Starting phenix.real_space_refine on Thu Jul 2 08:01:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fxc_29531/07_2026/8fxc_29531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxc_29531/07_2026/8fxc_29531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fxc_29531/07_2026/8fxc_29531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxc_29531/07_2026/8fxc_29531.map" model { file = "/net/cci-nas-00/data/ceres_data/8fxc_29531/07_2026/8fxc_29531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxc_29531/07_2026/8fxc_29531.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fxc_29531/07_2026/8fxc_29531.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fxc_29531/07_2026/8fxc_29531.cif" } resolution = 3.2 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= 0.135 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 Zn 1 6.06 5 S 44 5.16 5 C 4944 2.51 5 N 1308 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 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: 7639 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 707 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 917 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4509 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 21, 'GLN:plan1': 6, 'ASP:plan': 15, 'ASN:plan1': 7, 'HIS:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 191 Chain: "E" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1411 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 7, 'ASN:plan1': 5, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.72, per 1000 atoms: 0.23 Number of scatterers: 7639 At special positions: 0 Unit cell: (81, 100, 131, 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) Zn 1 29.99 S 44 16.00 O 1342 8.00 N 1308 7.00 C 4944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.06 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.04 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.16 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.07 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 BETA1-6 " NAG B 1 " - " FUC B 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 701 " - " ASN A 90 " " NAG A 702 " - " ASN A 53 " " NAG A 703 " - " ASN A 322 " " NAG A 704 " - " ASN A 103 " " NAG A 705 " - " ASN A 546 " " NAG B 1 " - " ASN E 343 " Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 452.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 706 " pdb="ZN ZN A 706 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 706 " - pdb=" NE2 HIS A 374 " 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1858 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 44.9% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.959A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.575A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.515A pdb=" N LYS A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 77 Processing helix chain 'A' and resid 78 through 83 removed outlier: 4.283A pdb=" N GLN A 81 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 98 removed outlier: 4.063A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.517A pdb=" N MET A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.502A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 220 through 249 removed outlier: 4.411A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.799A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.752A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.504A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.588A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.739A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 515 through 533 removed outlier: 3.552A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TYR A 521 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.616A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 597 removed outlier: 3.993A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.663A pdb=" N PHE E 342 " --> pdb=" O PHE E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.901A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 370 Processing helix chain 'E' and resid 386 through 389 Processing helix chain 'E' and resid 405 through 411 removed outlier: 4.862A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA E 411 " --> pdb=" O SER E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.514A pdb=" N TYR E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.571A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.571A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.668A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.668A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.332A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.290A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'E' and resid 391 through 392 removed outlier: 3.508A pdb=" N PHE E 392 " --> pdb=" O VAL E 524 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'E' and resid 473 through 474 363 hydrogen bonds defined for protein. 945 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: 1.08 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1506 1.33 - 1.46: 2444 1.46 - 1.59: 3830 1.59 - 1.72: 3 1.72 - 1.85: 68 Bond restraints: 7851 Sorted by residual: bond pdb=" CA ASP A 427 " pdb=" C ASP A 427 " ideal model delta sigma weight residual 1.524 1.613 -0.089 1.31e-02 5.83e+03 4.58e+01 bond pdb=" CA ASN E 477 " pdb=" C ASN E 477 " ideal model delta sigma weight residual 1.523 1.609 -0.087 1.41e-02 5.03e+03 3.78e+01 bond pdb=" N CYS L 23 " pdb=" CA CYS L 23 " ideal model delta sigma weight residual 1.461 1.398 0.063 1.19e-02 7.06e+03 2.79e+01 bond pdb=" CA CYS L 23 " pdb=" C CYS L 23 " ideal model delta sigma weight residual 1.522 1.577 -0.055 1.14e-02 7.69e+03 2.36e+01 bond pdb=" CA GLN A 287 " pdb=" C GLN A 287 " ideal model delta sigma weight residual 1.523 1.585 -0.063 1.41e-02 5.03e+03 1.97e+01 ... (remaining 7846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 10544 4.30 - 8.60: 137 8.60 - 12.91: 16 12.91 - 17.21: 0 17.21 - 21.51: 4 Bond angle restraints: 10701 Sorted by residual: angle pdb=" N GLU A 433 " pdb=" CA GLU A 433 " pdb=" C GLU A 433 " ideal model delta sigma weight residual 111.28 122.63 -11.35 1.09e+00 8.42e-01 1.08e+02 angle pdb=" CD1 LEU A 156 " pdb=" CG LEU A 156 " pdb=" CD2 LEU A 156 " ideal model delta sigma weight residual 110.80 132.31 -21.51 2.20e+00 2.07e-01 9.56e+01 angle pdb=" N ASN E 477 " pdb=" CA ASN E 477 " pdb=" C ASN E 477 " ideal model delta sigma weight residual 113.16 124.82 -11.66 1.24e+00 6.50e-01 8.85e+01 angle pdb=" CG1 VAL A 316 " pdb=" CB VAL A 316 " pdb=" CG2 VAL A 316 " ideal model delta sigma weight residual 110.80 130.93 -20.13 2.20e+00 2.07e-01 8.37e+01 angle pdb=" N LYS A 416 " pdb=" CA LYS A 416 " pdb=" C LYS A 416 " ideal model delta sigma weight residual 114.62 104.35 10.27 1.14e+00 7.69e-01 8.12e+01 ... (remaining 10696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 4260 17.39 - 34.79: 175 34.79 - 52.18: 41 52.18 - 69.58: 11 69.58 - 86.97: 7 Dihedral angle restraints: 4494 sinusoidal: 1588 harmonic: 2906 Sorted by residual: dihedral pdb=" N ASN E 487 " pdb=" C ASN E 487 " pdb=" CA ASN E 487 " pdb=" CB ASN E 487 " ideal model delta harmonic sigma weight residual 122.80 134.81 -12.01 0 2.50e+00 1.60e-01 2.31e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -122.59 36.59 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" N LYS A 288 " pdb=" C LYS A 288 " pdb=" CA LYS A 288 " pdb=" CB LYS A 288 " ideal model delta harmonic sigma weight residual 122.80 133.04 -10.24 0 2.50e+00 1.60e-01 1.68e+01 ... (remaining 4491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.307: 1155 0.307 - 0.614: 9 0.614 - 0.921: 1 0.921 - 1.228: 0 1.228 - 1.535: 1 Chirality restraints: 1166 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -0.86 -1.54 2.00e-01 2.50e+01 5.89e+01 chirality pdb=" C1 FUC B 2 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 2 " pdb=" O5 FUC B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.78e+01 chirality pdb=" CB VAL A 316 " pdb=" CA VAL A 316 " pdb=" CG1 VAL A 316 " pdb=" CG2 VAL A 316 " both_signs ideal model delta sigma weight residual False -2.63 -2.01 -0.62 2.00e-01 2.50e+01 9.67e+00 ... (remaining 1163 not shown) Planarity restraints: 1375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 322 " 0.026 2.00e-02 2.50e+03 2.74e-02 9.40e+00 pdb=" CG ASN A 322 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 322 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 322 " -0.042 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 473 " 0.036 2.00e-02 2.50e+03 1.78e-02 7.96e+00 pdb=" CG TRP A 473 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 473 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A 473 " -0.023 2.00e-02 2.50e+03 pdb=" NE1 TRP A 473 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 473 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 473 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 473 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 473 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 473 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 33 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C ASN A 33 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN A 33 " 0.017 2.00e-02 2.50e+03 pdb=" N HIS A 34 " 0.015 2.00e-02 2.50e+03 ... (remaining 1372 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 3026 2.90 - 3.40: 6841 3.40 - 3.90: 12432 3.90 - 4.40: 14584 4.40 - 4.90: 24292 Nonbonded interactions: 61175 Sorted by model distance: nonbonded pdb=" O VAL A 209 " pdb=" CG1 VAL A 209 " model vdw 2.403 3.460 nonbonded pdb=" OE1 GLU E 406 " pdb=" OH TYR E 495 " model vdw 2.484 3.040 nonbonded pdb=" NZ LYS A 187 " pdb=" OD2 ASP A 509 " model vdw 2.506 3.120 nonbonded pdb=" N SER A 280 " pdb=" N LEU A 281 " model vdw 2.506 2.560 nonbonded pdb=" N LYS A 416 " pdb=" N HIS A 417 " model vdw 2.507 2.560 ... (remaining 61170 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.200 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: 0.030 Process input model: 9.070 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.012 0.273 7869 Z= 0.662 Angle : 1.427 22.409 10740 Z= 0.957 Chirality : 0.098 1.535 1166 Planarity : 0.005 0.028 1369 Dihedral : 11.424 86.972 2609 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.34 % Favored : 95.95 % Rotamer: Outliers : 1.91 % Allowed : 2.06 % Favored : 96.04 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 4.55 % 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: -1.21 (0.24), residues: 988 helix: -1.07 (0.24), residues: 373 sheet: -0.19 (0.39), residues: 155 loop : -0.61 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 177 TYR 0.027 0.003 TYR A 385 PHE 0.017 0.002 PHE L 98 TRP 0.036 0.003 TRP A 473 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.01096 / 0.64 ( 7851) covalent geometry : angle 1.40165 / 0.95 (10701) SS BOND : bond 0.04660 / 1.83 ( 9) SS BOND : angle 3.38756 / 2.00 ( 18) hydrogen bonds : bond 0.22701 / 15.30 ( 348) hydrogen bonds : angle 7.13465 / 4.71 ( 945) metal coordination : bond 0.24004 / 11.87 ( 2) link_BETA1-6 : bond 0.05452 / 2.87 ( 1) link_BETA1-6 : angle 3.07763 / 1.55 ( 3) link_NAG-ASN : bond 0.04181 / 1.97 ( 6) link_NAG-ASN : angle 5.81447 / 2.33 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.282 Fit side-chains REVERT: L 55 ARG cc_start: 0.7660 (ttm110) cc_final: 0.7404 (ttm-80) REVERT: A 74 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7599 (mmtt) REVERT: A 144 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7087 (tp) REVERT: A 544 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.7046 (mt) REVERT: E 371 PHE cc_start: 0.5996 (OUTLIER) cc_final: 0.5178 (t80) outliers start: 13 outliers final: 5 residues processed: 142 average time/residue: 0.0970 time to fit residues: 18.4728 Evaluate side-chains 93 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 440 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN L 90 GLN A 401 HIS A 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.166874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.142906 restraints weight = 8404.288| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.57 r_work: 0.3749 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7869 Z= 0.137 Angle : 0.571 10.101 10740 Z= 0.299 Chirality : 0.043 0.371 1166 Planarity : 0.004 0.043 1369 Dihedral : 5.973 58.543 1107 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.50 % Allowed : 5.43 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.07 (0.26), residues: 988 helix: 0.49 (0.28), residues: 366 sheet: 0.19 (0.42), residues: 140 loop : -0.44 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 466 TYR 0.021 0.002 TYR H 54 PHE 0.013 0.002 PHE A 369 TRP 0.017 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 7851) covalent geometry : angle 0.55375 / 0.30 (10701) SS BOND : bond 0.00347 / 0.19 ( 9) SS BOND : angle 1.01738 / 0.56 ( 18) hydrogen bonds : bond 0.04613 / 3.12 ( 348) hydrogen bonds : angle 4.88408 / 3.21 ( 945) metal coordination : bond 0.01344 / 0.67 ( 2) link_BETA1-6 : bond 0.00210 / 0.11 ( 1) link_BETA1-6 : angle 1.66889 / 0.71 ( 3) link_NAG-ASN : bond 0.00656 / 0.39 ( 6) link_NAG-ASN : angle 3.25344 / 1.60 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7935 (ttm110) REVERT: A 30 ASP cc_start: 0.7755 (t0) cc_final: 0.7368 (t0) REVERT: A 74 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7628 (mptt) REVERT: A 142 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6919 (pp) REVERT: A 470 LYS cc_start: 0.7486 (ttmt) cc_final: 0.6974 (tppt) REVERT: A 559 ARG cc_start: 0.7999 (ppt-90) cc_final: 0.7488 (ptp-170) REVERT: E 371 PHE cc_start: 0.6082 (OUTLIER) cc_final: 0.5077 (t80) REVERT: E 440 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.6980 (pptt) outliers start: 17 outliers final: 8 residues processed: 113 average time/residue: 0.0906 time to fit residues: 14.1712 Evaluate side-chains 102 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN A 34 HIS A 522 GLN A 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.181553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.160552 restraints weight = 7825.425| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.85 r_work: 0.3522 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7869 Z= 0.193 Angle : 0.611 10.862 10740 Z= 0.316 Chirality : 0.046 0.373 1166 Planarity : 0.005 0.040 1369 Dihedral : 5.634 59.372 1101 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.06 % Allowed : 9.25 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.14 (0.26), residues: 988 helix: 0.31 (0.27), residues: 375 sheet: 0.34 (0.42), residues: 150 loop : -0.46 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 466 TYR 0.024 0.002 TYR A 385 PHE 0.015 0.002 PHE A 274 TRP 0.028 0.002 TRP A 473 HIS 0.006 0.002 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 ( 7851) covalent geometry : angle 0.59224 / 0.31 (10701) SS BOND : bond 0.00690 / 0.31 ( 9) SS BOND : angle 1.16903 / 0.68 ( 18) hydrogen bonds : bond 0.05119 / 3.48 ( 348) hydrogen bonds : angle 4.59997 / 3.06 ( 945) metal coordination : bond 0.00261 / 0.12 ( 2) link_BETA1-6 : bond 0.00425 / 0.22 ( 1) link_BETA1-6 : angle 1.85784 / 0.78 ( 3) link_NAG-ASN : bond 0.00460 / 0.26 ( 6) link_NAG-ASN : angle 3.49735 / 1.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8291 (ttm110) cc_final: 0.8006 (ttm110) REVERT: A 30 ASP cc_start: 0.7829 (t0) cc_final: 0.7540 (t0) REVERT: A 74 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7672 (mmtt) REVERT: A 470 LYS cc_start: 0.7719 (ttmt) cc_final: 0.7298 (tppt) REVERT: A 484 ILE cc_start: 0.8961 (mm) cc_final: 0.8583 (mt) REVERT: A 559 ARG cc_start: 0.8046 (ppt-90) cc_final: 0.7540 (ptp-170) REVERT: E 371 PHE cc_start: 0.6497 (OUTLIER) cc_final: 0.5402 (t80) outliers start: 14 outliers final: 10 residues processed: 88 average time/residue: 0.1024 time to fit residues: 12.2630 Evaluate side-chains 89 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN L 90 GLN A 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.183998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.168640 restraints weight = 7968.513| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 0.94 r_work: 0.3561 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7869 Z= 0.128 Angle : 0.516 10.614 10740 Z= 0.266 Chirality : 0.043 0.375 1166 Planarity : 0.004 0.039 1369 Dihedral : 5.381 59.947 1101 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.76 % Allowed : 9.99 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.11 (0.27), residues: 988 helix: 0.54 (0.28), residues: 375 sheet: 0.58 (0.43), residues: 147 loop : -0.38 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 466 TYR 0.017 0.001 TYR A 385 PHE 0.010 0.001 PHE A 369 TRP 0.015 0.001 TRP A 473 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 7851) covalent geometry : angle 0.49732 / 0.26 (10701) SS BOND : bond 0.00454 / 0.23 ( 9) SS BOND : angle 0.89333 / 0.50 ( 18) hydrogen bonds : bond 0.03980 / 2.71 ( 348) hydrogen bonds : angle 4.33960 / 2.90 ( 945) metal coordination : bond 0.00183 / 0.09 ( 2) link_BETA1-6 : bond 0.00315 / 0.17 ( 1) link_BETA1-6 : angle 1.59421 / 0.71 ( 3) link_NAG-ASN : bond 0.00491 / 0.29 ( 6) link_NAG-ASN : angle 3.29799 / 1.68 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7820 (t0) cc_final: 0.7502 (t0) REVERT: A 142 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6874 (pp) REVERT: A 470 LYS cc_start: 0.7560 (ttmt) cc_final: 0.7226 (tppt) REVERT: A 484 ILE cc_start: 0.8896 (mm) cc_final: 0.8534 (mt) REVERT: A 559 ARG cc_start: 0.7955 (ppt-90) cc_final: 0.7582 (ptp-170) REVERT: E 371 PHE cc_start: 0.6433 (OUTLIER) cc_final: 0.5387 (t80) REVERT: E 440 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.6764 (pptt) outliers start: 12 outliers final: 7 residues processed: 90 average time/residue: 0.1013 time to fit residues: 12.3159 Evaluate side-chains 88 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 92 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.182518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.167426 restraints weight = 8011.312| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 0.90 r_work: 0.3524 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7869 Z= 0.149 Angle : 0.540 10.715 10740 Z= 0.275 Chirality : 0.043 0.365 1166 Planarity : 0.004 0.036 1369 Dihedral : 5.077 59.962 1097 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.06 % Allowed : 11.01 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.07 (0.27), residues: 988 helix: 0.47 (0.27), residues: 383 sheet: 0.58 (0.43), residues: 147 loop : -0.39 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.019 0.002 TYR A 385 PHE 0.010 0.001 PHE A 28 TRP 0.017 0.001 TRP A 473 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 7851) covalent geometry : angle 0.52215 / 0.27 (10701) SS BOND : bond 0.00405 / 0.23 ( 9) SS BOND : angle 0.83798 / 0.50 ( 18) hydrogen bonds : bond 0.04213 / 2.87 ( 348) hydrogen bonds : angle 4.30706 / 2.89 ( 945) metal coordination : bond 0.00171 / 0.08 ( 2) link_BETA1-6 : bond 0.00170 / 0.09 ( 1) link_BETA1-6 : angle 1.62234 / 0.72 ( 3) link_NAG-ASN : bond 0.00467 / 0.27 ( 6) link_NAG-ASN : angle 3.31916 / 1.72 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7774 (ttm110) REVERT: A 30 ASP cc_start: 0.7788 (t0) cc_final: 0.7495 (t0) REVERT: A 142 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6843 (pp) REVERT: A 152 MET cc_start: 0.8303 (mmm) cc_final: 0.8014 (mmm) REVERT: A 279 TYR cc_start: 0.7405 (t80) cc_final: 0.7092 (t80) REVERT: A 470 LYS cc_start: 0.7634 (ttmt) cc_final: 0.7286 (tppt) REVERT: A 484 ILE cc_start: 0.8947 (mm) cc_final: 0.8612 (mt) REVERT: E 440 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.6647 (pptt) outliers start: 14 outliers final: 7 residues processed: 93 average time/residue: 0.0924 time to fit residues: 11.6664 Evaluate side-chains 89 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 80 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 33 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.184296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.168333 restraints weight = 7941.821| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.08 r_work: 0.3510 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7869 Z= 0.115 Angle : 0.502 10.243 10740 Z= 0.254 Chirality : 0.042 0.364 1166 Planarity : 0.004 0.034 1369 Dihedral : 4.728 59.513 1095 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.50 % Allowed : 10.72 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.20 (0.27), residues: 988 helix: 0.65 (0.28), residues: 383 sheet: 0.70 (0.44), residues: 146 loop : -0.40 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 192 TYR 0.015 0.001 TYR A 385 PHE 0.008 0.001 PHE A 28 TRP 0.013 0.001 TRP A 473 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 7851) covalent geometry : angle 0.48454 / 0.25 (10701) SS BOND : bond 0.00330 / 0.19 ( 9) SS BOND : angle 0.69010 / 0.41 ( 18) hydrogen bonds : bond 0.03672 / 2.50 ( 348) hydrogen bonds : angle 4.16089 / 2.79 ( 945) metal coordination : bond 0.00097 / 0.05 ( 2) link_BETA1-6 : bond 0.00189 / 0.10 ( 1) link_BETA1-6 : angle 1.47036 / 0.68 ( 3) link_NAG-ASN : bond 0.00479 / 0.28 ( 6) link_NAG-ASN : angle 3.14709 / 1.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7747 (ttm110) REVERT: A 30 ASP cc_start: 0.7843 (t0) cc_final: 0.7576 (t0) REVERT: A 142 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6805 (pp) REVERT: A 152 MET cc_start: 0.8234 (mmm) cc_final: 0.7994 (mmm) REVERT: A 470 LYS cc_start: 0.7668 (ttmt) cc_final: 0.7287 (tppt) REVERT: A 484 ILE cc_start: 0.8901 (mm) cc_final: 0.8571 (mt) REVERT: A 559 ARG cc_start: 0.8095 (ptt90) cc_final: 0.7451 (ptp-170) REVERT: E 440 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.6715 (pptt) outliers start: 17 outliers final: 7 residues processed: 103 average time/residue: 0.0867 time to fit residues: 12.2640 Evaluate side-chains 92 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 19 optimal weight: 0.0570 chunk 89 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 0.0270 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN A 493 HIS E 334 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.184489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.169037 restraints weight = 7955.839| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 0.95 r_work: 0.3550 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7869 Z= 0.112 Angle : 0.509 9.893 10740 Z= 0.258 Chirality : 0.042 0.351 1166 Planarity : 0.004 0.033 1369 Dihedral : 4.639 58.556 1095 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.20 % Allowed : 11.31 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.28 (0.27), residues: 988 helix: 0.70 (0.27), residues: 389 sheet: 0.56 (0.44), residues: 152 loop : -0.30 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 192 TYR 0.015 0.001 TYR A 385 PHE 0.008 0.001 PHE A 369 TRP 0.013 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 7851) covalent geometry : angle 0.49294 / 0.25 (10701) SS BOND : bond 0.00322 / 0.18 ( 9) SS BOND : angle 0.95867 / 0.53 ( 18) hydrogen bonds : bond 0.03558 / 2.41 ( 348) hydrogen bonds : angle 4.10928 / 2.76 ( 945) metal coordination : bond 0.00107 / 0.05 ( 2) link_BETA1-6 : bond 0.00132 / 0.07 ( 1) link_BETA1-6 : angle 1.37931 / 0.63 ( 3) link_NAG-ASN : bond 0.00465 / 0.27 ( 6) link_NAG-ASN : angle 3.02907 / 1.57 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7751 (ttm110) REVERT: A 142 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6766 (pp) REVERT: A 152 MET cc_start: 0.8272 (mmm) cc_final: 0.8027 (mmm) REVERT: A 279 TYR cc_start: 0.7419 (t80) cc_final: 0.7062 (t80) REVERT: A 360 MET cc_start: 0.8092 (ttt) cc_final: 0.7832 (ttt) REVERT: A 470 LYS cc_start: 0.7668 (ttmt) cc_final: 0.7320 (tppt) REVERT: A 484 ILE cc_start: 0.8867 (mm) cc_final: 0.8545 (mt) REVERT: E 440 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.6703 (pptt) outliers start: 15 outliers final: 9 residues processed: 97 average time/residue: 0.0895 time to fit residues: 11.8033 Evaluate side-chains 93 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 465 GLU Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.159174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.135156 restraints weight = 8538.375| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.52 r_work: 0.3391 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7869 Z= 0.153 Angle : 0.549 10.217 10740 Z= 0.278 Chirality : 0.043 0.347 1166 Planarity : 0.004 0.046 1369 Dihedral : 4.793 58.833 1095 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.06 % Allowed : 11.60 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.23 (0.27), residues: 988 helix: 0.66 (0.27), residues: 386 sheet: 0.53 (0.43), residues: 152 loop : -0.33 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 192 TYR 0.018 0.002 TYR A 385 PHE 0.009 0.001 PHE A 308 TRP 0.016 0.001 TRP A 473 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 ( 7851) covalent geometry : angle 0.53214 / 0.27 (10701) SS BOND : bond 0.00400 / 0.23 ( 9) SS BOND : angle 1.01182 / 0.56 ( 18) hydrogen bonds : bond 0.04101 / 2.77 ( 348) hydrogen bonds : angle 4.23852 / 2.84 ( 945) metal coordination : bond 0.00175 / 0.09 ( 2) link_BETA1-6 : bond 0.00311 / 0.16 ( 1) link_BETA1-6 : angle 1.60296 / 0.73 ( 3) link_NAG-ASN : bond 0.00435 / 0.25 ( 6) link_NAG-ASN : angle 3.13655 / 1.66 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.7935 (ttm110) REVERT: A 142 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6621 (pp) REVERT: A 152 MET cc_start: 0.8258 (mmm) cc_final: 0.8026 (mmm) REVERT: A 360 MET cc_start: 0.8207 (ttt) cc_final: 0.7934 (ttt) REVERT: A 470 LYS cc_start: 0.7836 (ttmt) cc_final: 0.7341 (tppt) REVERT: A 484 ILE cc_start: 0.8933 (mm) cc_final: 0.8657 (mt) REVERT: E 440 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.6689 (pptt) outliers start: 14 outliers final: 10 residues processed: 95 average time/residue: 0.0926 time to fit residues: 11.9988 Evaluate side-chains 92 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 465 GLU Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 84 optimal weight: 0.0170 chunk 65 optimal weight: 0.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.161809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.137626 restraints weight = 8562.290| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.61 r_work: 0.3437 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7869 Z= 0.110 Angle : 0.519 9.739 10740 Z= 0.262 Chirality : 0.042 0.350 1166 Planarity : 0.004 0.032 1369 Dihedral : 4.617 57.960 1095 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.62 % Allowed : 12.04 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.33 (0.27), residues: 988 helix: 0.78 (0.28), residues: 389 sheet: 0.60 (0.44), residues: 152 loop : -0.31 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 466 TYR 0.014 0.001 TYR A 385 PHE 0.011 0.001 PHE E 375 TRP 0.013 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 7851) covalent geometry : angle 0.50341 / 0.26 (10701) SS BOND : bond 0.00299 / 0.17 ( 9) SS BOND : angle 0.77469 / 0.43 ( 18) hydrogen bonds : bond 0.03455 / 2.33 ( 348) hydrogen bonds : angle 4.11564 / 2.76 ( 945) metal coordination : bond 0.00115 / 0.06 ( 2) link_BETA1-6 : bond 0.00261 / 0.14 ( 1) link_BETA1-6 : angle 1.50161 / 0.75 ( 3) link_NAG-ASN : bond 0.00449 / 0.27 ( 6) link_NAG-ASN : angle 2.99983 / 1.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8355 (ttm-80) cc_final: 0.7941 (ttm110) REVERT: A 74 LYS cc_start: 0.7895 (mmtt) cc_final: 0.7661 (mmtt) REVERT: A 89 GLN cc_start: 0.6570 (mp10) cc_final: 0.6321 (mt0) REVERT: A 142 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6739 (pp) REVERT: A 152 MET cc_start: 0.8199 (mmm) cc_final: 0.7982 (mmm) REVERT: A 470 LYS cc_start: 0.7785 (ttmt) cc_final: 0.7299 (tppt) REVERT: A 484 ILE cc_start: 0.8897 (mm) cc_final: 0.8615 (mt) REVERT: E 440 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.6771 (pptt) outliers start: 11 outliers final: 8 residues processed: 92 average time/residue: 0.0915 time to fit residues: 11.6888 Evaluate side-chains 93 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.0670 chunk 44 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.159085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134999 restraints weight = 8539.114| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.50 r_work: 0.3414 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7869 Z= 0.159 Angle : 0.569 10.046 10740 Z= 0.287 Chirality : 0.044 0.339 1166 Planarity : 0.004 0.033 1369 Dihedral : 4.791 58.686 1095 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.62 % Allowed : 12.78 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.27 (0.27), residues: 988 helix: 0.70 (0.27), residues: 386 sheet: 0.58 (0.43), residues: 152 loop : -0.32 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 245 TYR 0.018 0.001 TYR A 385 PHE 0.012 0.001 PHE E 375 TRP 0.016 0.001 TRP A 473 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 7851) covalent geometry : angle 0.55324 / 0.28 (10701) SS BOND : bond 0.00406 / 0.23 ( 9) SS BOND : angle 0.96088 / 0.55 ( 18) hydrogen bonds : bond 0.04102 / 2.77 ( 348) hydrogen bonds : angle 4.26831 / 2.86 ( 945) metal coordination : bond 0.00251 / 0.12 ( 2) link_BETA1-6 : bond 0.00381 / 0.20 ( 1) link_BETA1-6 : angle 1.75903 / 0.81 ( 3) link_NAG-ASN : bond 0.00426 / 0.25 ( 6) link_NAG-ASN : angle 3.07221 / 1.63 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.7952 (ttm110) REVERT: A 89 GLN cc_start: 0.6431 (mp10) cc_final: 0.6165 (mt0) REVERT: A 152 MET cc_start: 0.8300 (mmm) cc_final: 0.8084 (mmm) REVERT: A 360 MET cc_start: 0.8465 (ptm) cc_final: 0.8180 (ptm) REVERT: A 470 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7171 (tppt) REVERT: A 484 ILE cc_start: 0.8948 (mm) cc_final: 0.8687 (mt) REVERT: E 440 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.6727 (pptt) outliers start: 11 outliers final: 10 residues processed: 90 average time/residue: 0.0777 time to fit residues: 9.7551 Evaluate side-chains 92 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 465 GLU Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 87 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.186349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.170254 restraints weight = 8045.081| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 0.99 r_work: 0.3554 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7869 Z= 0.113 Angle : 0.532 10.747 10740 Z= 0.267 Chirality : 0.042 0.340 1166 Planarity : 0.004 0.046 1369 Dihedral : 4.630 57.446 1095 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.76 % Allowed : 12.48 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.38 (0.28), residues: 988 helix: 0.81 (0.28), residues: 389 sheet: 0.65 (0.44), residues: 152 loop : -0.29 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 55 TYR 0.015 0.001 TYR A 279 PHE 0.012 0.001 PHE A 315 TRP 0.013 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 7851) covalent geometry : angle 0.51740 / 0.26 (10701) SS BOND : bond 0.00309 / 0.18 ( 9) SS BOND : angle 0.77867 / 0.44 ( 18) hydrogen bonds : bond 0.03523 / 2.38 ( 348) hydrogen bonds : angle 4.13727 / 2.77 ( 945) metal coordination : bond 0.00148 / 0.07 ( 2) link_BETA1-6 : bond 0.00031 / 0.02 ( 1) link_BETA1-6 : angle 1.39486 / 0.66 ( 3) link_NAG-ASN : bond 0.00441 / 0.26 ( 6) link_NAG-ASN : angle 2.93296 / 1.54 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2058.84 seconds wall clock time: 35 minutes 59.44 seconds (2159.44 seconds total)