Starting phenix.real_space_refine on Tue May 20 00:45:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9btg_44889/05_2025/9btg_44889_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9btg_44889/05_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_44889/05_2025/9btg_44889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9btg_44889/05_2025/9btg_44889.map" model { file = "/net/cci-nas-00/data/ceres_data/9btg_44889/05_2025/9btg_44889_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9btg_44889/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.14, per 1000 atoms: 0.53 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: 4.68 Conformation dependent library (CDL) restraints added in 1.4 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: 1.44 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: 6.98 Time building geometry restraints manager: 5.72 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: 11.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.310 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 41.710 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:3.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.820 ------------------------------------------------------------------------------- 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 : 1.405 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: 0.5808 time to fit residues: 92.6022 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 : 1.597 ------------------------------------------------------------------------------- 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 = 0.064123 restraints weight = 59915.827| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.38 r_work: 0.2728 rms_B_bonded: 3.22 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 : 1.395 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: 0.4643 time to fit residues: 56.6643 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 : 1.442 ------------------------------------------------------------------------------- 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: 0.9980 chunk 81 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 8 optimal weight: 0.0060 chunk 6 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 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 = 0.079787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.064202 restraints weight = 59896.709| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.28 r_work: 0.2744 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10113 Z= 0.128 Angle : 0.548 12.459 13746 Z= 0.291 Chirality : 0.042 0.178 1515 Planarity : 0.004 0.035 1743 Dihedral : 5.832 46.566 1555 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: -0.22 (0.24), residues: 1179 helix: -0.00 (0.29), residues: 317 sheet: -0.15 (0.26), residues: 340 loop : -0.03 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.003 0.001 HIS B 425 PHE 0.010 0.001 PHE B 261 TYR 0.011 0.001 TYR B 427 ARG 0.004 0.000 ARG C 333 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 7) link_NAG-ASN : angle 1.50973 ( 21) link_BETA1-4 : bond 0.00266 ( 3) link_BETA1-4 : angle 1.48883 ( 9) hydrogen bonds : bond 0.04753 ( 320) hydrogen bonds : angle 5.21821 ( 879) SS BOND : bond 0.00372 ( 24) SS BOND : angle 2.35467 ( 48) covalent geometry : bond 0.00279 (10079) covalent geometry : angle 0.52671 (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 : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8272 (tm-30) REVERT: C 413 SER cc_start: 0.9365 (m) cc_final: 0.8956 (p) outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.4094 time to fit residues: 49.1600 Evaluate side-chains 78 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 47 optimal weight: 0.0000 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 352 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.078501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.063283 restraints weight = 60627.379| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.29 r_work: 0.2715 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10113 Z= 0.169 Angle : 0.512 7.372 13746 Z= 0.274 Chirality : 0.042 0.171 1515 Planarity : 0.004 0.037 1743 Dihedral : 5.464 41.953 1555 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.74 % Allowed : 4.26 % Favored : 95.00 % 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: -0.01 (0.24), residues: 1179 helix: 0.33 (0.29), residues: 318 sheet: -0.11 (0.27), residues: 340 loop : 0.06 (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 C 233 PHE 0.011 0.001 PHE B 261 TYR 0.010 0.001 TYR C 433 ARG 0.002 0.000 ARG B 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 7) link_NAG-ASN : angle 1.50253 ( 21) link_BETA1-4 : bond 0.00230 ( 3) link_BETA1-4 : angle 1.63464 ( 9) hydrogen bonds : bond 0.04252 ( 320) hydrogen bonds : angle 4.97745 ( 879) SS BOND : bond 0.00328 ( 24) SS BOND : angle 1.33169 ( 48) covalent geometry : bond 0.00387 (10079) covalent geometry : angle 0.50221 (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 87 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9230 (tp30) cc_final: 0.8846 (tp30) REVERT: B 292 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8380 (tm-30) REVERT: C 413 SER cc_start: 0.9372 (m) cc_final: 0.8974 (p) outliers start: 8 outliers final: 6 residues processed: 82 average time/residue: 0.4277 time to fit residues: 51.1306 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 : 1.405 ------------------------------------------------------------------------------- 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: 2.9990 chunk 109 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.078263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.063103 restraints weight = 60967.026| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.30 r_work: 0.2709 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10113 Z= 0.162 Angle : 0.507 7.394 13746 Z= 0.269 Chirality : 0.041 0.165 1515 Planarity : 0.003 0.037 1743 Dihedral : 5.273 40.513 1555 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.56 % Allowed : 5.64 % Favored : 93.80 % 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: 0.15 (0.24), residues: 1179 helix: 0.60 (0.29), residues: 318 sheet: -0.10 (0.27), residues: 341 loop : 0.11 (0.28), residues: 520 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 0.006 0.000 ARG A 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 7) link_NAG-ASN : angle 1.39886 ( 21) link_BETA1-4 : bond 0.00167 ( 3) link_BETA1-4 : angle 1.49503 ( 9) hydrogen bonds : bond 0.04114 ( 320) hydrogen bonds : angle 4.86550 ( 879) SS BOND : bond 0.00376 ( 24) SS BOND : angle 1.15677 ( 48) covalent geometry : bond 0.00371 (10079) covalent geometry : angle 0.49970 (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 79 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9249 (tp30) cc_final: 0.8841 (tp30) REVERT: A 432 MET cc_start: 0.8962 (mmm) cc_final: 0.8696 (mpp) REVERT: B 292 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8399 (tm-30) REVERT: C 413 SER cc_start: 0.9368 (m) cc_final: 0.8974 (p) outliers start: 6 outliers final: 6 residues processed: 76 average time/residue: 0.4327 time to fit residues: 49.1739 Evaluate side-chains 77 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 1.574 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- 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: 2.9990 chunk 84 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3117 r_free = 0.3117 target = 0.075288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.060457 restraints weight = 61480.558| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.24 r_work: 0.2682 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 10113 Z= 0.276 Angle : 0.570 12.499 13746 Z= 0.303 Chirality : 0.044 0.309 1515 Planarity : 0.004 0.035 1743 Dihedral : 5.441 41.385 1555 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.02 % Allowed : 5.64 % Favored : 93.34 % 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: 0.10 (0.24), residues: 1179 helix: 0.60 (0.29), residues: 319 sheet: -0.16 (0.27), residues: 337 loop : 0.08 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 470 HIS 0.006 0.001 HIS A 473 PHE 0.012 0.001 PHE B 261 TYR 0.010 0.001 TYR C 433 ARG 0.004 0.000 ARG A 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 7) link_NAG-ASN : angle 1.59466 ( 21) link_BETA1-4 : bond 0.00549 ( 3) link_BETA1-4 : angle 1.84712 ( 9) hydrogen bonds : bond 0.04335 ( 320) hydrogen bonds : angle 4.92611 ( 879) SS BOND : bond 0.00981 ( 24) SS BOND : angle 1.83442 ( 48) covalent geometry : bond 0.00635 (10079) covalent geometry : angle 0.55541 (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 81 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9261 (tp30) cc_final: 0.8841 (tp30) REVERT: A 432 MET cc_start: 0.8942 (mmm) cc_final: 0.8678 (mpp) REVERT: A 443 MET cc_start: 0.8820 (tpt) cc_final: 0.8073 (ttp) REVERT: B 292 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8418 (tm-30) REVERT: C 413 SER cc_start: 0.9360 (m) cc_final: 0.8972 (p) outliers start: 11 outliers final: 9 residues processed: 76 average time/residue: 0.4323 time to fit residues: 48.9106 Evaluate side-chains 78 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 1.545 ------------------------------------------------------------------------------- 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 A residue 431 GLN Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 465 GLU 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: 0.5980 chunk 107 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3157 r_free = 0.3157 target = 0.078478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.062843 restraints weight = 60666.619| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.37 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: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10113 Z= 0.125 Angle : 0.505 11.876 13746 Z= 0.267 Chirality : 0.042 0.303 1515 Planarity : 0.003 0.037 1743 Dihedral : 5.180 41.158 1555 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.83 % Allowed : 5.74 % Favored : 93.43 % 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: 0.27 (0.25), residues: 1179 helix: 0.91 (0.30), residues: 318 sheet: -0.11 (0.28), residues: 336 loop : 0.08 (0.28), residues: 525 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 0.007 0.001 TYR C 433 ARG 0.004 0.000 ARG A 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 7) link_NAG-ASN : angle 1.26118 ( 21) link_BETA1-4 : bond 0.00221 ( 3) link_BETA1-4 : angle 1.36017 ( 9) hydrogen bonds : bond 0.03854 ( 320) hydrogen bonds : angle 4.70493 ( 879) SS BOND : bond 0.00630 ( 24) SS BOND : angle 1.47729 ( 48) covalent geometry : bond 0.00286 (10079) covalent geometry : angle 0.49495 (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 84 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9265 (tp30) cc_final: 0.8844 (tp30) REVERT: A 432 MET cc_start: 0.8935 (mmm) cc_final: 0.8671 (mpp) REVERT: B 292 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8399 (tm-30) REVERT: C 413 SER cc_start: 0.9356 (m) cc_final: 0.8969 (p) outliers start: 9 outliers final: 8 residues processed: 79 average time/residue: 0.4075 time to fit residues: 47.9023 Evaluate side-chains 81 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 399 CYS Chi-restraints excluded: chain A residue 431 GLN Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain C residue 232 LEU 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: 2.9990 chunk 114 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.077166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.062174 restraints weight = 60123.502| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.26 r_work: 0.2697 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10113 Z= 0.191 Angle : 0.517 11.252 13746 Z= 0.274 Chirality : 0.042 0.294 1515 Planarity : 0.003 0.035 1743 Dihedral : 5.114 41.424 1554 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.65 % Allowed : 6.20 % Favored : 93.15 % 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: 0.22 (0.25), residues: 1179 helix: 0.87 (0.30), residues: 325 sheet: -0.22 (0.27), residues: 344 loop : 0.13 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.00202 ( 7) link_NAG-ASN : angle 1.34045 ( 21) link_BETA1-4 : bond 0.00321 ( 3) link_BETA1-4 : angle 1.61270 ( 9) hydrogen bonds : bond 0.03942 ( 320) hydrogen bonds : angle 4.70726 ( 879) SS BOND : bond 0.00616 ( 24) SS BOND : angle 1.51029 ( 48) covalent geometry : bond 0.00438 (10079) covalent geometry : angle 0.50608 (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 81 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9267 (tp30) cc_final: 0.8836 (tp30) REVERT: A 432 MET cc_start: 0.8930 (mmm) cc_final: 0.8649 (mpp) REVERT: B 292 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8397 (tm-30) REVERT: C 413 SER cc_start: 0.9349 (m) cc_final: 0.8967 (p) outliers start: 7 outliers final: 7 residues processed: 78 average time/residue: 0.4285 time to fit residues: 49.8764 Evaluate side-chains 79 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 196 CYS Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 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: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3149 r_free = 0.3149 target = 0.077403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.062152 restraints weight = 60494.710| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.33 r_work: 0.2697 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10113 Z= 0.185 Angle : 0.524 11.227 13746 Z= 0.277 Chirality : 0.042 0.285 1515 Planarity : 0.003 0.036 1743 Dihedral : 5.097 41.469 1554 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.83 % Allowed : 6.20 % Favored : 92.97 % 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: 0.23 (0.25), residues: 1179 helix: 0.90 (0.30), residues: 325 sheet: -0.22 (0.27), residues: 344 loop : 0.12 (0.28), residues: 510 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 0.009 0.001 TYR C 433 ARG 0.004 0.000 ARG A 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 7) link_NAG-ASN : angle 1.30050 ( 21) link_BETA1-4 : bond 0.00221 ( 3) link_BETA1-4 : angle 1.54231 ( 9) hydrogen bonds : bond 0.03908 ( 320) hydrogen bonds : angle 4.67287 ( 879) SS BOND : bond 0.00584 ( 24) SS BOND : angle 1.46314 ( 48) covalent geometry : bond 0.00425 (10079) covalent geometry : angle 0.51384 (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 81 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 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: 0.9269 (tp30) cc_final: 0.8840 (tp30) REVERT: A 432 MET cc_start: 0.8926 (mmm) cc_final: 0.8647 (mpp) REVERT: B 292 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8393 (tm-30) REVERT: C 413 SER cc_start: 0.9349 (m) cc_final: 0.8972 (p) outliers start: 9 outliers final: 9 residues processed: 77 average time/residue: 0.4391 time to fit residues: 50.5893 Evaluate side-chains 81 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 1.851 ------------------------------------------------------------------------------- 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 A residue 431 GLN Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 37 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3154 r_free = 0.3154 target = 0.078238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.062685 restraints weight = 60983.457| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.40 r_work: 0.2705 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10113 Z= 0.143 Angle : 0.495 10.817 13746 Z= 0.261 Chirality : 0.041 0.267 1515 Planarity : 0.003 0.035 1743 Dihedral : 4.947 41.317 1554 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.74 % Allowed : 6.11 % Favored : 93.15 % 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: 0.35 (0.25), residues: 1179 helix: 0.98 (0.30), residues: 326 sheet: -0.07 (0.28), residues: 338 loop : 0.14 (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 0.010 0.001 PHE B 261 TYR 0.008 0.001 TYR C 433 ARG 0.003 0.000 ARG A 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 7) link_NAG-ASN : angle 1.16067 ( 21) link_BETA1-4 : bond 0.00175 ( 3) link_BETA1-4 : angle 1.38421 ( 9) hydrogen bonds : bond 0.03685 ( 320) hydrogen bonds : angle 4.58233 ( 879) SS BOND : bond 0.00544 ( 24) SS BOND : angle 1.33284 ( 48) covalent geometry : bond 0.00330 (10079) covalent geometry : angle 0.48650 (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 81 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9261 (tp30) cc_final: 0.8832 (tp30) REVERT: A 432 MET cc_start: 0.8929 (mmm) cc_final: 0.8633 (mpp) REVERT: A 443 MET cc_start: 0.8788 (tpt) cc_final: 0.8032 (ttp) REVERT: B 292 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8391 (tm-30) REVERT: C 413 SER cc_start: 0.9348 (m) cc_final: 0.8974 (p) outliers start: 8 outliers final: 7 residues processed: 78 average time/residue: 0.4235 time to fit residues: 49.6857 Evaluate side-chains 79 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.724 ------------------------------------------------------------------------------- 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 A residue 431 GLN Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain C residue 330 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: 0.7980 chunk 44 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.077897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.062595 restraints weight = 61481.136| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.35 r_work: 0.2706 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10113 Z= 0.150 Angle : 0.518 14.418 13746 Z= 0.271 Chirality : 0.042 0.379 1515 Planarity : 0.003 0.036 1743 Dihedral : 4.949 41.239 1554 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.65 % Allowed : 6.29 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.37 (0.25), residues: 1179 helix: 1.00 (0.30), residues: 326 sheet: -0.06 (0.28), residues: 338 loop : 0.15 (0.28), residues: 515 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 0.009 0.001 PHE B 261 TYR 0.008 0.001 TYR C 217 ARG 0.003 0.000 ARG A 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 7) link_NAG-ASN : angle 1.18284 ( 21) link_BETA1-4 : bond 0.00187 ( 3) link_BETA1-4 : angle 1.45314 ( 9) hydrogen bonds : bond 0.03761 ( 320) hydrogen bonds : angle 4.56108 ( 879) SS BOND : bond 0.00607 ( 24) SS BOND : angle 1.36182 ( 48) covalent geometry : bond 0.00344 (10079) covalent geometry : angle 0.51020 (13668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6943.46 seconds wall clock time: 121 minutes 23.81 seconds (7283.81 seconds total)