Starting phenix.real_space_refine on Thu Jul 2 18:45:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mn5_23916/07_2026/7mn5_23916.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mn5_23916/07_2026/7mn5_23916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mn5_23916/07_2026/7mn5_23916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mn5_23916/07_2026/7mn5_23916.map" model { file = "/net/cci-nas-00/data/ceres_data/7mn5_23916/07_2026/7mn5_23916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mn5_23916/07_2026/7mn5_23916.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mn5_23916/07_2026/7mn5_23916.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mn5_23916/07_2026/7mn5_23916.cif" } resolution = 2.93 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= 0.001 sd= 0.054 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: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 5896 2.51 5 N 1695 2.21 5 O 1817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9526 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4496 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 37, 'TRANS': 547} Chain breaks: 2 Chain: "H" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain breaks: 1 Chain: "B" Number of atoms: 4471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4471 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 38, 'TRANS': 540} Chain breaks: 3 Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 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 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 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 chiralities: 3 Chain: "B" 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 chiralities: 2 Time building chain proxies: 2.13, per 1000 atoms: 0.22 Number of scatterers: 9526 At special positions: 0 Unit cell: (80.995, 141.115, 131.095, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 118 16.00 O 1817 8.00 N 1695 7.00 C 5896 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 56 " distance=2.02 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 218 " distance=2.02 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 226 " distance=2.04 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 231 " - pdb=" SG CYS A 243 " distance=1.71 Simple disulfide: pdb=" SG CYS A 246 " - pdb=" SG CYS A 255 " distance=2.04 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 493 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 509 " distance=2.02 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 517 " distance=2.04 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 529 " distance=2.02 Simple disulfide: pdb=" SG CYS A 533 " - pdb=" SG CYS A 549 " distance=2.02 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 573 " distance=2.02 Simple disulfide: pdb=" SG CYS A 576 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 610 " distance=2.05 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 621 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 629 " distance=2.05 Simple disulfide: pdb=" SG CYS H 182 " - pdb=" SG CYS H 196 " distance=2.11 Simple disulfide: pdb=" SG CYS H 190 " - pdb=" SG CYS H 210 " distance=2.02 Simple disulfide: pdb=" SG CYS H 212 " - pdb=" SG CYS H 221 " distance=2.02 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 53 " distance=2.05 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 204 " distance=2.07 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.04 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.04 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 295 " distance=2.05 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=2.04 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 331 " distance=2.04 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 338 " distance=2.12 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 504 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 540 " distance=2.02 Simple disulfide: pdb=" SG CYS B 544 " - pdb=" SG CYS B 560 " distance=2.02 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 596 " distance=2.06 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 623 " distance=2.04 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 Atom "HETATM 9524 O5 NAG B1502 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1101 " - " ASN A 408 " " NAG A1102 " - " ASN A 353 " " NAG A1103 " - " ASN A 414 " " NAG B1501 " - " ASN B 530 " " NAG B1502 " - " ASN B 187 " " NAG C 1 " - " ASN B 259 " " NAG D 1 " - " ASN A 469 " " NAG E 1 " - " ASN A 250 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 290.0 milliseconds 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2222 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 26 sheets defined 15.7% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.181A pdb=" N TRP A 79 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.920A pdb=" N ILE A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 380 through 390 removed outlier: 4.123A pdb=" N THR A 389 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 463 through 468 removed outlier: 3.591A pdb=" N HIS A 466 " --> pdb=" O CYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'H' and resid 186 through 190 removed outlier: 3.802A pdb=" N CYS H 190 " --> pdb=" O LYS H 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 199 through 203 removed outlier: 4.197A pdb=" N ARG B 203 " --> pdb=" O LYS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.888A pdb=" N CYS B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 360 through 365 Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.575A pdb=" N PHE B 381 " --> pdb=" O PRO B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.995A pdb=" N GLN B 398 " --> pdb=" O PRO B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 481 through 485 Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 7.288A pdb=" N CYS A 29 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 6.965A pdb=" N VAL A 38 " --> pdb=" O CYS H 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 5.372A pdb=" N GLY A 146 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 235 removed outlier: 7.732A pdb=" N GLY A 234 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N CYS A 243 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 249 through 251 Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 282 Processing sheet with id=AA7, first strand: chain 'A' and resid 300 through 302 removed outlier: 7.190A pdb=" N VAL A 296 " --> pdb=" O CYS A 320 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 363 removed outlier: 6.376A pdb=" N LEU A 397 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N MET A 433 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 399 " --> pdb=" O MET A 433 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE A 428 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N TYR A 455 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU A 430 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N SER A 457 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 432 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LYS A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE A 456 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 523 through 525 removed outlier: 3.535A pdb=" N TYR A 523 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 528 " --> pdb=" O ARG A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 542 through 545 Processing sheet with id=AB3, first strand: chain 'A' and resid 579 through 581 Processing sheet with id=AB4, first strand: chain 'A' and resid 593 through 595 Processing sheet with id=AB5, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AB6, first strand: chain 'H' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB8, first strand: chain 'B' and resid 60 through 63 removed outlier: 7.319A pdb=" N LEU B 154 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 115 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLN B 156 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU B 117 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B 153 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 258 through 260 Processing sheet with id=AC1, first strand: chain 'B' and resid 272 through 275 removed outlier: 3.622A pdb=" N GLU B 280 " --> pdb=" O ASN B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 289 through 291 Processing sheet with id=AC3, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AC4, first strand: chain 'B' and resid 342 through 343 removed outlier: 6.889A pdb=" N CYS B 342 " --> pdb=" O PHE B 371 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 374 through 376 removed outlier: 6.621A pdb=" N LEU B 374 " --> pdb=" O TYR B 411 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU B 465 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 443 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR B 496 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE B 468 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 553 through 556 Processing sheet with id=AC7, first strand: chain 'B' and resid 590 through 592 Processing sheet with id=AC8, first strand: chain 'B' and resid 615 through 617 187 hydrogen bonds defined for protein. 333 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: 1.51 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2062 1.33 - 1.45: 2147 1.45 - 1.57: 5398 1.57 - 1.69: 2 1.69 - 1.81: 134 Bond restraints: 9743 Sorted by residual: bond pdb=" CA HIS A 578 " pdb=" C HIS A 578 " ideal model delta sigma weight residual 1.520 1.549 -0.029 4.80e-03 4.34e+04 3.77e+01 bond pdb=" N PRO A 512 " pdb=" CD PRO A 512 " ideal model delta sigma weight residual 1.473 1.399 0.074 1.40e-02 5.10e+03 2.79e+01 bond pdb=" CA PRO A 403 " pdb=" C PRO A 403 " ideal model delta sigma weight residual 1.514 1.542 -0.028 5.50e-03 3.31e+04 2.62e+01 bond pdb=" N PRO B 316 " pdb=" CD PRO B 316 " ideal model delta sigma weight residual 1.473 1.410 0.063 1.40e-02 5.10e+03 2.02e+01 bond pdb=" CA SER A 401 " pdb=" C SER A 401 " ideal model delta sigma weight residual 1.521 1.576 -0.055 1.26e-02 6.30e+03 1.89e+01 ... (remaining 9738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 10558 1.74 - 3.49: 2248 3.49 - 5.23: 359 5.23 - 6.98: 51 6.98 - 8.72: 5 Bond angle restraints: 13221 Sorted by residual: angle pdb=" C GLU B 348 " pdb=" CA GLU B 348 " pdb=" CB GLU B 348 " ideal model delta sigma weight residual 116.54 109.39 7.15 1.15e+00 7.56e-01 3.87e+01 angle pdb=" CA LYS B 336 " pdb=" C LYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 117.68 121.52 -3.84 7.10e-01 1.98e+00 2.93e+01 angle pdb=" N ALA B 87 " pdb=" CA ALA B 87 " pdb=" C ALA B 87 " ideal model delta sigma weight residual 108.99 117.42 -8.43 1.57e+00 4.06e-01 2.88e+01 angle pdb=" C SER B 335 " pdb=" N LYS B 336 " pdb=" CA LYS B 336 " ideal model delta sigma weight residual 122.07 128.95 -6.88 1.44e+00 4.82e-01 2.28e+01 angle pdb=" CA ASP B 421 " pdb=" CB ASP B 421 " pdb=" CG ASP B 421 " ideal model delta sigma weight residual 112.60 117.36 -4.76 1.00e+00 1.00e+00 2.27e+01 ... (remaining 13216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5606 17.81 - 35.63: 203 35.63 - 53.44: 51 53.44 - 71.26: 29 71.26 - 89.07: 6 Dihedral angle restraints: 5895 sinusoidal: 2436 harmonic: 3459 Sorted by residual: dihedral pdb=" CB CYS A 290 " pdb=" SG CYS A 290 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 -177.93 -89.07 1 1.00e+01 1.00e-02 9.44e+01 dihedral pdb=" CB CYS B 268 " pdb=" SG CYS B 268 " pdb=" SG CYS B 295 " pdb=" CB CYS B 295 " ideal model delta sinusoidal sigma weight residual 93.00 166.55 -73.55 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS B 199 " pdb=" SG CYS B 199 " pdb=" SG CYS B 212 " pdb=" CB CYS B 212 " ideal model delta sinusoidal sigma weight residual -86.00 -157.79 71.79 1 1.00e+01 1.00e-02 6.60e+01 ... (remaining 5892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1266 0.101 - 0.203: 174 0.203 - 0.304: 20 0.304 - 0.405: 12 0.405 - 0.507: 1 Chirality restraints: 1473 Sorted by residual: chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.47 -0.07 2.00e-02 2.50e+03 1.26e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.13e+01 chirality pdb=" C1 NAG B1502 " pdb=" ND2 ASN B 187 " pdb=" C2 NAG B1502 " pdb=" O5 NAG B1502 " both_signs ideal model delta sigma weight residual False -2.40 -2.91 0.51 2.00e-01 2.50e+01 6.42e+00 ... (remaining 1470 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 187 " 0.058 2.00e-02 2.50e+03 1.19e-01 1.77e+02 pdb=" CG ASN B 187 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 187 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN B 187 " -0.215 2.00e-02 2.50e+03 pdb=" C1 NAG B1502 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 469 " -0.101 2.00e-02 2.50e+03 1.16e-01 1.70e+02 pdb=" CG ASN A 469 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 469 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 469 " 0.192 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 408 " 0.064 2.00e-02 2.50e+03 8.78e-02 9.64e+01 pdb=" CG ASN A 408 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 408 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 408 " -0.155 2.00e-02 2.50e+03 pdb=" C1 NAG A1101 " 0.100 2.00e-02 2.50e+03 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2314 2.83 - 3.35: 8451 3.35 - 3.86: 15566 3.86 - 4.38: 18729 4.38 - 4.90: 30639 Nonbonded interactions: 75699 Sorted by model distance: nonbonded pdb=" OG1 THR A 334 " pdb=" O PHE A 340 " model vdw 2.311 3.040 nonbonded pdb=" OD1 ASP A 581 " pdb=" NZ LYS A 602 " model vdw 2.389 3.120 nonbonded pdb=" O GLN A 298 " pdb=" OG1 THR A 299 " model vdw 2.434 3.040 nonbonded pdb=" CG ASN B 187 " pdb=" O5 NAG B1502 " model vdw 2.443 2.616 nonbonded pdb=" O4 BMA C 3 " pdb=" O6 BMA C 3 " model vdw 2.456 3.040 ... (remaining 75694 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 'D' selection = chain 'E' } 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: 3.210 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.100 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 : 0.013 0.324 9806 Z= 0.827 Angle : 1.637 45.300 13360 Z= 1.038 Chirality : 0.080 0.507 1473 Planarity : 0.008 0.115 1740 Dihedral : 10.995 81.829 3523 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.05 (0.24), residues: 1195 helix: -2.59 (0.50), residues: 69 sheet: -1.10 (0.39), residues: 153 loop : 0.45 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 487 TYR 0.051 0.003 TYR B 163 PHE 0.041 0.002 PHE A 535 TRP 0.075 0.006 TRP B 415 HIS 0.001 0.000 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.01255 / 0.80 ( 9743) covalent geometry : angle 1.46496 / 1.01 (13221) SS BOND : bond 0.04995 / 4.92 ( 50) SS BOND : angle 3.67442 / 2.52 ( 100) hydrogen bonds : bond 0.22484 / 15.68 ( 187) hydrogen bonds : angle 8.06506 / 5.74 ( 333) link_ALPHA1-3 : bond 0.05225 / 2.75 ( 1) link_ALPHA1-3 : angle 1.86259 / 0.99 ( 3) link_BETA1-4 : bond 0.04047 / 1.92 ( 4) link_BETA1-4 : angle 3.41923 / 1.95 ( 12) link_NAG-ASN : bond 0.07113 / 3.01 ( 8) link_NAG-ASN : angle 15.69677 / 11.09 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 PHE cc_start: 0.4206 (p90) cc_final: 0.3542 (p90) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.6460 time to fit residues: 100.2315 Evaluate side-chains 55 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 30.0000 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 HIS B 470 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.127916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.087862 restraints weight = 16643.887| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.22 r_work: 0.3297 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9806 Z= 0.176 Angle : 0.691 14.974 13360 Z= 0.358 Chirality : 0.049 0.211 1473 Planarity : 0.005 0.039 1740 Dihedral : 5.165 20.193 1302 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.19 % Allowed : 6.95 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.34 (0.24), residues: 1195 helix: -2.42 (0.47), residues: 95 sheet: -0.78 (0.42), residues: 138 loop : 0.17 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 354 TYR 0.014 0.002 TYR B 343 PHE 0.016 0.002 PHE A 94 TRP 0.013 0.002 TRP B 205 HIS 0.013 0.001 HIS B 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 ( 9743) covalent geometry : angle 0.67613 / 0.35 (13221) SS BOND : bond 0.00620 / 0.41 ( 50) SS BOND : angle 1.22740 / 0.79 ( 100) hydrogen bonds : bond 0.04596 / 3.27 ( 187) hydrogen bonds : angle 6.11356 / 4.39 ( 333) link_ALPHA1-3 : bond 0.00775 / 0.41 ( 1) link_ALPHA1-3 : angle 1.53339 / 0.82 ( 3) link_BETA1-4 : bond 0.00416 / 0.20 ( 4) link_BETA1-4 : angle 2.00050 / 1.17 ( 12) link_NAG-ASN : bond 0.00393 / 0.19 ( 8) link_NAG-ASN : angle 2.39598 / 1.81 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.7939 (t0) cc_final: 0.7689 (t0) REVERT: A 158 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7699 (mmp) REVERT: H 181 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8145 (tmtt) REVERT: B 538 GLN cc_start: 0.7788 (pt0) cc_final: 0.6964 (pp30) outliers start: 23 outliers final: 8 residues processed: 70 average time/residue: 0.5835 time to fit residues: 44.0741 Evaluate side-chains 53 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 HIS B 362 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.127045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.086894 restraints weight = 16524.256| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.23 r_work: 0.3279 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9806 Z= 0.124 Angle : 0.586 15.896 13360 Z= 0.297 Chirality : 0.046 0.172 1473 Planarity : 0.005 0.040 1740 Dihedral : 4.781 19.741 1302 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.52 % Allowed : 7.90 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.29 (0.24), residues: 1195 helix: -1.78 (0.54), residues: 82 sheet: -0.76 (0.44), residues: 138 loop : 0.10 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 354 TYR 0.010 0.001 TYR B 274 PHE 0.013 0.001 PHE A 543 TRP 0.008 0.001 TRP B 521 HIS 0.005 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 9743) covalent geometry : angle 0.57347 / 0.29 (13221) SS BOND : bond 0.00388 / 0.29 ( 50) SS BOND : angle 0.90229 / 0.59 ( 100) hydrogen bonds : bond 0.03734 / 2.65 ( 187) hydrogen bonds : angle 5.73506 / 4.12 ( 333) link_ALPHA1-3 : bond 0.00470 / 0.25 ( 1) link_ALPHA1-3 : angle 1.35670 / 0.73 ( 3) link_BETA1-4 : bond 0.00508 / 0.22 ( 4) link_BETA1-4 : angle 1.75870 / 1.03 ( 12) link_NAG-ASN : bond 0.00394 / 0.32 ( 8) link_NAG-ASN : angle 2.19104 / 1.63 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8051 (t0) cc_final: 0.7698 (t0) REVERT: A 490 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7873 (tpp-160) REVERT: H 181 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8237 (tmtt) REVERT: B 238 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8180 (pt0) REVERT: B 538 GLN cc_start: 0.7816 (pt0) cc_final: 0.6992 (pp30) outliers start: 16 outliers final: 7 residues processed: 57 average time/residue: 0.6176 time to fit residues: 37.9426 Evaluate side-chains 51 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 307 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 55 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.122108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.081354 restraints weight = 16896.788| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.24 r_work: 0.3176 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 9806 Z= 0.228 Angle : 0.663 19.107 13360 Z= 0.332 Chirality : 0.049 0.152 1473 Planarity : 0.005 0.037 1740 Dihedral : 5.149 21.350 1302 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.48 % Allowed : 7.43 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.56 (0.24), residues: 1195 helix: -1.88 (0.55), residues: 76 sheet: -0.86 (0.43), residues: 143 loop : -0.13 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 138 TYR 0.019 0.002 TYR B 274 PHE 0.019 0.002 PHE A 94 TRP 0.010 0.001 TRP B 521 HIS 0.008 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.23 ( 9743) covalent geometry : angle 0.65014 / 0.33 (13221) SS BOND : bond 0.00506 / 0.40 ( 50) SS BOND : angle 1.04276 / 0.69 ( 100) hydrogen bonds : bond 0.04125 / 2.96 ( 187) hydrogen bonds : angle 5.74149 / 4.13 ( 333) link_ALPHA1-3 : bond 0.00906 / 0.48 ( 1) link_ALPHA1-3 : angle 1.72539 / 0.91 ( 3) link_BETA1-4 : bond 0.00297 / 0.12 ( 4) link_BETA1-4 : angle 1.90952 / 1.09 ( 12) link_NAG-ASN : bond 0.00267 / 0.15 ( 8) link_NAG-ASN : angle 2.28892 / 1.77 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8145 (t0) cc_final: 0.7686 (t0) REVERT: A 490 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7796 (tpp-160) REVERT: H 181 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8243 (tmtt) REVERT: H 186 GLU cc_start: 0.7290 (pt0) cc_final: 0.7033 (pt0) REVERT: B 538 GLN cc_start: 0.7844 (pt0) cc_final: 0.7025 (pp30) outliers start: 26 outliers final: 11 residues processed: 68 average time/residue: 0.5338 time to fit residues: 39.4543 Evaluate side-chains 52 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 318 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.123148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.082692 restraints weight = 16812.811| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.23 r_work: 0.3189 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9806 Z= 0.146 Angle : 0.607 17.733 13360 Z= 0.298 Chirality : 0.046 0.163 1473 Planarity : 0.004 0.037 1740 Dihedral : 4.929 19.441 1302 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.48 % Allowed : 8.19 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.56 (0.24), residues: 1195 helix: -1.75 (0.56), residues: 76 sheet: -0.84 (0.44), residues: 143 loop : -0.15 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 330 TYR 0.011 0.001 TYR B 274 PHE 0.011 0.001 PHE A 94 TRP 0.008 0.001 TRP B 205 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 9743) covalent geometry : angle 0.58149 / 0.29 (13221) SS BOND : bond 0.00361 / 0.27 ( 50) SS BOND : angle 1.13962 / 0.60 ( 100) hydrogen bonds : bond 0.03559 / 2.54 ( 187) hydrogen bonds : angle 5.56282 / 4.01 ( 333) link_ALPHA1-3 : bond 0.00403 / 0.21 ( 1) link_ALPHA1-3 : angle 1.47617 / 0.78 ( 3) link_BETA1-4 : bond 0.00369 / 0.16 ( 4) link_BETA1-4 : angle 1.65999 / 0.99 ( 12) link_NAG-ASN : bond 0.00211 / 0.12 ( 8) link_NAG-ASN : angle 3.39752 / 2.27 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8163 (t0) cc_final: 0.7675 (t0) REVERT: A 475 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6348 (mmt-90) REVERT: A 490 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7791 (tpp-160) REVERT: H 181 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8208 (tmtt) REVERT: H 186 GLU cc_start: 0.7104 (pt0) cc_final: 0.6815 (pt0) REVERT: B 538 GLN cc_start: 0.7806 (pt0) cc_final: 0.7017 (pp30) outliers start: 26 outliers final: 13 residues processed: 62 average time/residue: 0.5638 time to fit residues: 37.9156 Evaluate side-chains 55 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 320 GLN Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.8980 chunk 52 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 43 optimal weight: 0.0070 chunk 116 optimal weight: 0.0370 chunk 95 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 67 optimal weight: 0.0170 overall best weight: 0.1514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 HIS A 435 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 318 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.126180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.086140 restraints weight = 16652.822| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.20 r_work: 0.3255 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9806 Z= 0.083 Angle : 0.524 14.120 13360 Z= 0.260 Chirality : 0.044 0.185 1473 Planarity : 0.004 0.039 1740 Dihedral : 4.475 18.019 1302 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.19 % Allowed : 8.00 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.44 (0.25), residues: 1195 helix: -1.55 (0.55), residues: 81 sheet: -0.84 (0.45), residues: 136 loop : -0.05 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 354 TYR 0.008 0.001 TYR A 86 PHE 0.016 0.001 PHE A 543 TRP 0.009 0.001 TRP B 205 HIS 0.002 0.000 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.08 ( 9743) covalent geometry : angle 0.51188 / 0.26 (13221) SS BOND : bond 0.00179 / 0.14 ( 50) SS BOND : angle 0.81516 / 0.46 ( 100) hydrogen bonds : bond 0.02683 / 1.89 ( 187) hydrogen bonds : angle 5.20595 / 3.76 ( 333) link_ALPHA1-3 : bond 0.00407 / 0.21 ( 1) link_ALPHA1-3 : angle 1.39131 / 0.74 ( 3) link_BETA1-4 : bond 0.00415 / 0.19 ( 4) link_BETA1-4 : angle 1.45232 / 0.88 ( 12) link_NAG-ASN : bond 0.00470 / 0.34 ( 8) link_NAG-ASN : angle 2.07892 / 1.52 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 47 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8150 (mmp) REVERT: A 318 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7712 (mttp) REVERT: A 490 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7781 (tpp-160) REVERT: A 534 ASN cc_start: 0.7179 (m-40) cc_final: 0.6970 (m-40) REVERT: H 181 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8147 (tmtt) REVERT: H 186 GLU cc_start: 0.6967 (pt0) cc_final: 0.6672 (pt0) REVERT: H 209 LEU cc_start: 0.8328 (mp) cc_final: 0.8020 (tt) REVERT: B 538 GLN cc_start: 0.7730 (pt0) cc_final: 0.7013 (pp30) outliers start: 23 outliers final: 7 residues processed: 64 average time/residue: 0.4915 time to fit residues: 34.5776 Evaluate side-chains 51 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 193 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 83 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 chunk 115 optimal weight: 10.0000 chunk 39 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 318 HIS B 320 GLN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.121555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.080965 restraints weight = 16947.885| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.21 r_work: 0.3171 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9806 Z= 0.206 Angle : 0.641 18.590 13360 Z= 0.313 Chirality : 0.048 0.154 1473 Planarity : 0.005 0.036 1740 Dihedral : 4.874 24.626 1302 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.38 % Allowed : 8.76 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.52 (0.24), residues: 1195 helix: -1.56 (0.58), residues: 75 sheet: -0.87 (0.44), residues: 143 loop : -0.12 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 203 TYR 0.018 0.002 TYR A 523 PHE 0.017 0.002 PHE A 94 TRP 0.010 0.001 TRP B 452 HIS 0.006 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.21 ( 9743) covalent geometry : angle 0.62467 / 0.31 (13221) SS BOND : bond 0.00447 / 0.35 ( 50) SS BOND : angle 1.06896 / 0.60 ( 100) hydrogen bonds : bond 0.03760 / 2.71 ( 187) hydrogen bonds : angle 5.47906 / 3.95 ( 333) link_ALPHA1-3 : bond 0.00379 / 0.20 ( 1) link_ALPHA1-3 : angle 1.40768 / 0.74 ( 3) link_BETA1-4 : bond 0.00348 / 0.15 ( 4) link_BETA1-4 : angle 1.75137 / 1.02 ( 12) link_NAG-ASN : bond 0.00240 / 0.12 ( 8) link_NAG-ASN : angle 2.63402 / 1.90 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 41 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8217 (t0) cc_final: 0.7706 (t0) REVERT: A 490 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7769 (tpp-160) REVERT: H 181 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8432 (tmtt) REVERT: B 538 GLN cc_start: 0.7852 (pt0) cc_final: 0.6998 (pp30) outliers start: 25 outliers final: 14 residues processed: 61 average time/residue: 0.5201 time to fit residues: 34.7597 Evaluate side-chains 57 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 63 optimal weight: 0.0040 chunk 4 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 HIS A 215 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 318 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.122352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.082009 restraints weight = 16787.782| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.21 r_work: 0.3193 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9806 Z= 0.144 Angle : 0.593 17.536 13360 Z= 0.292 Chirality : 0.046 0.163 1473 Planarity : 0.004 0.036 1740 Dihedral : 4.786 23.004 1302 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.81 % Allowed : 9.52 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.41 (0.25), residues: 1195 helix: -1.18 (0.62), residues: 68 sheet: -0.72 (0.46), residues: 138 loop : -0.11 (0.21), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 354 TYR 0.015 0.001 TYR A 523 PHE 0.013 0.001 PHE A 543 TRP 0.007 0.001 TRP B 205 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.14 ( 9743) covalent geometry : angle 0.57454 / 0.29 (13221) SS BOND : bond 0.00348 / 0.27 ( 50) SS BOND : angle 1.22405 / 0.60 ( 100) hydrogen bonds : bond 0.03344 / 2.38 ( 187) hydrogen bonds : angle 5.37697 / 3.88 ( 333) link_ALPHA1-3 : bond 0.00370 / 0.19 ( 1) link_ALPHA1-3 : angle 1.41505 / 0.74 ( 3) link_BETA1-4 : bond 0.00281 / 0.12 ( 4) link_BETA1-4 : angle 1.58061 / 0.95 ( 12) link_NAG-ASN : bond 0.00235 / 0.17 ( 8) link_NAG-ASN : angle 2.43316 / 1.77 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8205 (t0) cc_final: 0.7689 (t0) REVERT: A 475 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6016 (mmt-90) REVERT: A 490 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7748 (tpp-160) REVERT: H 181 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8393 (tmtt) REVERT: H 186 GLU cc_start: 0.7226 (pt0) cc_final: 0.6956 (pt0) REVERT: B 538 GLN cc_start: 0.7854 (pt0) cc_final: 0.7002 (pp30) outliers start: 19 outliers final: 9 residues processed: 61 average time/residue: 0.5953 time to fit residues: 39.1887 Evaluate side-chains 51 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.9990 chunk 33 optimal weight: 0.0980 chunk 1 optimal weight: 5.9990 chunk 36 optimal weight: 0.0020 chunk 81 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.124481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.084337 restraints weight = 16641.949| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.19 r_work: 0.3218 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9806 Z= 0.093 Angle : 0.544 15.396 13360 Z= 0.270 Chirality : 0.045 0.179 1473 Planarity : 0.004 0.038 1740 Dihedral : 4.515 19.700 1302 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.24 % Allowed : 10.57 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.36 (0.25), residues: 1195 helix: -1.42 (0.59), residues: 74 sheet: -0.70 (0.48), residues: 133 loop : -0.04 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 354 TYR 0.016 0.001 TYR A 523 PHE 0.009 0.001 PHE B 577 TRP 0.009 0.001 TRP B 205 HIS 0.003 0.000 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.09 ( 9743) covalent geometry : angle 0.53089 / 0.27 (13221) SS BOND : bond 0.00212 / 0.16 ( 50) SS BOND : angle 0.88825 / 0.48 ( 100) hydrogen bonds : bond 0.02787 / 1.97 ( 187) hydrogen bonds : angle 5.13255 / 3.72 ( 333) link_ALPHA1-3 : bond 0.00391 / 0.21 ( 1) link_ALPHA1-3 : angle 1.39667 / 0.74 ( 3) link_BETA1-4 : bond 0.00372 / 0.17 ( 4) link_BETA1-4 : angle 1.44538 / 0.88 ( 12) link_NAG-ASN : bond 0.00358 / 0.24 ( 8) link_NAG-ASN : angle 2.26631 / 1.63 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8149 (t0) cc_final: 0.7681 (t0) REVERT: A 319 MET cc_start: 0.7920 (mpt) cc_final: 0.7026 (mpt) REVERT: A 475 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6361 (mmt-90) REVERT: H 181 LYS cc_start: 0.8657 (mmpt) cc_final: 0.8410 (tmtt) REVERT: H 187 LYS cc_start: 0.8773 (tptm) cc_final: 0.8434 (tptt) REVERT: B 538 GLN cc_start: 0.7823 (pt0) cc_final: 0.6996 (pp30) outliers start: 13 outliers final: 8 residues processed: 56 average time/residue: 0.5538 time to fit residues: 33.6685 Evaluate side-chains 52 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 193 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 116 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 318 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.121273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.080913 restraints weight = 16801.044| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.20 r_work: 0.3170 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9806 Z= 0.201 Angle : 0.642 18.606 13360 Z= 0.313 Chirality : 0.048 0.156 1473 Planarity : 0.005 0.041 1740 Dihedral : 4.821 20.659 1302 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.24 % Allowed : 10.95 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.46 (0.25), residues: 1195 helix: -1.18 (0.62), residues: 68 sheet: -0.89 (0.44), residues: 153 loop : -0.10 (0.21), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 354 TYR 0.016 0.001 TYR B 274 PHE 0.014 0.002 PHE A 219 TRP 0.008 0.001 TRP B 452 HIS 0.006 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.20 ( 9743) covalent geometry : angle 0.62565 / 0.31 (13221) SS BOND : bond 0.00442 / 0.34 ( 50) SS BOND : angle 1.07935 / 0.61 ( 100) hydrogen bonds : bond 0.03609 / 2.58 ( 187) hydrogen bonds : angle 5.34575 / 3.87 ( 333) link_ALPHA1-3 : bond 0.00370 / 0.19 ( 1) link_ALPHA1-3 : angle 1.41572 / 0.74 ( 3) link_BETA1-4 : bond 0.00316 / 0.14 ( 4) link_BETA1-4 : angle 1.62383 / 0.97 ( 12) link_NAG-ASN : bond 0.00241 / 0.13 ( 8) link_NAG-ASN : angle 2.76895 / 1.94 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8191 (t0) cc_final: 0.7701 (t0) REVERT: A 475 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6045 (mmt-90) REVERT: H 186 GLU cc_start: 0.7659 (pm20) cc_final: 0.7069 (pm20) REVERT: B 538 GLN cc_start: 0.7877 (pt0) cc_final: 0.7031 (pp30) outliers start: 13 outliers final: 10 residues processed: 54 average time/residue: 0.5171 time to fit residues: 30.4590 Evaluate side-chains 51 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 18 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 318 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.122636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.082445 restraints weight = 16612.427| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.16 r_work: 0.3196 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9806 Z= 0.122 Angle : 0.580 16.760 13360 Z= 0.285 Chirality : 0.045 0.166 1473 Planarity : 0.004 0.048 1740 Dihedral : 4.649 19.589 1302 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.05 % Allowed : 11.05 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.47 (0.25), residues: 1195 helix: -1.48 (0.58), residues: 74 sheet: -0.71 (0.46), residues: 148 loop : -0.11 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 354 TYR 0.015 0.001 TYR A 523 PHE 0.010 0.001 PHE A 219 TRP 0.008 0.001 TRP B 205 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 9743) covalent geometry : angle 0.56557 / 0.28 (13221) SS BOND : bond 0.00288 / 0.22 ( 50) SS BOND : angle 0.89193 / 0.50 ( 100) hydrogen bonds : bond 0.03122 / 2.22 ( 187) hydrogen bonds : angle 5.20253 / 3.77 ( 333) link_ALPHA1-3 : bond 0.00363 / 0.19 ( 1) link_ALPHA1-3 : angle 1.41027 / 0.74 ( 3) link_BETA1-4 : bond 0.00317 / 0.14 ( 4) link_BETA1-4 : angle 1.51324 / 0.92 ( 12) link_NAG-ASN : bond 0.00276 / 0.20 ( 8) link_NAG-ASN : angle 2.53139 / 1.79 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3195.11 seconds wall clock time: 55 minutes 24.61 seconds (3324.61 seconds total)