Starting phenix.real_space_refine on Wed Jan 22 22:49:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9btg_44889/01_2025/9btg_44889_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9btg_44889/01_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_44889/01_2025/9btg_44889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9btg_44889/01_2025/9btg_44889.map" model { file = "/net/cci-nas-00/data/ceres_data/9btg_44889/01_2025/9btg_44889_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9btg_44889/01_2025/9btg_44889_trim.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 94 5.16 5 C 6251 2.51 5 N 1613 2.21 5 O 1880 1.98 5 H 9273 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 10.51, per 1000 atoms: 0.55 Number of scatterers: 19111 At special positions: 0 Unit cell: (104.195, 107.401, 94.577, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 O 1880 8.00 N 1613 7.00 C 6251 6.00 H 9273 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 272 " distance=2.04 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 189 " distance=2.04 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 203 " distance=2.03 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 444 " distance=2.03 Simple disulfide: pdb=" SG CYS A 390 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS A 399 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 401 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 272 " distance=2.03 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 203 " distance=2.04 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 444 " distance=2.03 Simple disulfide: pdb=" SG CYS B 390 " - pdb=" SG CYS B 440 " distance=2.04 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 401 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 267 " distance=2.03 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 457 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 453 " distance=2.03 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 449 " distance=2.03 Simple disulfide: pdb=" SG CYS C 407 " - pdb=" SG CYS C 434 " distance=2.03 Simple disulfide: pdb=" SG CYS C 409 " - pdb=" SG CYS C 423 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 701 " - " ASN A 141 " " NAG A 703 " - " ASN A 449 " " NAG B 701 " - " ASN B 141 " " NAG B 703 " - " ASN B 449 " " NAG D 1 " - " ASN A 260 " " NAG E 1 " - " ASN B 207 " " NAG F 1 " - " ASN C 271 " Time building additional restraints: 5.17 Conformation dependent library (CDL) restraints added in 1.5 seconds 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2300 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 12 sheets defined 34.2% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 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: 6.11 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: 5.720 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: 0.320 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 42.390 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.090 ------------------------------------------------------------------------------- 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 10079 Z= 0.312 Angle : 0.766 7.929 13668 Z= 0.433 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 *********************** 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 : 1.594 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: 0.6276 time to fit residues: 99.8751 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 : 1.587 ------------------------------------------------------------------------------- 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 10079 Z= 0.205 Angle : 0.584 9.765 13668 Z= 0.321 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 *********************** 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 : 1.601 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: 0.5075 time to fit residues: 61.7650 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 : 1.596 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 GLN B 425 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.080074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.064503 restraints weight = 59955.187| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.28 r_work: 0.2721 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10079 Z= 0.170 Angle : 0.524 11.203 13668 Z= 0.280 Chirality : 0.042 0.175 1515 Planarity : 0.004 0.035 1743 Dihedral : 5.753 46.238 1555 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.65 % Allowed : 3.79 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1179 helix: 0.07 (0.29), residues: 317 sheet: -0.13 (0.26), residues: 340 loop : -0.02 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 470 HIS 0.004 0.001 HIS B 425 PHE 0.010 0.001 PHE B 261 TYR 0.012 0.001 TYR B 427 ARG 0.002 0.000 ARG B 125 *********************** 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 86 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8294 (tm-30) REVERT: C 413 SER cc_start: 0.9362 (m) cc_final: 0.8946 (p) outliers start: 7 outliers final: 4 residues processed: 82 average time/residue: 0.4473 time to fit residues: 55.1006 Evaluate side-chains 78 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 0.0570 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 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: 1.4106 ------------------------------------------------------------------------------- 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 = 0.3145 r_free = 0.3145 target = 0.077890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.062648 restraints weight = 60932.477| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 3.29 r_work: 0.2701 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10079 Z= 0.312 Angle : 0.516 6.481 13668 Z= 0.278 Chirality : 0.042 0.173 1515 Planarity : 0.004 0.038 1743 Dihedral : 5.536 41.870 1555 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.65 % Allowed : 4.53 % Favored : 94.82 % 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: -0.03 (0.24), residues: 1179 helix: 0.23 (0.29), residues: 324 sheet: -0.12 (0.27), residues: 340 loop : 0.10 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 470 HIS 0.004 0.001 HIS A 473 PHE 0.011 0.001 PHE B 261 TYR 0.010 0.001 TYR C 433 ARG 0.002 0.000 ARG B 200 *********************** 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 88 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9242 (tp30) cc_final: 0.8842 (tp30) REVERT: A 395 MET cc_start: 0.8596 (ttt) cc_final: 0.8384 (tpt) REVERT: B 292 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8410 (tm-30) REVERT: C 413 SER cc_start: 0.9374 (m) cc_final: 0.8975 (p) outliers start: 7 outliers final: 6 residues processed: 84 average time/residue: 0.4993 time to fit residues: 61.7768 Evaluate side-chains 80 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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: 1.9990 chunk 90 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.077884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.062372 restraints weight = 61259.945| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.33 r_work: 0.2700 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10079 Z= 0.275 Angle : 0.511 7.687 13668 Z= 0.273 Chirality : 0.042 0.167 1515 Planarity : 0.004 0.038 1743 Dihedral : 5.366 40.897 1555 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.65 % Allowed : 5.37 % Favored : 93.99 % 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: 0.09 (0.24), residues: 1179 helix: 0.43 (0.29), residues: 325 sheet: -0.14 (0.27), residues: 341 loop : 0.17 (0.28), residues: 513 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 0.011 0.001 PHE B 261 TYR 0.009 0.001 TYR C 433 ARG 0.009 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9256 (tp30) cc_final: 0.8853 (tp30) REVERT: B 292 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8412 (tm-30) REVERT: C 413 SER cc_start: 0.9372 (m) cc_final: 0.8982 (p) outliers start: 7 outliers final: 6 residues processed: 79 average time/residue: 0.4357 time to fit residues: 51.0968 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 : 1.525 ------------------------------------------------------------------------------- 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: 0.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3122 r_free = 0.3122 target = 0.075474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.060644 restraints weight = 61230.658| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.27 r_work: 0.2685 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10079 Z= 0.331 Angle : 0.517 7.689 13668 Z= 0.277 Chirality : 0.042 0.163 1515 Planarity : 0.003 0.033 1743 Dihedral : 5.330 41.507 1555 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.56 % Allowed : 5.83 % Favored : 93.62 % 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: 0.09 (0.25), residues: 1179 helix: 0.69 (0.30), residues: 319 sheet: -0.27 (0.27), residues: 344 loop : 0.09 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 470 HIS 0.005 0.001 HIS A 473 PHE 0.011 0.001 PHE B 261 TYR 0.010 0.001 TYR C 433 ARG 0.002 0.000 ARG B 200 *********************** 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 80 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9264 (tp30) cc_final: 0.8837 (tp30) REVERT: B 292 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8397 (tm-30) REVERT: C 413 SER cc_start: 0.9353 (m) cc_final: 0.8973 (p) outliers start: 6 outliers final: 5 residues processed: 76 average time/residue: 0.4604 time to fit residues: 51.9597 Evaluate side-chains 73 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain 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: 2.9990 chunk 16 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3155 r_free = 0.3155 target = 0.077715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.062688 restraints weight = 59950.478| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.27 r_work: 0.2712 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10079 Z= 0.185 Angle : 0.474 7.186 13668 Z= 0.252 Chirality : 0.041 0.161 1515 Planarity : 0.003 0.037 1743 Dihedral : 5.065 41.216 1554 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.83 % Allowed : 6.11 % Favored : 93.06 % 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: 0.85 (0.30), residues: 325 sheet: -0.22 (0.27), residues: 337 loop : 0.13 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.003 0.001 HIS C 439 PHE 0.009 0.001 PHE B 261 TYR 0.008 0.001 TYR C 508 ARG 0.004 0.000 ARG A 125 *********************** 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 81 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9266 (tp30) cc_final: 0.8842 (tp30) REVERT: B 292 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8379 (tm-30) REVERT: C 413 SER cc_start: 0.9353 (m) cc_final: 0.8976 (p) outliers start: 9 outliers final: 7 residues processed: 77 average time/residue: 0.3828 time to fit residues: 45.9062 Evaluate side-chains 76 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 399 CYS Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain C residue 330 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 104 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 431 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.077421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.061885 restraints weight = 60926.122| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.35 r_work: 0.2687 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.005 0.040 10079 Z= 0.301 Angle : 0.504 7.890 13668 Z= 0.268 Chirality : 0.042 0.158 1515 Planarity : 0.003 0.034 1743 Dihedral : 5.080 41.451 1554 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: 0.18 (0.25), residues: 1179 helix: 0.85 (0.30), residues: 326 sheet: -0.28 (0.28), residues: 339 loop : 0.12 (0.28), residues: 514 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 *********************** 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 78 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9277 (tp30) cc_final: 0.8847 (tp30) REVERT: B 292 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8399 (tm-30) REVERT: C 413 SER cc_start: 0.9366 (m) cc_final: 0.8994 (p) outliers start: 9 outliers final: 8 residues processed: 74 average time/residue: 0.4204 time to fit residues: 48.2314 Evaluate side-chains 75 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 416 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3141 r_free = 0.3141 target = 0.076878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.061972 restraints weight = 60528.301| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.27 r_work: 0.2696 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10079 Z= 0.269 Angle : 0.489 6.976 13668 Z= 0.260 Chirality : 0.041 0.159 1515 Planarity : 0.003 0.037 1743 Dihedral : 5.040 41.705 1554 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.93 % Allowed : 5.92 % 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: 0.94 (0.30), residues: 320 sheet: -0.24 (0.28), residues: 341 loop : 0.10 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.004 0.001 HIS 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 *********************** 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 77 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.9269 (tp30) cc_final: 0.8839 (tp30) REVERT: B 292 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8384 (tm-30) outliers start: 10 outliers final: 8 residues processed: 73 average time/residue: 0.4102 time to fit residues: 46.7971 Evaluate side-chains 74 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 1.735 ------------------------------------------------------------------------------- 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 416 ASN 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.2983 > 50: distance: 106 - 124: 17.743 distance: 124 - 125: 15.930 distance: 124 - 132: 20.983 distance: 125 - 126: 18.293 distance: 125 - 128: 5.505 distance: 125 - 133: 12.161 distance: 126 - 127: 13.675 distance: 126 - 138: 11.380 distance: 128 - 129: 12.931 distance: 128 - 134: 18.485 distance: 128 - 135: 15.424 distance: 129 - 130: 13.503 distance: 129 - 131: 3.421 distance: 131 - 136: 15.493 distance: 131 - 137: 18.385 distance: 138 - 139: 13.823 distance: 138 - 152: 22.560 distance: 139 - 140: 12.933 distance: 139 - 142: 10.835 distance: 139 - 153: 5.092 distance: 140 - 141: 11.981 distance: 140 - 162: 6.222 distance: 142 - 143: 7.672 distance: 142 - 154: 10.374 distance: 142 - 155: 9.101 distance: 143 - 144: 4.590 distance: 143 - 145: 7.490 distance: 144 - 146: 5.551 distance: 144 - 156: 4.658 distance: 146 - 157: 3.817 distance: 148 - 158: 3.112 distance: 150 - 151: 3.029 distance: 162 - 163: 6.635 distance: 162 - 166: 7.740 distance: 163 - 164: 11.303 distance: 163 - 167: 6.303 distance: 163 - 168: 15.272 distance: 164 - 165: 8.332 distance: 164 - 169: 12.819 distance: 169 - 170: 10.870 distance: 169 - 177: 17.386 distance: 170 - 171: 7.773 distance: 170 - 173: 18.019 distance: 170 - 178: 5.816 distance: 171 - 172: 16.566 distance: 171 - 186: 7.417 distance: 173 - 174: 15.574 distance: 173 - 179: 19.040 distance: 173 - 180: 20.040 distance: 174 - 175: 11.396 distance: 174 - 181: 7.660 distance: 174 - 182: 14.190 distance: 175 - 176: 5.615 distance: 176 - 183: 5.101 distance: 176 - 184: 6.151 distance: 176 - 185: 5.427 distance: 186 - 187: 9.925 distance: 186 - 193: 5.760 distance: 187 - 188: 20.007 distance: 187 - 190: 7.531 distance: 187 - 194: 10.153 distance: 188 - 189: 8.008 distance: 188 - 200: 8.758 distance: 190 - 191: 11.197 distance: 190 - 192: 12.131 distance: 190 - 195: 20.040 distance: 191 - 196: 10.260 distance: 192 - 197: 4.416 distance: 192 - 199: 4.685 distance: 200 - 201: 13.775 distance: 200 - 209: 12.931 distance: 201 - 202: 8.410 distance: 201 - 204: 11.713 distance: 201 - 210: 16.964 distance: 202 - 203: 13.953 distance: 202 - 215: 7.007 distance: 204 - 205: 8.239 distance: 204 - 211: 20.016 distance: 204 - 212: 23.039 distance: 205 - 206: 13.622 distance: 205 - 213: 8.463 distance: 205 - 214: 13.976 distance: 206 - 207: 3.916 distance: 206 - 208: 9.481 distance: 215 - 216: 12.492 distance: 215 - 224: 8.128 distance: 216 - 217: 8.809 distance: 216 - 219: 5.640 distance: 216 - 225: 15.870 distance: 217 - 218: 15.708 distance: 217 - 237: 8.933 distance: 219 - 220: 9.590 distance: 219 - 226: 10.856 distance: 219 - 227: 12.824 distance: 220 - 221: 5.494 distance: 220 - 229: 4.918 distance: 221 - 222: 3.269 distance: 221 - 231: 3.065 distance: 237 - 238: 14.072 distance: 237 - 242: 19.322 distance: 238 - 239: 13.761 distance: 238 - 241: 5.014 distance: 238 - 243: 23.305 distance: 239 - 240: 31.698 distance: 239 - 247: 26.364 distance: 241 - 244: 5.688 distance: 241 - 245: 4.909 distance: 241 - 246: 5.302 distance: 247 - 248: 38.920 distance: 247 - 255: 38.478 distance: 248 - 249: 25.922 distance: 248 - 251: 28.792 distance: 248 - 256: 19.730 distance: 249 - 250: 24.890 distance: 249 - 266: 12.056 distance: 251 - 252: 35.671 distance: 251 - 257: 17.401 distance: 251 - 258: 37.491 distance: 252 - 254: 8.860 distance: 252 - 259: 8.249 distance: 253 - 260: 4.704 distance: 253 - 261: 9.790 distance: 253 - 262: 6.027 distance: 254 - 263: 3.436 distance: 254 - 264: 8.408 distance: 254 - 265: 3.647 distance: 266 - 267: 19.859 distance: 266 - 272: 12.692 distance: 267 - 268: 7.686 distance: 267 - 270: 16.794 distance: 267 - 273: 9.156 distance: 268 - 269: 7.322 distance: 268 - 280: 6.590 distance: 270 - 271: 20.876 distance: 270 - 274: 32.022 distance: 270 - 275: 34.461 distance: 271 - 272: 9.165 distance: 271 - 276: 11.851 distance: 271 - 277: 7.382 distance: 272 - 278: 10.077 distance: 272 - 279: 9.955