Starting phenix.real_space_refine on Fri Jun 6 12:42:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fxc_29531/06_2025/8fxc_29531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxc_29531/06_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_29531/06_2025/8fxc_29531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxc_29531/06_2025/8fxc_29531.map" model { file = "/net/cci-nas-00/data/ceres_data/8fxc_29531/06_2025/8fxc_29531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxc_29531/06_2025/8fxc_29531.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLN:plan1': 6, 'ASP:plan': 15, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 1, 'GLU:plan': 21, 'ARG: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: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 7} 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: 5.18, per 1000 atoms: 0.68 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: 2.06 Conformation dependent library (CDL) restraints added in 864.9 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: 1.13 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: 2.18 Time building geometry restraints manager: 2.37 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: 0.790 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.470 Find NCS groups from input model: 0.070 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.700 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (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 TRP 0.036 0.003 TRP A 473 HIS 0.005 0.001 HIS A 34 PHE 0.017 0.002 PHE L 98 TYR 0.027 0.003 TYR A 385 ARG 0.004 0.001 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.04181 ( 6) link_NAG-ASN : angle 5.81447 ( 18) hydrogen bonds : bond 0.22701 ( 348) hydrogen bonds : angle 7.13465 ( 945) link_BETA1-6 : bond 0.05452 ( 1) link_BETA1-6 : angle 3.07763 ( 3) metal coordination : bond 0.24004 ( 2) SS BOND : bond 0.04660 ( 9) SS BOND : angle 3.38756 ( 18) covalent geometry : bond 0.01096 ( 7851) covalent geometry : angle 1.40165 (10701) *********************** 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 : 0.781 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: 0.2105 time to fit residues: 39.5474 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 : 0.769 ------------------------------------------------------------------------------- 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 82 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 88 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.166475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.142348 restraints weight = 8328.405| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.55 r_work: 0.3521 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2031 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= 0.142 Angle : 0.580 11.057 10740 Z= 0.301 Chirality : 0.044 0.382 1166 Planarity : 0.004 0.044 1369 Dihedral : 6.613 58.657 1250 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.50 % Allowed : 5.29 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 988 helix: 0.48 (0.28), residues: 372 sheet: 0.14 (0.42), residues: 150 loop : -0.39 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 473 HIS 0.004 0.001 HIS A 374 PHE 0.013 0.002 PHE A 369 TYR 0.021 0.002 TYR H 54 ARG 0.003 0.000 ARG E 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 6) link_NAG-ASN : angle 3.45018 ( 18) hydrogen bonds : bond 0.04617 ( 348) hydrogen bonds : angle 4.88006 ( 945) link_BETA1-6 : bond 0.00147 ( 1) link_BETA1-6 : angle 1.68532 ( 3) metal coordination : bond 0.00036 ( 2) SS BOND : bond 0.00546 ( 9) SS BOND : angle 0.99800 ( 18) covalent geometry : bond 0.00317 ( 7851) covalent geometry : angle 0.56173 (10701) *********************** 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 : 0.772 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7915 (ttm110) REVERT: A 30 ASP cc_start: 0.7897 (t0) cc_final: 0.7499 (t0) REVERT: A 74 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7658 (mptt) REVERT: A 142 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6880 (pp) REVERT: A 470 LYS cc_start: 0.7510 (ttmt) cc_final: 0.7030 (tppt) REVERT: A 559 ARG cc_start: 0.8048 (ppt-90) cc_final: 0.7547 (ptp-170) REVERT: E 371 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.5157 (t80) REVERT: E 440 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.6980 (pptt) outliers start: 17 outliers final: 8 residues processed: 113 average time/residue: 0.1916 time to fit residues: 29.7436 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 : 0.746 ------------------------------------------------------------------------------- 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 77 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.154350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.130290 restraints weight = 8618.540| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.52 r_work: 0.3351 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 7869 Z= 0.300 Angle : 0.732 12.743 10740 Z= 0.379 Chirality : 0.051 0.415 1166 Planarity : 0.006 0.046 1369 Dihedral : 6.443 57.011 1244 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.20 % Allowed : 9.84 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.26), residues: 988 helix: -0.18 (0.26), residues: 379 sheet: 0.40 (0.43), residues: 146 loop : -0.62 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 473 HIS 0.009 0.002 HIS A 374 PHE 0.018 0.003 PHE A 274 TYR 0.028 0.003 TYR A 385 ARG 0.005 0.001 ARG A 161 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 6) link_NAG-ASN : angle 4.10726 ( 18) hydrogen bonds : bond 0.06228 ( 348) hydrogen bonds : angle 4.99513 ( 945) link_BETA1-6 : bond 0.00638 ( 1) link_BETA1-6 : angle 2.29229 ( 3) metal coordination : bond 0.00479 ( 2) SS BOND : bond 0.00681 ( 9) SS BOND : angle 1.44937 ( 18) covalent geometry : bond 0.00726 ( 7851) covalent geometry : angle 0.70972 (10701) *********************** 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 97 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7919 (t0) cc_final: 0.7518 (t0) REVERT: A 360 MET cc_start: 0.8156 (ttt) cc_final: 0.7890 (ttt) REVERT: A 470 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7252 (tppt) REVERT: A 484 ILE cc_start: 0.9071 (mm) cc_final: 0.8757 (mt) REVERT: E 371 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.5717 (t80) REVERT: E 440 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.6731 (mptt) outliers start: 15 outliers final: 10 residues processed: 90 average time/residue: 0.2254 time to fit residues: 27.7091 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 : 0.842 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 75 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 68 optimal weight: 0.0070 chunk 54 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.183171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.167310 restraints weight = 7865.873| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.08 r_work: 0.3517 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7869 Z= 0.113 Angle : 0.529 11.545 10740 Z= 0.270 Chirality : 0.043 0.410 1166 Planarity : 0.004 0.039 1369 Dihedral : 5.493 59.392 1240 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.62 % Allowed : 10.87 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.27), residues: 988 helix: 0.37 (0.28), residues: 375 sheet: 0.57 (0.44), residues: 147 loop : -0.51 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 PHE 0.009 0.001 PHE A 369 TYR 0.016 0.001 TYR A 385 ARG 0.003 0.000 ARG E 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 6) link_NAG-ASN : angle 3.56421 ( 18) hydrogen bonds : bond 0.03978 ( 348) hydrogen bonds : angle 4.42587 ( 945) link_BETA1-6 : bond 0.00194 ( 1) link_BETA1-6 : angle 1.75788 ( 3) metal coordination : bond 0.00124 ( 2) SS BOND : bond 0.00369 ( 9) SS BOND : angle 1.06773 ( 18) covalent geometry : bond 0.00255 ( 7851) covalent geometry : angle 0.50631 (10701) *********************** 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 97 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7778 (t0) cc_final: 0.7438 (t0) REVERT: A 142 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6742 (pp) REVERT: A 360 MET cc_start: 0.8049 (ttt) cc_final: 0.7829 (ttt) REVERT: A 470 LYS cc_start: 0.7634 (ttmt) cc_final: 0.7216 (tppt) REVERT: A 484 ILE cc_start: 0.8931 (mm) cc_final: 0.8592 (mt) REVERT: E 371 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.5512 (t80) REVERT: E 440 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.6688 (pptt) outliers start: 11 outliers final: 6 residues processed: 92 average time/residue: 0.2137 time to fit residues: 26.7622 Evaluate side-chains 90 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 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 86 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 0.0670 chunk 10 optimal weight: 0.0270 chunk 27 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.186585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.170855 restraints weight = 7877.310| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 0.98 r_work: 0.3581 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7869 Z= 0.096 Angle : 0.482 10.392 10740 Z= 0.245 Chirality : 0.041 0.377 1166 Planarity : 0.004 0.034 1369 Dihedral : 5.124 59.480 1240 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.91 % Allowed : 11.45 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.27), residues: 988 helix: 0.52 (0.27), residues: 390 sheet: 0.63 (0.44), residues: 147 loop : -0.39 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 477 HIS 0.002 0.001 HIS L 92 PHE 0.009 0.001 PHE A 315 TYR 0.013 0.001 TYR A 385 ARG 0.002 0.000 ARG E 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 6) link_NAG-ASN : angle 3.17686 ( 18) hydrogen bonds : bond 0.03330 ( 348) hydrogen bonds : angle 4.13503 ( 945) link_BETA1-6 : bond 0.00216 ( 1) link_BETA1-6 : angle 1.38624 ( 3) metal coordination : bond 0.00007 ( 2) SS BOND : bond 0.00301 ( 9) SS BOND : angle 0.78422 ( 18) covalent geometry : bond 0.00211 ( 7851) covalent geometry : angle 0.46300 (10701) *********************** 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 107 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7695 (t0) cc_final: 0.7479 (t0) REVERT: A 142 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6734 (pp) REVERT: A 152 MET cc_start: 0.8227 (mmm) cc_final: 0.7910 (mmm) REVERT: A 360 MET cc_start: 0.8143 (ttt) cc_final: 0.7886 (ttt) REVERT: A 470 LYS cc_start: 0.7539 (ttmt) cc_final: 0.7233 (tppt) REVERT: A 484 ILE cc_start: 0.8884 (mm) cc_final: 0.8541 (mt) REVERT: A 559 ARG cc_start: 0.8110 (ptt90) cc_final: 0.7460 (ptp-170) REVERT: E 440 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.6704 (pptt) outliers start: 13 outliers final: 6 residues processed: 103 average time/residue: 0.2036 time to fit residues: 28.8583 Evaluate side-chains 89 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 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 49 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN E 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.177758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.161709 restraints weight = 7922.364| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.00 r_work: 0.3464 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 7869 Z= 0.243 Angle : 0.642 11.958 10740 Z= 0.327 Chirality : 0.047 0.378 1166 Planarity : 0.005 0.041 1369 Dihedral : 5.594 58.845 1238 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.50 % Allowed : 11.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.27), residues: 988 helix: 0.19 (0.27), residues: 382 sheet: 0.48 (0.43), residues: 146 loop : -0.60 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 473 HIS 0.007 0.002 HIS A 374 PHE 0.013 0.002 PHE A 274 TYR 0.023 0.002 TYR A 385 ARG 0.003 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 6) link_NAG-ASN : angle 3.71440 ( 18) hydrogen bonds : bond 0.05275 ( 348) hydrogen bonds : angle 4.60089 ( 945) link_BETA1-6 : bond 0.00428 ( 1) link_BETA1-6 : angle 2.04120 ( 3) metal coordination : bond 0.00357 ( 2) SS BOND : bond 0.00549 ( 9) SS BOND : angle 1.09114 ( 18) covalent geometry : bond 0.00596 ( 7851) covalent geometry : angle 0.62204 (10701) *********************** 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 99 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7802 (t0) cc_final: 0.7546 (t0) REVERT: A 38 ASP cc_start: 0.7454 (m-30) cc_final: 0.7246 (m-30) REVERT: A 142 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6703 (pp) REVERT: A 152 MET cc_start: 0.8319 (mmm) cc_final: 0.8070 (mmm) REVERT: A 360 MET cc_start: 0.8177 (ttt) cc_final: 0.7964 (ttt) REVERT: A 470 LYS cc_start: 0.7871 (ttmt) cc_final: 0.7270 (tppt) REVERT: A 484 ILE cc_start: 0.9007 (mm) cc_final: 0.8737 (mt) outliers start: 17 outliers final: 11 residues processed: 96 average time/residue: 0.2155 time to fit residues: 28.7047 Evaluate side-chains 91 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 43 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 74 optimal weight: 4.9990 chunk 89 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.158415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.134539 restraints weight = 8523.048| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.51 r_work: 0.3405 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7869 Z= 0.146 Angle : 0.554 11.090 10740 Z= 0.281 Chirality : 0.043 0.381 1166 Planarity : 0.004 0.045 1369 Dihedral : 5.304 59.162 1238 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.06 % Allowed : 12.78 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.27), residues: 988 helix: 0.31 (0.27), residues: 394 sheet: 0.39 (0.43), residues: 152 loop : -0.66 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 PHE 0.010 0.001 PHE A 400 TYR 0.016 0.001 TYR A 385 ARG 0.004 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 6) link_NAG-ASN : angle 3.42968 ( 18) hydrogen bonds : bond 0.04111 ( 348) hydrogen bonds : angle 4.35531 ( 945) link_BETA1-6 : bond 0.00310 ( 1) link_BETA1-6 : angle 1.75777 ( 3) metal coordination : bond 0.00224 ( 2) SS BOND : bond 0.00378 ( 9) SS BOND : angle 1.24751 ( 18) covalent geometry : bond 0.00349 ( 7851) covalent geometry : angle 0.53336 (10701) *********************** 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 100 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7941 (t0) cc_final: 0.7641 (t0) REVERT: A 142 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6704 (pp) REVERT: A 152 MET cc_start: 0.8272 (mmm) cc_final: 0.8026 (mmm) REVERT: A 360 MET cc_start: 0.8359 (ttt) cc_final: 0.8141 (ttt) REVERT: A 470 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7238 (tppt) REVERT: A 484 ILE cc_start: 0.8987 (mm) cc_final: 0.8728 (mt) REVERT: E 440 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.6586 (pptt) outliers start: 14 outliers final: 7 residues processed: 96 average time/residue: 0.2094 time to fit residues: 27.1848 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 : 0.804 ------------------------------------------------------------------------------- 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 487 VAL Chi-restraints excluded: chain E residue 440 LYS 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 53 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.180027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.165740 restraints weight = 7974.188| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 0.90 r_work: 0.3503 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7869 Z= 0.224 Angle : 0.617 11.466 10740 Z= 0.314 Chirality : 0.046 0.376 1166 Planarity : 0.005 0.044 1369 Dihedral : 5.531 57.928 1238 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.06 % Allowed : 13.22 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.27), residues: 988 helix: 0.18 (0.27), residues: 388 sheet: 0.36 (0.43), residues: 152 loop : -0.75 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 473 HIS 0.006 0.002 HIS A 374 PHE 0.012 0.002 PHE E 375 TYR 0.021 0.002 TYR A 385 ARG 0.006 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 6) link_NAG-ASN : angle 3.57314 ( 18) hydrogen bonds : bond 0.04935 ( 348) hydrogen bonds : angle 4.55132 ( 945) link_BETA1-6 : bond 0.00382 ( 1) link_BETA1-6 : angle 1.89662 ( 3) metal coordination : bond 0.00278 ( 2) SS BOND : bond 0.00508 ( 9) SS BOND : angle 1.25875 ( 18) covalent geometry : bond 0.00547 ( 7851) covalent geometry : angle 0.59731 (10701) *********************** 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 96 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7878 (t0) cc_final: 0.7614 (t0) REVERT: A 142 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6695 (pp) REVERT: A 152 MET cc_start: 0.8281 (mmm) cc_final: 0.8052 (mmm) REVERT: A 360 MET cc_start: 0.8225 (ttt) cc_final: 0.8023 (ttt) REVERT: A 484 ILE cc_start: 0.8980 (mm) cc_final: 0.8708 (mt) outliers start: 14 outliers final: 12 residues processed: 93 average time/residue: 0.2875 time to fit residues: 37.3586 Evaluate side-chains 93 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 43 SER 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 88 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 66 optimal weight: 0.3980 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4067 r_free = 0.4067 target = 0.184681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.168754 restraints weight = 8014.495| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 0.97 r_work: 0.3525 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 0.031 7869 Z= 0.117 Angle : 0.521 10.697 10740 Z= 0.265 Chirality : 0.043 0.376 1166 Planarity : 0.004 0.040 1369 Dihedral : 5.135 59.305 1238 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.06 % Allowed : 12.92 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.27), residues: 988 helix: 0.45 (0.27), residues: 394 sheet: 0.49 (0.44), residues: 152 loop : -0.68 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 PHE 0.010 0.001 PHE E 375 TYR 0.015 0.001 TYR A 385 ARG 0.001 0.000 ARG E 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00502 ( 6) link_NAG-ASN : angle 3.29448 ( 18) hydrogen bonds : bond 0.03700 ( 348) hydrogen bonds : angle 4.24321 ( 945) link_BETA1-6 : bond 0.00093 ( 1) link_BETA1-6 : angle 1.56569 ( 3) metal coordination : bond 0.00144 ( 2) SS BOND : bond 0.00327 ( 9) SS BOND : angle 0.84169 ( 18) covalent geometry : bond 0.00270 ( 7851) covalent geometry : angle 0.50208 (10701) *********************** 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 99 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7781 (t0) cc_final: 0.7561 (t0) REVERT: A 142 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6788 (pp) REVERT: A 152 MET cc_start: 0.8233 (mmm) cc_final: 0.7978 (mmm) REVERT: A 360 MET cc_start: 0.8294 (ttt) cc_final: 0.8075 (ttt) REVERT: A 484 ILE cc_start: 0.8935 (mm) cc_final: 0.8662 (mt) REVERT: E 440 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.6609 (pptt) outliers start: 14 outliers final: 11 residues processed: 96 average time/residue: 0.2024 time to fit residues: 27.0753 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 : 0.868 ------------------------------------------------------------------------------- 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 43 SER 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 95 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 2 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.5364 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.180553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.159035 restraints weight = 8069.129| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.93 r_work: 0.3449 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7869 Z= 0.204 Angle : 0.610 11.127 10740 Z= 0.309 Chirality : 0.045 0.369 1166 Planarity : 0.005 0.041 1369 Dihedral : 5.399 58.510 1238 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.06 % Allowed : 13.07 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.27), residues: 988 helix: 0.21 (0.27), residues: 398 sheet: 0.41 (0.43), residues: 152 loop : -0.69 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 473 HIS 0.006 0.001 HIS A 374 PHE 0.012 0.002 PHE A 28 TYR 0.020 0.002 TYR A 385 ARG 0.003 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 6) link_NAG-ASN : angle 3.44226 ( 18) hydrogen bonds : bond 0.04709 ( 348) hydrogen bonds : angle 4.48447 ( 945) link_BETA1-6 : bond 0.00422 ( 1) link_BETA1-6 : angle 1.89491 ( 3) metal coordination : bond 0.00259 ( 2) SS BOND : bond 0.00475 ( 9) SS BOND : angle 1.17581 ( 18) covalent geometry : bond 0.00496 ( 7851) covalent geometry : angle 0.59146 (10701) ********************** 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 93 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8011 (t0) cc_final: 0.7758 (t0) REVERT: A 142 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6648 (pp) REVERT: A 152 MET cc_start: 0.8299 (mmm) cc_final: 0.8075 (mmm) REVERT: A 360 MET cc_start: 0.8364 (ttt) cc_final: 0.8140 (ttt) REVERT: A 484 ILE cc_start: 0.8990 (mm) cc_final: 0.8742 (mt) outliers start: 14 outliers final: 12 residues processed: 89 average time/residue: 0.2179 time to fit residues: 27.7686 Evaluate side-chains 91 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 43 SER 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 42 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 80 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 0.0970 chunk 96 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.183758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.168099 restraints weight = 7926.952| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 0.96 r_work: 0.3534 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7869 Z= 0.108 Angle : 0.515 10.381 10740 Z= 0.260 Chirality : 0.042 0.367 1166 Planarity : 0.004 0.039 1369 Dihedral : 5.001 59.680 1238 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.06 % Allowed : 12.92 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.27), residues: 988 helix: 0.46 (0.27), residues: 401 sheet: 0.52 (0.44), residues: 152 loop : -0.56 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 PHE 0.009 0.001 PHE E 375 TYR 0.015 0.001 TYR A 385 ARG 0.001 0.000 ARG A 161 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 6) link_NAG-ASN : angle 3.16422 ( 18) hydrogen bonds : bond 0.03479 ( 348) hydrogen bonds : angle 4.17842 ( 945) link_BETA1-6 : bond 0.00019 ( 1) link_BETA1-6 : angle 1.52067 ( 3) metal coordination : bond 0.00175 ( 2) SS BOND : bond 0.00298 ( 9) SS BOND : angle 0.78760 ( 18) covalent geometry : bond 0.00246 ( 7851) covalent geometry : angle 0.49778 (10701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4442.03 seconds wall clock time: 78 minutes 17.31 seconds (4697.31 seconds total)