Starting phenix.real_space_refine on Fri Aug 22 20:33:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fxc_29531/08_2025/8fxc_29531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxc_29531/08_2025/8fxc_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_29531/08_2025/8fxc_29531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxc_29531/08_2025/8fxc_29531.map" model { file = "/net/cci-nas-00/data/ceres_data/8fxc_29531/08_2025/8fxc_29531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxc_29531/08_2025/8fxc_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-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.09, per 1000 atoms: 0.27 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: 0.71 Conformation dependent library (CDL) restraints added in 448.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.35 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: 1.34 Time building geometry restraints manager: 0.95 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: 4396 17.39 - 34.79: 178 34.79 - 52.18: 45 52.18 - 69.58: 11 69.58 - 86.97: 7 Dihedral angle restraints: 4637 sinusoidal: 1731 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 4634 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: 1.420 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.310 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 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 : 11.352 86.972 2752 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 aren 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 covalent geometry : bond 0.01096 ( 7851) covalent geometry : angle 1.40165 (10701) SS BOND : bond 0.04660 ( 9) SS BOND : angle 3.38756 ( 18) hydrogen bonds : bond 0.22701 ( 348) hydrogen bonds : angle 7.13465 ( 945) metal coordination : bond 0.24004 ( 2) link_BETA1-6 : bond 0.05452 ( 1) link_BETA1-6 : angle 3.07763 ( 3) link_NAG-ASN : bond 0.04181 ( 6) link_NAG-ASN : angle 5.81447 ( 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 : 0.283 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: 0.7307 (OUTLIER) cc_final: 0.7087 (tp) REVERT: A 544 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.7045 (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: 0.1039 time to fit residues: 19.6820 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 : 0.350 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.166802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.143505 restraints weight = 8387.715| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.48 r_work: 0.3727 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7869 Z= 0.137 Angle : 0.579 11.182 10740 Z= 0.301 Chirality : 0.044 0.391 1166 Planarity : 0.004 0.044 1369 Dihedral : 6.606 58.773 1250 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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 aren not related in a simple way. whole: -0.03 (0.26), residues: 988 helix: 0.50 (0.28), residues: 372 sheet: 0.12 (0.42), residues: 150 loop : -0.39 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 466 TYR 0.023 0.002 TYR H 54 PHE 0.014 0.002 PHE A 369 TRP 0.017 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7851) covalent geometry : angle 0.56044 (10701) SS BOND : bond 0.00350 ( 9) SS BOND : angle 1.01486 ( 18) hydrogen bonds : bond 0.04743 ( 348) hydrogen bonds : angle 4.89403 ( 945) metal coordination : bond 0.00237 ( 2) link_BETA1-6 : bond 0.00195 ( 1) link_BETA1-6 : angle 1.62102 ( 3) link_NAG-ASN : bond 0.00547 ( 6) link_NAG-ASN : angle 3.45045 ( 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 121 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8209 (ttm110) cc_final: 0.7973 (ttm110) REVERT: A 30 ASP cc_start: 0.7829 (t0) cc_final: 0.7446 (t0) REVERT: A 74 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7677 (mptt) REVERT: A 142 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6922 (pp) REVERT: A 470 LYS cc_start: 0.7529 (ttmt) cc_final: 0.7050 (tppt) REVERT: A 559 ARG cc_start: 0.8090 (ppt-90) cc_final: 0.7566 (ptp-170) REVERT: E 371 PHE cc_start: 0.6067 (OUTLIER) cc_final: 0.5072 (t80) REVERT: E 440 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.6959 (pptt) outliers start: 17 outliers final: 8 residues processed: 112 average time/residue: 0.0923 time to fit residues: 14.2260 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 : 0.214 ------------------------------------------------------------------------------- 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: 3.9990 chunk 13 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4056 r_free = 0.4056 target = 0.183091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.166704 restraints weight = 7789.981| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.07 r_work: 0.3590 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2737 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= 0.171 Angle : 0.581 11.092 10740 Z= 0.301 Chirality : 0.045 0.388 1166 Planarity : 0.004 0.040 1369 Dihedral : 5.935 59.797 1244 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.06 % Allowed : 8.96 % Favored : 88.99 % 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 aren not related in a simple way. whole: -0.02 (0.26), residues: 988 helix: 0.47 (0.27), residues: 373 sheet: 0.36 (0.42), residues: 150 loop : -0.44 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.022 0.002 TYR A 385 PHE 0.013 0.002 PHE A 274 TRP 0.025 0.002 TRP A 473 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 7851) covalent geometry : angle 0.56168 (10701) SS BOND : bond 0.00423 ( 9) SS BOND : angle 1.19640 ( 18) hydrogen bonds : bond 0.04795 ( 348) hydrogen bonds : angle 4.55047 ( 945) metal coordination : bond 0.00110 ( 2) link_BETA1-6 : bond 0.00200 ( 1) link_BETA1-6 : angle 1.81874 ( 3) link_NAG-ASN : bond 0.00502 ( 6) link_NAG-ASN : angle 3.42840 ( 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 96 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8333 (ttm110) cc_final: 0.8073 (ttm110) REVERT: A 30 ASP cc_start: 0.7888 (t0) cc_final: 0.7646 (t0) REVERT: A 255 TYR cc_start: 0.7696 (m-10) cc_final: 0.7438 (m-10) REVERT: A 470 LYS cc_start: 0.7729 (ttmt) cc_final: 0.7371 (tppt) REVERT: A 484 ILE cc_start: 0.8886 (mm) cc_final: 0.8482 (mt) REVERT: A 559 ARG cc_start: 0.8145 (ppt-90) cc_final: 0.7742 (ptp-170) REVERT: E 371 PHE cc_start: 0.6433 (OUTLIER) cc_final: 0.5364 (t80) outliers start: 14 outliers final: 10 residues processed: 89 average time/residue: 0.1030 time to fit residues: 12.3735 Evaluate side-chains 89 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3728 r_free = 0.3728 target = 0.158681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.134511 restraints weight = 8589.503| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.53 r_work: 0.3393 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7869 Z= 0.183 Angle : 0.572 11.640 10740 Z= 0.294 Chirality : 0.045 0.389 1166 Planarity : 0.004 0.040 1369 Dihedral : 5.568 58.883 1240 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.47 % Allowed : 10.43 % Favored : 88.11 % 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 aren not related in a simple way. whole: -0.02 (0.26), residues: 988 helix: 0.38 (0.27), residues: 376 sheet: 0.54 (0.43), residues: 147 loop : -0.42 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.022 0.002 TYR A 385 PHE 0.013 0.002 PHE A 274 TRP 0.021 0.002 TRP A 473 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 7851) covalent geometry : angle 0.55159 (10701) SS BOND : bond 0.00792 ( 9) SS BOND : angle 0.96737 ( 18) hydrogen bonds : bond 0.04647 ( 348) hydrogen bonds : angle 4.50054 ( 945) metal coordination : bond 0.00196 ( 2) link_BETA1-6 : bond 0.00568 ( 1) link_BETA1-6 : angle 1.83310 ( 3) link_NAG-ASN : bond 0.00485 ( 6) link_NAG-ASN : angle 3.54547 ( 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 92 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8033 (t0) cc_final: 0.7824 (t0) REVERT: A 142 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6672 (pp) REVERT: A 152 MET cc_start: 0.8372 (mmm) cc_final: 0.7704 (mmt) REVERT: A 470 LYS cc_start: 0.7773 (ttmt) cc_final: 0.7288 (tppt) REVERT: A 484 ILE cc_start: 0.8989 (mm) cc_final: 0.8665 (mt) REVERT: A 559 ARG cc_start: 0.8093 (ppt-90) cc_final: 0.7581 (ptp-170) REVERT: E 440 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.6677 (mptt) outliers start: 10 outliers final: 7 residues processed: 88 average time/residue: 0.1016 time to fit residues: 12.0545 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 : 0.319 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.167641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144877 restraints weight = 8405.427| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.43 r_work: 0.3444 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7869 Z= 0.182 Angle : 0.571 11.489 10740 Z= 0.293 Chirality : 0.044 0.385 1166 Planarity : 0.004 0.036 1369 Dihedral : 5.438 58.853 1238 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.76 % Allowed : 10.87 % Favored : 87.37 % 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 aren not related in a simple way. whole: -0.11 (0.27), residues: 988 helix: 0.34 (0.27), residues: 377 sheet: 0.54 (0.43), residues: 147 loop : -0.53 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.021 0.002 TYR A 385 PHE 0.011 0.002 PHE A 28 TRP 0.019 0.002 TRP A 473 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 7851) covalent geometry : angle 0.55075 (10701) SS BOND : bond 0.00448 ( 9) SS BOND : angle 0.91063 ( 18) hydrogen bonds : bond 0.04584 ( 348) hydrogen bonds : angle 4.43883 ( 945) metal coordination : bond 0.00227 ( 2) link_BETA1-6 : bond 0.00373 ( 1) link_BETA1-6 : angle 1.86054 ( 3) link_NAG-ASN : bond 0.00502 ( 6) link_NAG-ASN : angle 3.56575 ( 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 96 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.7892 (ttm110) REVERT: A 30 ASP cc_start: 0.7972 (t0) cc_final: 0.7658 (t0) REVERT: A 142 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6735 (pp) REVERT: A 470 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7202 (tppt) REVERT: A 484 ILE cc_start: 0.8993 (mm) cc_final: 0.8686 (mt) REVERT: E 440 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.6757 (mptt) outliers start: 12 outliers final: 7 residues processed: 92 average time/residue: 0.0951 time to fit residues: 11.9152 Evaluate side-chains 88 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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: 0.9990 chunk 68 optimal weight: 0.0040 chunk 87 optimal weight: 0.5980 chunk 79 optimal weight: 0.0570 chunk 83 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.4712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.184820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.169486 restraints weight = 7976.787| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 0.93 r_work: 0.3564 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7869 Z= 0.100 Angle : 0.493 10.531 10740 Z= 0.251 Chirality : 0.041 0.376 1166 Planarity : 0.004 0.033 1369 Dihedral : 5.040 59.659 1238 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.06 % Allowed : 10.72 % Favored : 87.22 % 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 aren not related in a simple way. whole: 0.19 (0.27), residues: 988 helix: 0.65 (0.28), residues: 377 sheet: 0.75 (0.44), residues: 147 loop : -0.43 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 55 TYR 0.014 0.001 TYR A 385 PHE 0.008 0.001 PHE A 315 TRP 0.014 0.001 TRP A 477 HIS 0.002 0.001 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 7851) covalent geometry : angle 0.47318 (10701) SS BOND : bond 0.00298 ( 9) SS BOND : angle 0.91022 ( 18) hydrogen bonds : bond 0.03483 ( 348) hydrogen bonds : angle 4.15770 ( 945) metal coordination : bond 0.00097 ( 2) link_BETA1-6 : bond 0.00140 ( 1) link_BETA1-6 : angle 1.46018 ( 3) link_NAG-ASN : bond 0.00516 ( 6) link_NAG-ASN : angle 3.23478 ( 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 107 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7773 (ttm110) REVERT: A 30 ASP cc_start: 0.7778 (t0) cc_final: 0.7553 (t0) REVERT: A 142 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6805 (pp) REVERT: A 470 LYS cc_start: 0.7686 (ttmt) cc_final: 0.7335 (tppt) REVERT: A 484 ILE cc_start: 0.8869 (mm) cc_final: 0.8537 (mt) REVERT: A 559 ARG cc_start: 0.8066 (ptt90) cc_final: 0.7476 (ptp-170) REVERT: E 440 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.6600 (pptt) outliers start: 14 outliers final: 6 residues processed: 103 average time/residue: 0.0945 time to fit residues: 13.2741 Evaluate side-chains 91 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 19 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 61 optimal weight: 0.0070 chunk 68 optimal weight: 0.0470 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3719 r_free = 0.3719 target = 0.157853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133823 restraints weight = 8572.641| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.52 r_work: 0.3382 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7869 Z= 0.168 Angle : 0.568 10.972 10740 Z= 0.289 Chirality : 0.044 0.367 1166 Planarity : 0.004 0.034 1369 Dihedral : 5.240 59.916 1238 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.91 % Allowed : 12.63 % Favored : 85.46 % 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 aren not related in a simple way. whole: -0.03 (0.27), residues: 988 helix: 0.42 (0.27), residues: 392 sheet: 0.49 (0.43), residues: 152 loop : -0.51 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 192 TYR 0.019 0.002 TYR A 385 PHE 0.010 0.002 PHE A 274 TRP 0.017 0.001 TRP A 473 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 7851) covalent geometry : angle 0.54979 (10701) SS BOND : bond 0.00430 ( 9) SS BOND : angle 1.03248 ( 18) hydrogen bonds : bond 0.04354 ( 348) hydrogen bonds : angle 4.30807 ( 945) metal coordination : bond 0.00157 ( 2) link_BETA1-6 : bond 0.00317 ( 1) link_BETA1-6 : angle 1.75997 ( 3) link_NAG-ASN : bond 0.00457 ( 6) link_NAG-ASN : angle 3.35746 ( 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 99 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.7986 (ttm110) REVERT: A 30 ASP cc_start: 0.8083 (t0) cc_final: 0.7766 (t0) REVERT: A 142 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6685 (pp) REVERT: A 152 MET cc_start: 0.8351 (mmm) cc_final: 0.8098 (mmm) REVERT: A 470 LYS cc_start: 0.7884 (ttmt) cc_final: 0.7383 (tppt) REVERT: A 484 ILE cc_start: 0.8979 (mm) cc_final: 0.8699 (mt) REVERT: E 440 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.6684 (pptt) outliers start: 13 outliers final: 10 residues processed: 95 average time/residue: 0.1028 time to fit residues: 13.1644 Evaluate side-chains 94 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 1 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.157869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.133761 restraints weight = 8554.201| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.53 r_work: 0.3385 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3617 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= 0.168 Angle : 0.566 10.788 10740 Z= 0.287 Chirality : 0.044 0.370 1166 Planarity : 0.004 0.038 1369 Dihedral : 5.267 59.732 1238 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.06 % Allowed : 12.19 % 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 aren not related in a simple way. whole: -0.11 (0.27), residues: 988 helix: 0.40 (0.27), residues: 392 sheet: 0.50 (0.43), residues: 152 loop : -0.61 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 192 TYR 0.018 0.002 TYR A 385 PHE 0.010 0.001 PHE A 28 TRP 0.016 0.001 TRP A 473 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 7851) covalent geometry : angle 0.54845 (10701) SS BOND : bond 0.00430 ( 9) SS BOND : angle 0.97422 ( 18) hydrogen bonds : bond 0.04302 ( 348) hydrogen bonds : angle 4.36016 ( 945) metal coordination : bond 0.00211 ( 2) link_BETA1-6 : bond 0.00356 ( 1) link_BETA1-6 : angle 1.81858 ( 3) link_NAG-ASN : bond 0.00455 ( 6) link_NAG-ASN : angle 3.33055 ( 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 98 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8000 (t0) cc_final: 0.7724 (t0) REVERT: A 142 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6660 (pp) REVERT: A 152 MET cc_start: 0.8286 (mmm) cc_final: 0.8050 (mmm) REVERT: A 360 MET cc_start: 0.8232 (ttt) cc_final: 0.7983 (ttt) REVERT: A 470 LYS cc_start: 0.7894 (ttmt) cc_final: 0.7196 (tppt) REVERT: A 484 ILE cc_start: 0.8982 (mm) cc_final: 0.8714 (mt) REVERT: E 440 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.6588 (pptt) outliers start: 14 outliers final: 9 residues processed: 95 average time/residue: 0.0941 time to fit residues: 12.1466 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 : 0.297 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.158442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.134280 restraints weight = 8613.678| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.54 r_work: 0.3402 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7869 Z= 0.153 Angle : 0.552 10.630 10740 Z= 0.279 Chirality : 0.044 0.366 1166 Planarity : 0.004 0.047 1369 Dihedral : 5.219 59.891 1238 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.20 % Allowed : 12.04 % 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 aren not related in a simple way. whole: -0.06 (0.27), residues: 988 helix: 0.47 (0.27), residues: 392 sheet: 0.52 (0.44), residues: 152 loop : -0.61 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 192 TYR 0.018 0.002 TYR A 385 PHE 0.011 0.001 PHE E 375 TRP 0.014 0.001 TRP A 473 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7851) covalent geometry : angle 0.53472 (10701) SS BOND : bond 0.00395 ( 9) SS BOND : angle 0.89686 ( 18) hydrogen bonds : bond 0.04123 ( 348) hydrogen bonds : angle 4.31876 ( 945) metal coordination : bond 0.00205 ( 2) link_BETA1-6 : bond 0.00292 ( 1) link_BETA1-6 : angle 1.64662 ( 3) link_NAG-ASN : bond 0.00468 ( 6) link_NAG-ASN : angle 3.26713 ( 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 101 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7965 (t0) cc_final: 0.7701 (t0) REVERT: A 142 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6753 (pp) REVERT: A 152 MET cc_start: 0.8273 (mmm) cc_final: 0.8008 (mmm) REVERT: A 470 LYS cc_start: 0.7860 (ttmt) cc_final: 0.7143 (ttmt) REVERT: A 484 ILE cc_start: 0.8955 (mm) cc_final: 0.8699 (mt) REVERT: E 440 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.6635 (pptt) outliers start: 15 outliers final: 10 residues processed: 97 average time/residue: 0.0989 time to fit residues: 13.1243 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 : 0.280 ------------------------------------------------------------------------------- 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 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 349 SER 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 43 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.183107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.167920 restraints weight = 7950.461| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 0.95 r_work: 0.3527 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7869 Z= 0.119 Angle : 0.538 10.219 10740 Z= 0.271 Chirality : 0.043 0.365 1166 Planarity : 0.004 0.047 1369 Dihedral : 5.005 59.219 1238 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.91 % Allowed : 12.48 % 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 aren not related in a simple way. whole: 0.05 (0.27), residues: 988 helix: 0.56 (0.27), residues: 395 sheet: 0.57 (0.44), residues: 152 loop : -0.55 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.015 0.001 TYR A 385 PHE 0.013 0.001 PHE E 375 TRP 0.014 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7851) covalent geometry : angle 0.52157 (10701) SS BOND : bond 0.00337 ( 9) SS BOND : angle 0.76696 ( 18) hydrogen bonds : bond 0.03650 ( 348) hydrogen bonds : angle 4.21580 ( 945) metal coordination : bond 0.00117 ( 2) link_BETA1-6 : bond 0.00114 ( 1) link_BETA1-6 : angle 1.60013 ( 3) link_NAG-ASN : bond 0.00480 ( 6) link_NAG-ASN : angle 3.12993 ( 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 95 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 142 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6791 (pp) REVERT: A 152 MET cc_start: 0.8197 (mmm) cc_final: 0.7958 (mmm) REVERT: A 360 MET cc_start: 0.8300 (ptm) cc_final: 0.8055 (ptm) REVERT: A 470 LYS cc_start: 0.7776 (ttmt) cc_final: 0.7139 (ttmt) REVERT: A 484 ILE cc_start: 0.8902 (mm) cc_final: 0.8626 (mt) REVERT: E 440 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.6610 (pptt) outliers start: 13 outliers final: 10 residues processed: 90 average time/residue: 0.0954 time to fit residues: 11.7758 Evaluate side-chains 94 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 349 SER Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.180430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.165308 restraints weight = 8026.305| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 0.90 r_work: 0.3487 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7869 Z= 0.170 Angle : 0.577 10.562 10740 Z= 0.291 Chirality : 0.044 0.355 1166 Planarity : 0.004 0.043 1369 Dihedral : 5.189 59.586 1238 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.91 % Allowed : 12.33 % 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 aren not related in a simple way. whole: -0.03 (0.27), residues: 988 helix: 0.48 (0.27), residues: 392 sheet: 0.51 (0.44), residues: 152 loop : -0.57 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.018 0.002 TYR A 385 PHE 0.012 0.002 PHE E 375 TRP 0.016 0.002 TRP A 473 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 7851) covalent geometry : angle 0.56049 (10701) SS BOND : bond 0.00425 ( 9) SS BOND : angle 0.93981 ( 18) hydrogen bonds : bond 0.04290 ( 348) hydrogen bonds : angle 4.35385 ( 945) metal coordination : bond 0.00218 ( 2) link_BETA1-6 : bond 0.00330 ( 1) link_BETA1-6 : angle 1.78960 ( 3) link_NAG-ASN : bond 0.00464 ( 6) link_NAG-ASN : angle 3.20783 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2065.34 seconds wall clock time: 36 minutes 5.39 seconds (2165.39 seconds total)