00 -143.18 57.18 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CA LYS C 91 " pdb=" C LYS C 91 " pdb=" N LEU C 92 " pdb=" CA LEU C 92 " ideal model delta harmonic sigma weight residual 180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA PRO B 409 " pdb=" C PRO B 409 " pdb=" N ARG B 410 " pdb=" CA ARG B 410 " ideal model delta harmonic sigma weight residual -180.00 -155.77 -24.23 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 9484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1012 0.044 - 0.089: 382 0.089 - 0.133: 97 0.133 - 0.178: 22 0.178 - 0.222: 2 Chirality restraints: 1515 Sorted by residual: chirality pdb=" C1 NAG B 703 " pdb=" ND2 ASN B 449 " pdb=" C2 NAG B 703 " pdb=" O5 NAG B 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE C 331 " pdb=" N ILE C 331 " pdb=" C ILE C 331 " pdb=" CB ILE C 331 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA ILE B 97 " pdb=" N ILE B 97 " pdb=" C ILE B 97 " pdb=" CB ILE B 97 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.66e-01 ... (remaining 1512 not shown) Planarity restraints: 2882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 353 " 0.200 9.50e-02 1.11e+02 6.69e-02 4.81e+00 pdb=" NE ARG B 353 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 353 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 353 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 353 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 353 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 353 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 353 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG B 353 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 261 " 0.019 2.00e-02 2.50e+03 9.47e-03 2.69e+00 pdb=" CG PHE C 261 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE C 261 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE C 261 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 261 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 261 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 261 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE C 261 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE C 261 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE C 261 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE C 261 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE C 261 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 379 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 380 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 380 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 380 " -0.021 5.00e-02 4.00e+02 ... (remaining 2879 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 1960 2.26 - 2.84: 41669 2.84 - 3.43: 47581 3.43 - 4.01: 68049 4.01 - 4.60: 103750 Nonbonded interactions: 263009 Sorted by model distance: nonbonded pdb=" OE1 GLN C 227 " pdb=" HG SER C 323 " model vdw 1.673 2.450 nonbonded pdb=" H ILE B 301 " pdb=" O GLY B 491 " model vdw 1.674 2.450 nonbonded pdb=" HG SER C 366 " pdb=" O CYS C 372 " model vdw 1.687 2.450 nonbonded pdb=" O ILE C 393 " pdb=" HG SER C 397 " model vdw 1.695 2.450 nonbonded pdb=" HH TYR C 107 " pdb=" OE1 GLU C 118 " model vdw 1.698 2.450 ... (remaining 263004 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 79 through 159 or (resid 160 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 161 through 167 or resid 180 through 186 or (resid 187 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1)) or resid 188 through 206 or (resid 207 and (name N or \ name CA or name C or name O or name CB or name CG or name OD1 or name ND2 or na \ me H or name HA or name HB2 or name HB3 or name HD21)) or resid 208 through 360 \ or (resid 361 and (name N or name CA or name C or name O or name CB or name SG o \ r name H or name HA or name HB2 or name HB3)) or resid 362 through 424 or (resid \ 425 and (name N or name CA or name C or name O or name CB or name CG or name ND \ 1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name H \ B3 or name HD2 or name HE1 or name HE2)) or resid 426 through 447 or (resid 448 \ and (name N or name CA or name C or name O or name CB or name SG or name H or na \ me HA or name HB2 or name HB3)) or resid 449 through 511 or resid 701 through 70 \ 3)) selection = (chain 'B' and (resid 79 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 250 through 255 or (resid 256 and (name N or name CA or name C or na \ me O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or res \ id 257 through 259 or (resid 260 and (name N or name CA or name C or name O or n \ ame CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or na \ me HB3 or name HD21)) or resid 261 through 320 or (resid 321 and (name N or name \ CA or name C or name O or name CB or name CG or name ND1 or name CD2 or name CE \ 1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name H \ D2 or name HE1)) or resid 322 through 480 or resid 487 through 511 or resid 701 \ through 703)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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=1.00 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: 94.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.340 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 44.450 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 : 0.005 0.052 10113 Z= 0.232 Angle : 0.787 9.477 13746 Z= 0.437 Chirality : 0.050 0.222 1515 Planarity : 0.006 0.087 1743 Dihedral : 12.603 89.953 3874 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 0.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.28 % Allowed : 0.65 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.22), residues: 1179 helix: -1.88 (0.25), residues: 315 sheet: 0.01 (0.26), residues: 327 loop : -0.61 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 229 HIS 0.009 0.002 HIS C 358 PHE 0.027 0.002 PHE C 261 TYR 0.019 0.002 TYR B 335 ARG 0.004 0.001 ARG B 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00707 ( 7) link_NAG-ASN : angle 3.21156 ( 21) link_BETA1-4 : bond 0.00980 ( 3) link_BETA1-4 : angle 4.58102 ( 9) hydrogen bonds : bond 0.18072 ( 320) hydrogen bonds : angle 7.63133 ( 879) SS BOND : bond 0.00431 ( 24) SS BOND : angle 1.31686 ( 48) covalent geometry : bond 0.00487 (10079) covalent geometry : angle 0.76629 (13668) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 MET cc_start: 0.8753 (ttt) cc_final: 0.8397 (ttt) outliers start: 3 outliers final: 2 residues processed: 119 average time/residue: 0.6440 time to fit residues: 104.4260 Evaluate side-chains 77 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 256 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A 431 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.080173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.064121 restraints weight = 59915.775| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.38 r_work: 0.2728 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10113 Z= 0.144 Angle : 0.593 9.765 13746 Z= 0.323 Chirality : 0.044 0.202 1515 Planarity : 0.005 0.040 1743 Dihedral : 6.645 51.287 1555 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.56 % Allowed : 3.33 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.23), residues: 1179 helix: -0.78 (0.27), residues: 321 sheet: -0.18 (0.25), residues: 343 loop : -0.12 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 229 HIS 0.004 0.001 HIS A 473 PHE 0.013 0.001 PHE B 293 TYR 0.013 0.001 TYR C 107 ARG 0.006 0.000 ARG C 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 7) link_NAG-ASN : angle 1.95159 ( 21) link_BETA1-4 : bond 0.00158 ( 3) link_BETA1-4 : angle 1.67295 ( 9) hydrogen bonds : bond 0.05830 ( 320) hydrogen bonds : angle 5.75510 ( 879) SS BOND : bond 0.00413 ( 24) SS BOND : angle 1.14786 ( 48) covalent geometry : bond 0.00321 (10079) covalent geometry : angle 0.58383 (13668) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 85 average time/residue: 0.5800 time to fit residues: 73.2403 Evaluate side-chains 77 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 365 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 83 optimal weight: 0.0570 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 GLN B 425 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.079734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.064162 restraints weight = 60073.452| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.28 r_work: 0.2746 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10113 Z= 0.129 Angle : 0.540 11.028 13746 Z= 0.286 Chirality : 0.042 0.173 1515 Planarity : 0.004 0.036 1743 Dihedral : 5.736 45.622 1555 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.65 % Allowed : 3.89 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.24), residues: 1179 helix: 0.08 (0.29), residues: 317 sheet: -0.14 (0.26), residues: 340 loop : -0.02 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 470 HIS 0.005 0.001 HIS B 425 PHE 0.011 0.001 PHE B 261 TYR 0.014 0.001 TYR B 427 ARG 0.003 0.000 ARG C 333 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 7) link_NAG-ASN : angle 1.45936 ( 21) link_BETA1-4 : bond 0.00269 ( 3) link_BETA1-4 : angle 1.49360 ( 9) hydrogen bonds : bond 0.04636 ( 320) hydrogen bonds : angle 5.16200 ( 879) SS BOND : bond 0.00347 ( 24) SS BOND : angle 2.11998 ( 48) covalent geometry : bond 0.00283 (10079) covalent geometry : angle 0.52230 (13668) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8287 (tm-30) REVERT: C 413 SER cc_start: 0.9366 (m) cc_final: 0.8959 (p) outliers start: 7 outliers final: 4 residues processed: 80 average time/residue: 0.5132 time to fit residues: 60.4090 Evaluate side-chains 77 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.0000 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN B 352 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.062779 restraints weight = 60859.620| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.30 r_work: 0.2702 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10113 Z= 0.189 Angle : 0.518 7.816 13746 Z= 0.276 Chirality : 0.042 0.171 1515 Planarity : 0.004 0.038 1743 Dihedral : 5.491 41.555 1555 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.74 % Allowed : 4.63 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.24), residues: 1179 helix: 0.35 (0.29), residues: 318 sheet: -0.15 (0.27), residues: 340 loop : 0.05 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 470 HIS 0.003 0.001 HIS A 473 PHE 0.011 0.001 PHE B 261 TYR 0.010 0.001 TYR C 433 ARG 0.002 0.000 ARG B 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 7) link_NAG-ASN : angle 1.54318 ( 21) link_BETA1-4 : bond 0.00252 ( 3) link_BETA1-4 : angle 1.70493 ( 9) hydrogen bonds : bond 0.04342 ( 320) hydrogen bonds : angle 4.98905 ( 879) SS BOND : bond 0.00307 ( 24) SS BOND : angle 1.37280 ( 48) covalent geometry : bond 0.00429 (10079) covalent geometry : angle 0.50746 (13668) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9239 (tp30) cc_final: 0.8838 (tp30) REVERT: B 292 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8408 (tm-30) REVERT: C 413 SER cc_start: 0.9373 (m) cc_final: 0.8974 (p) outliers start: 8 outliers final: 6 residues processed: 84 average time/residue: 0.5983 time to fit residues: 75.0135 Evaluate side-chains 80 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 471 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 109 optimal weight: 0.0030 chunk 18 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.078263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.062742 restraints weight = 61142.351| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.34 r_work: 0.2706 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10113 Z= 0.167 Angle : 0.512 7.878 13746 Z= 0.271 Chirality : 0.042 0.166 1515 Planarity : 0.003 0.039 1743 Dihedral : 5.273 40.881 1555 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.65 % Allowed : 5.18 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.24), residues: 1179 helix: 0.62 (0.29), residues: 319 sheet: -0.17 (0.27), residues: 342 loop : 0.13 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 470 HIS 0.004 0.001 HIS B 425 PHE 0.010 0.001 PHE B 261 TYR 0.009 0.001 TYR C 433 ARG 0.008 0.000 ARG A 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 7) link_NAG-ASN : angle 1.36820 ( 21) link_BETA1-4 : bond 0.00172 ( 3) link_BETA1-4 : angle 1.45768 ( 9) hydrogen bonds : bond 0.04087 ( 320) hydrogen bonds : angle 4.84753 ( 879) SS BOND : bond 0.00296 ( 24) SS BOND : angle 1.17864 ( 48) covalent geometry : bond 0.00382 (10079) covalent geometry : angle 0.50435 (13668) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9260 (tp30) cc_final: 0.8853 (tp30) REVERT: B 292 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8419 (tm-30) REVERT: C 413 SER cc_start: 0.9371 (m) cc_final: 0.8974 (p) outliers start: 7 outliers final: 6 residues processed: 79 average time/residue: 0.4260 time to fit residues: 50.2256 Evaluate side-chains 78 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 399 CYS Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 471 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 18 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 66 optimal weight: 0.0770 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.077515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.062082 restraints weight = 61793.401| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.35 r_work: 0.2690 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10113 Z= 0.199 Angle : 0.508 6.566 13746 Z= 0.269 Chirality : 0.042 0.163 1515 Planarity : 0.003 0.035 1743 Dihedral : 5.224 41.319 1555 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.56 % Allowed : 5.55 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1179 helix: 0.68 (0.29), residues: 325 sheet: -0.18 (0.27), residues: 336 loop : 0.15 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.004 0.001 HIS A 473 PHE 0.011 0.001 PHE B 261 TYR 0.009 0.001 TYR C 433 ARG 0.002 0.000 ARG A 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 7) link_NAG-ASN : angle 1.42370 ( 21) link_BETA1-4 : bond 0.00260 ( 3) link_BETA1-4 : angle 1.63674 ( 9) hydrogen bonds : bond 0.04074 ( 320) hydrogen bonds : angle 4.81219 ( 879) SS BOND : bond 0.00431 ( 24) SS BOND : angle 1.14870 ( 48) covalent geometry : bond 0.00456 (10079) covalent geometry : angle 0.50008 (13668) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9270 (tp30) cc_final: 0.8846 (tp30) REVERT: B 292 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8400 (tm-30) REVERT: C 413 SER cc_start: 0.9362 (m) cc_final: 0.8974 (p) outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 0.4309 time to fit residues: 47.3547 Evaluate side-chains 74 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 68 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.078591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.063234 restraints weight = 60537.758| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.33 r_work: 0.2715 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10113 Z= 0.112 Angle : 0.470 6.693 13746 Z= 0.248 Chirality : 0.041 0.161 1515 Planarity : 0.003 0.036 1743 Dihedral : 4.938 40.896 1554 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.56 % Allowed : 5.74 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1179 helix: 1.01 (0.30), residues: 319 sheet: -0.16 (0.28), residues: 337 loop : 0.15 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.003 0.001 HIS C 439 PHE 0.009 0.001 PHE B 261 TYR 0.008 0.001 TYR C 433 ARG 0.004 0.000 ARG A 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 7) link_NAG-ASN : angle 1.17674 ( 21) link_BETA1-4 : bond 0.00207 ( 3) link_BETA1-4 : angle 1.29636 ( 9) hydrogen bonds : bond 0.03671 ( 320) hydrogen bonds : angle 4.64732 ( 879) SS BOND : bond 0.00427 ( 24) SS BOND : angle 1.02956 ( 48) covalent geometry : bond 0.00258 (10079) covalent geometry : angle 0.46352 (13668) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9270 (tp30) cc_final: 0.8849 (tp30) REVERT: B 292 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8402 (tm-30) REVERT: C 413 SER cc_start: 0.9358 (m) cc_final: 0.8972 (p) outliers start: 6 outliers final: 5 residues processed: 77 average time/residue: 0.4356 time to fit residues: 50.1425 Evaluate side-chains 76 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 471 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 104 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.076715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.061630 restraints weight = 60014.015| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.31 r_work: 0.2706 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10113 Z= 0.168 Angle : 0.490 6.932 13746 Z= 0.259 Chirality : 0.041 0.167 1515 Planarity : 0.003 0.035 1743 Dihedral : 4.914 41.033 1554 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.74 % Allowed : 5.74 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1179 helix: 0.94 (0.30), residues: 326 sheet: -0.20 (0.28), residues: 337 loop : 0.21 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.004 0.001 HIS C 439 PHE 0.010 0.001 PHE B 261 TYR 0.008 0.001 TYR C 433 ARG 0.004 0.000 ARG A 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 7) link_NAG-ASN : angle 1.28120 ( 21) link_BETA1-4 : bond 0.00196 ( 3) link_BETA1-4 : angle 1.53037 ( 9) hydrogen bonds : bond 0.03788 ( 320) hydrogen bonds : angle 4.66393 ( 879) SS BOND : bond 0.00331 ( 24) SS BOND : angle 1.05630 ( 48) covalent geometry : bond 0.00387 (10079) covalent geometry : angle 0.48345 (13668) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9274 (tp30) cc_final: 0.8849 (tp30) REVERT: B 292 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8401 (tm-30) REVERT: C 413 SER cc_start: 0.9355 (m) cc_final: 0.8973 (p) outliers start: 8 outliers final: 6 residues processed: 75 average time/residue: 0.4381 time to fit residues: 49.2213 Evaluate side-chains 76 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 399 CYS Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 471 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 431 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.077369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.061985 restraints weight = 61245.595| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.37 r_work: 0.2690 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10113 Z= 0.189 Angle : 0.498 6.917 13746 Z= 0.263 Chirality : 0.042 0.162 1515 Planarity : 0.003 0.036 1743 Dihedral : 4.971 41.139 1554 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.74 % Allowed : 5.74 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1179 helix: 1.01 (0.30), residues: 320 sheet: -0.24 (0.28), residues: 339 loop : 0.21 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.004 0.001 HIS A 473 PHE 0.010 0.001 PHE B 261 TYR 0.009 0.001 TYR C 433 ARG 0.004 0.000 ARG A 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 7) link_NAG-ASN : angle 1.29056 ( 21) link_BETA1-4 : bond 0.00123 ( 3) link_BETA1-4 : angle 1.57173 ( 9) hydrogen bonds : bond 0.03897 ( 320) hydrogen bonds : angle 4.66028 ( 879) SS BOND : bond 0.00403 ( 24) SS BOND : angle 1.09427 ( 48) covalent geometry : bond 0.00434 (10079) covalent geometry : angle 0.49108 (13668) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9277 (tp30) cc_final: 0.8847 (tp30) REVERT: A 395 MET cc_start: 0.8574 (tpt) cc_final: 0.8295 (tpp) REVERT: B 292 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8386 (tm-30) REVERT: C 413 SER cc_start: 0.9352 (m) cc_final: 0.8978 (p) outliers start: 8 outliers final: 7 residues processed: 73 average time/residue: 0.4305 time to fit residues: 46.8090 Evaluate side-chains 75 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 399 CYS Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 37 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 0.0070 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.077987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.063088 restraints weight = 59991.898| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.29 r_work: 0.2716 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10113 Z= 0.107 Angle : 0.465 6.430 13746 Z= 0.244 Chirality : 0.041 0.160 1515 Planarity : 0.003 0.036 1743 Dihedral : 4.776 40.848 1554 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.56 % Allowed : 5.74 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1179 helix: 1.16 (0.30), residues: 320 sheet: -0.17 (0.28), residues: 344 loop : 0.17 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.003 0.001 HIS C 439 PHE 0.009 0.001 PHE B 261 TYR 0.007 0.001 TYR C 284 ARG 0.003 0.000 ARG A 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 7) link_NAG-ASN : angle 1.10268 ( 21) link_BETA1-4 : bond 0.00187 ( 3) link_BETA1-4 : angle 1.31407 ( 9) hydrogen bonds : bond 0.03564 ( 320) hydrogen bonds : angle 4.53892 ( 879) SS BOND : bond 0.00296 ( 24) SS BOND : angle 1.02266 ( 48) covalent geometry : bond 0.00246 (10079) covalent geometry : angle 0.45899 (13668) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9276 (tp30) cc_final: 0.8847 (tp30) REVERT: B 292 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8387 (tm-30) REVERT: C 413 SER cc_start: 0.9345 (m) cc_final: 0.8966 (p) outliers start: 6 outliers final: 6 residues processed: 73 average time/residue: 0.4318 time to fit residues: 47.0325 Evaluate side-chains 76 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 399 CYS Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 471 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 0.0170 chunk 16 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.079554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.064068 restraints weight = 60772.013| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.42 r_work: 0.2735 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10113 Z= 0.088 Angle : 0.446 5.765 13746 Z= 0.233 Chirality : 0.040 0.160 1515 Planarity : 0.003 0.038 1743 Dihedral : 4.509 40.929 1554 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.56 % Allowed : 5.74 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1179 helix: 1.31 (0.30), residues: 320 sheet: -0.10 (0.28), residues: 344 loop : 0.23 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.003 0.001 HIS C 439 PHE 0.008 0.001 PHE B 261 TYR 0.009 0.001 TYR C 433 ARG 0.003 0.000 ARG A 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 7) link_NAG-ASN : angle 0.98915 ( 21) link_BETA1-4 : bond 0.00222 ( 3) link_BETA1-4 : angle 1.21157 ( 9) hydrogen bonds : bond 0.03277 ( 320) hydrogen bonds : angle 4.41599 ( 879) SS BOND : bond 0.00230 ( 24) SS BOND : angle 0.90397 ( 48) covalent geometry : bond 0.00203 (10079) covalent geometry : angle 0.44151 (13668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8335.50 seconds wall clock time: 146 minutes 58.71 seconds (8818.71 seconds total)