Starting phenix.real_space_refine on Thu Sep 18 18:49:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9btg_44889/09_2025/9btg_44889_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9btg_44889/09_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_44889/09_2025/9btg_44889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9btg_44889/09_2025/9btg_44889.map" model { file = "/net/cci-nas-00/data/ceres_data/9btg_44889/09_2025/9btg_44889_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9btg_44889/09_2025/9btg_44889_trim.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.29, per 1000 atoms: 0.17 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: 1.55 Conformation dependent library (CDL) restraints added in 565.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.43 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: 4.26 Time building geometry restraints manager: 2.22 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 703)) 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: 5.740 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: 0.100 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.560 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG B 206 TYR 0.019 0.002 TYR B 335 PHE 0.027 0.002 PHE C 261 TRP 0.015 0.002 TRP C 229 HIS 0.009 0.002 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00487 (10079) covalent geometry : angle 0.76629 (13668) SS BOND : bond 0.00431 ( 24) SS BOND : angle 1.31686 ( 48) hydrogen bonds : bond 0.18072 ( 320) hydrogen bonds : angle 7.63133 ( 879) link_BETA1-4 : bond 0.00980 ( 3) link_BETA1-4 : angle 4.58102 ( 9) link_NAG-ASN : bond 0.00707 ( 7) link_NAG-ASN : angle 3.21156 ( 21) *********************** 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 : 0.454 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: 0.8399 (ttt) outliers start: 3 outliers final: 2 residues processed: 119 average time/residue: 0.2728 time to fit residues: 43.3755 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 : 0.514 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.080303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.064134 restraints weight = 60013.956| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 3.40 r_work: 0.2694 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10113 Z= 0.150 Angle : 0.586 9.412 13746 Z= 0.317 Chirality : 0.043 0.196 1515 Planarity : 0.005 0.040 1743 Dihedral : 6.608 51.273 1555 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.56 % Allowed : 3.24 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.23), residues: 1179 helix: -0.74 (0.27), residues: 321 sheet: -0.23 (0.25), residues: 344 loop : -0.11 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 270 TYR 0.014 0.001 TYR C 107 PHE 0.017 0.001 PHE B 293 TRP 0.009 0.001 TRP C 229 HIS 0.004 0.001 HIS A 473 Details of bonding type rmsd covalent geometry : bond 0.00331 (10079) covalent geometry : angle 0.57780 (13668) SS BOND : bond 0.00503 ( 24) SS BOND : angle 1.17874 ( 48) hydrogen bonds : bond 0.05648 ( 320) hydrogen bonds : angle 5.72100 ( 879) link_BETA1-4 : bond 0.00210 ( 3) link_BETA1-4 : angle 1.55839 ( 9) link_NAG-ASN : bond 0.00163 ( 7) link_NAG-ASN : angle 1.89325 ( 21) *********************** 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 : 0.401 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: 0.2152 time to fit residues: 26.1878 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 : 0.533 ------------------------------------------------------------------------------- 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 113 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.078822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.063504 restraints weight = 60640.702| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.27 r_work: 0.2720 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10113 Z= 0.165 Angle : 0.558 12.513 13746 Z= 0.297 Chirality : 0.042 0.173 1515 Planarity : 0.004 0.035 1743 Dihedral : 5.866 45.275 1555 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.74 % Allowed : 3.52 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.24), residues: 1179 helix: -0.07 (0.28), residues: 323 sheet: -0.16 (0.26), residues: 340 loop : 0.02 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 333 TYR 0.014 0.001 TYR B 427 PHE 0.012 0.001 PHE B 261 TRP 0.011 0.001 TRP A 470 HIS 0.006 0.001 HIS B 425 Details of bonding type rmsd covalent geometry : bond 0.00369 (10079) covalent geometry : angle 0.53725 (13668) SS BOND : bond 0.00447 ( 24) SS BOND : angle 2.29054 ( 48) hydrogen bonds : bond 0.04867 ( 320) hydrogen bonds : angle 5.23816 ( 879) link_BETA1-4 : bond 0.00211 ( 3) link_BETA1-4 : angle 1.65555 ( 9) link_NAG-ASN : bond 0.00126 ( 7) link_NAG-ASN : angle 1.59811 ( 21) *********************** 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 82 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 413 SER cc_start: 0.9369 (m) cc_final: 0.8965 (p) outliers start: 8 outliers final: 6 residues processed: 77 average time/residue: 0.1807 time to fit residues: 20.7770 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 : 0.532 ------------------------------------------------------------------------------- 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 C residue 232 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 102 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3143 r_free = 0.3143 target = 0.077720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.062529 restraints weight = 61156.409| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.29 r_work: 0.2700 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10113 Z= 0.185 Angle : 0.521 7.433 13746 Z= 0.278 Chirality : 0.042 0.171 1515 Planarity : 0.004 0.037 1743 Dihedral : 5.570 41.449 1555 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.65 % Allowed : 4.81 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.24), residues: 1179 helix: 0.29 (0.29), residues: 318 sheet: -0.17 (0.26), residues: 340 loop : 0.01 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 200 TYR 0.010 0.001 TYR C 217 PHE 0.011 0.001 PHE B 261 TRP 0.010 0.001 TRP A 470 HIS 0.003 0.001 HIS A 473 Details of bonding type rmsd covalent geometry : bond 0.00424 (10079) covalent geometry : angle 0.50976 (13668) SS BOND : bond 0.00306 ( 24) SS BOND : angle 1.45926 ( 48) hydrogen bonds : bond 0.04342 ( 320) hydrogen bonds : angle 5.01208 ( 879) link_BETA1-4 : bond 0.00212 ( 3) link_BETA1-4 : angle 1.61465 ( 9) link_NAG-ASN : bond 0.00196 ( 7) link_NAG-ASN : angle 1.51415 ( 21) *********************** 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 84 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9243 (tp30) cc_final: 0.8848 (tp30) REVERT: A 432 MET cc_start: 0.8959 (mmm) cc_final: 0.8693 (mpp) REVERT: B 292 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8390 (tm-30) REVERT: C 413 SER cc_start: 0.9372 (m) cc_final: 0.8973 (p) outliers start: 7 outliers final: 6 residues processed: 80 average time/residue: 0.2143 time to fit residues: 25.0093 Evaluate side-chains 81 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 35 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.0370 chunk 67 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.079021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.063435 restraints weight = 60586.189| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.37 r_work: 0.2721 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10113 Z= 0.107 Angle : 0.488 7.329 13746 Z= 0.258 Chirality : 0.041 0.165 1515 Planarity : 0.003 0.036 1743 Dihedral : 5.221 40.385 1555 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.46 % Allowed : 5.27 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.24), residues: 1179 helix: 0.59 (0.29), residues: 318 sheet: -0.11 (0.27), residues: 341 loop : 0.12 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 125 TYR 0.008 0.001 TYR C 433 PHE 0.009 0.001 PHE B 261 TRP 0.009 0.001 TRP A 470 HIS 0.004 0.001 HIS B 425 Details of bonding type rmsd covalent geometry : bond 0.00241 (10079) covalent geometry : angle 0.48103 (13668) SS BOND : bond 0.00451 ( 24) SS BOND : angle 1.10006 ( 48) hydrogen bonds : bond 0.03926 ( 320) hydrogen bonds : angle 4.81196 ( 879) link_BETA1-4 : bond 0.00209 ( 3) link_BETA1-4 : angle 1.35415 ( 9) link_NAG-ASN : bond 0.00102 ( 7) link_NAG-ASN : angle 1.28948 ( 21) *********************** 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 84 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9247 (tp30) cc_final: 0.8847 (tp30) REVERT: A 432 MET cc_start: 0.8937 (mmm) cc_final: 0.8671 (mpp) REVERT: B 292 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8398 (tm-30) REVERT: C 413 SER cc_start: 0.9367 (m) cc_final: 0.8969 (p) outliers start: 5 outliers final: 5 residues processed: 80 average time/residue: 0.1964 time to fit residues: 23.5407 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 : 0.524 ------------------------------------------------------------------------------- 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 431 GLN 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 103 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 100 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 0.0770 chunk 75 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.079181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.063662 restraints weight = 60302.640| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.34 r_work: 0.2729 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10113 Z= 0.107 Angle : 0.494 11.253 13746 Z= 0.262 Chirality : 0.042 0.333 1515 Planarity : 0.003 0.036 1743 Dihedral : 5.029 40.299 1554 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.83 % Allowed : 5.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.24), residues: 1179 helix: 0.82 (0.30), residues: 318 sheet: -0.08 (0.27), residues: 341 loop : 0.15 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.008 0.001 TYR C 433 PHE 0.009 0.001 PHE B 261 TRP 0.009 0.001 TRP A 470 HIS 0.003 0.001 HIS C 439 Details of bonding type rmsd covalent geometry : bond 0.00244 (10079) covalent geometry : angle 0.48350 (13668) SS BOND : bond 0.00659 ( 24) SS BOND : angle 1.52892 ( 48) hydrogen bonds : bond 0.03743 ( 320) hydrogen bonds : angle 4.71814 ( 879) link_BETA1-4 : bond 0.00197 ( 3) link_BETA1-4 : angle 1.35274 ( 9) link_NAG-ASN : bond 0.00081 ( 7) link_NAG-ASN : angle 1.25459 ( 21) *********************** 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 85 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9256 (tp30) cc_final: 0.8849 (tp30) REVERT: A 432 MET cc_start: 0.8921 (mmm) cc_final: 0.8655 (mpp) REVERT: B 292 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8401 (tm-30) REVERT: C 413 SER cc_start: 0.9366 (m) cc_final: 0.8964 (p) outliers start: 9 outliers final: 8 residues processed: 81 average time/residue: 0.2110 time to fit residues: 25.4057 Evaluate side-chains 82 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 431 GLN Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 471 ILE 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 70 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.076141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.061042 restraints weight = 60574.714| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.32 r_work: 0.2696 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10113 Z= 0.225 Angle : 0.541 11.723 13746 Z= 0.287 Chirality : 0.042 0.310 1515 Planarity : 0.003 0.041 1743 Dihedral : 5.135 40.905 1554 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.93 % Allowed : 5.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.25), residues: 1179 helix: 0.78 (0.30), residues: 325 sheet: -0.19 (0.27), residues: 345 loop : 0.15 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 125 TYR 0.010 0.001 TYR C 433 PHE 0.011 0.001 PHE B 328 TRP 0.010 0.001 TRP A 470 HIS 0.005 0.001 HIS A 473 Details of bonding type rmsd covalent geometry : bond 0.00512 (10079) covalent geometry : angle 0.53024 (13668) SS BOND : bond 0.00655 ( 24) SS BOND : angle 1.50870 ( 48) hydrogen bonds : bond 0.04089 ( 320) hydrogen bonds : angle 4.78148 ( 879) link_BETA1-4 : bond 0.00262 ( 3) link_BETA1-4 : angle 1.75959 ( 9) link_NAG-ASN : bond 0.00308 ( 7) link_NAG-ASN : angle 1.46652 ( 21) *********************** 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: 10 poor density : 74 time to evaluate : 0.505 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: 0.8854 (tp30) REVERT: A 432 MET cc_start: 0.8931 (mmm) cc_final: 0.8654 (mpp) REVERT: A 443 MET cc_start: 0.8864 (tpt) cc_final: 0.8103 (ttp) REVERT: B 292 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8394 (tm-30) REVERT: C 413 SER cc_start: 0.9360 (m) cc_final: 0.8971 (p) outliers start: 10 outliers final: 9 residues processed: 80 average time/residue: 0.2071 time to fit residues: 24.5101 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 : 0.543 ------------------------------------------------------------------------------- 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 B residue 465 GLU 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 80 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.078055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.062703 restraints weight = 61049.549| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.34 r_work: 0.2704 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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 : 0.004 0.049 10113 Z= 0.157 Angle : 0.504 11.241 13746 Z= 0.267 Chirality : 0.042 0.288 1515 Planarity : 0.003 0.037 1743 Dihedral : 5.026 40.964 1554 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.93 % Allowed : 5.83 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.25), residues: 1179 helix: 0.88 (0.30), residues: 325 sheet: -0.19 (0.27), residues: 344 loop : 0.17 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 125 TYR 0.008 0.001 TYR C 433 PHE 0.010 0.001 PHE B 261 TRP 0.009 0.001 TRP A 470 HIS 0.003 0.001 HIS C 439 Details of bonding type rmsd covalent geometry : bond 0.00361 (10079) covalent geometry : angle 0.49463 (13668) SS BOND : bond 0.00585 ( 24) SS BOND : angle 1.45175 ( 48) hydrogen bonds : bond 0.03823 ( 320) hydrogen bonds : angle 4.65560 ( 879) link_BETA1-4 : bond 0.00176 ( 3) link_BETA1-4 : angle 1.40745 ( 9) link_NAG-ASN : bond 0.00108 ( 7) link_NAG-ASN : angle 1.25688 ( 21) *********************** 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 84 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9285 (tp30) cc_final: 0.8864 (tp30) REVERT: A 432 MET cc_start: 0.8923 (mmm) cc_final: 0.8636 (mpp) REVERT: B 292 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8397 (tm-30) REVERT: C 413 SER cc_start: 0.9356 (m) cc_final: 0.8968 (p) outliers start: 10 outliers final: 10 residues processed: 78 average time/residue: 0.2053 time to fit residues: 23.8417 Evaluate side-chains 83 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 21 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.077775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.062852 restraints weight = 59959.326| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.27 r_work: 0.2714 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2892 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= 0.141 Angle : 0.503 10.969 13746 Z= 0.265 Chirality : 0.041 0.269 1515 Planarity : 0.003 0.035 1743 Dihedral : 4.935 40.905 1554 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.93 % Allowed : 6.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.25), residues: 1179 helix: 0.99 (0.30), residues: 325 sheet: -0.12 (0.28), residues: 336 loop : 0.17 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 125 TYR 0.008 0.001 TYR C 433 PHE 0.009 0.001 PHE B 261 TRP 0.009 0.001 TRP A 470 HIS 0.003 0.001 HIS C 439 Details of bonding type rmsd covalent geometry : bond 0.00326 (10079) covalent geometry : angle 0.49400 (13668) SS BOND : bond 0.00550 ( 24) SS BOND : angle 1.35674 ( 48) hydrogen bonds : bond 0.03696 ( 320) hydrogen bonds : angle 4.58874 ( 879) link_BETA1-4 : bond 0.00188 ( 3) link_BETA1-4 : angle 1.43979 ( 9) link_NAG-ASN : bond 0.00098 ( 7) link_NAG-ASN : angle 1.20877 ( 21) *********************** 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 85 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9278 (tp30) cc_final: 0.8851 (tp30) REVERT: A 432 MET cc_start: 0.8916 (mmm) cc_final: 0.8610 (mpp) REVERT: B 292 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8391 (tm-30) REVERT: C 413 SER cc_start: 0.9357 (m) cc_final: 0.8970 (p) outliers start: 10 outliers final: 9 residues processed: 80 average time/residue: 0.1754 time to fit residues: 21.2366 Evaluate side-chains 83 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 A residue 399 CYS 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 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 100 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 chunk 115 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.078664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.063389 restraints weight = 60516.089| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.34 r_work: 0.2723 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10113 Z= 0.115 Angle : 0.485 9.515 13746 Z= 0.255 Chirality : 0.041 0.245 1515 Planarity : 0.003 0.038 1743 Dihedral : 4.755 40.747 1554 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.83 % Allowed : 6.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.25), residues: 1179 helix: 1.15 (0.30), residues: 320 sheet: -0.08 (0.28), residues: 336 loop : 0.16 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 125 TYR 0.008 0.001 TYR C 217 PHE 0.009 0.001 PHE B 261 TRP 0.008 0.001 TRP A 470 HIS 0.003 0.001 HIS C 439 Details of bonding type rmsd covalent geometry : bond 0.00267 (10079) covalent geometry : angle 0.47539 (13668) SS BOND : bond 0.00438 ( 24) SS BOND : angle 1.46647 ( 48) hydrogen bonds : bond 0.03530 ( 320) hydrogen bonds : angle 4.50570 ( 879) link_BETA1-4 : bond 0.00188 ( 3) link_BETA1-4 : angle 1.29273 ( 9) link_NAG-ASN : bond 0.00064 ( 7) link_NAG-ASN : angle 1.09569 ( 21) ********************** 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 84 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9263 (tp30) cc_final: 0.8851 (tp30) REVERT: A 432 MET cc_start: 0.8908 (mmm) cc_final: 0.8613 (mpp) REVERT: A 443 MET cc_start: 0.8796 (tpt) cc_final: 0.8095 (ttp) REVERT: B 292 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8391 (tm-30) REVERT: B 510 SER cc_start: 0.8813 (m) cc_final: 0.8333 (p) REVERT: C 413 SER cc_start: 0.9356 (m) cc_final: 0.8969 (p) outliers start: 9 outliers final: 9 residues processed: 80 average time/residue: 0.1809 time to fit residues: 21.8082 Evaluate side-chains 83 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 B residue 471 ILE 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 89 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.078425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.063383 restraints weight = 60764.252| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.31 r_work: 0.2725 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10113 Z= 0.120 Angle : 0.484 9.833 13746 Z= 0.254 Chirality : 0.041 0.245 1515 Planarity : 0.003 0.035 1743 Dihedral : 4.640 41.057 1554 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.08 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.25), residues: 1179 helix: 1.21 (0.30), residues: 320 sheet: -0.09 (0.28), residues: 336 loop : 0.19 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 125 TYR 0.009 0.001 TYR C 433 PHE 0.008 0.001 PHE B 261 TRP 0.008 0.001 TRP A 470 HIS 0.003 0.001 HIS C 439 Details of bonding type rmsd covalent geometry : bond 0.00279 (10079) covalent geometry : angle 0.47340 (13668) SS BOND : bond 0.00455 ( 24) SS BOND : angle 1.51951 ( 48) hydrogen bonds : bond 0.03482 ( 320) hydrogen bonds : angle 4.46744 ( 879) link_BETA1-4 : bond 0.00179 ( 3) link_BETA1-4 : angle 1.35110 ( 9) link_NAG-ASN : bond 0.00076 ( 7) link_NAG-ASN : angle 1.10464 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3668.49 seconds wall clock time: 63 minutes 10.65 seconds (3790.65 seconds total)