Starting phenix.real_space_refine on Tue Aug 4 21:10:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u4o_63852/08_2026/9u4o_63852_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u4o_63852/08_2026/9u4o_63852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u4o_63852/08_2026/9u4o_63852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u4o_63852/08_2026/9u4o_63852.map" model { file = "/net/cci-nas-00/data/ceres_data/9u4o_63852/08_2026/9u4o_63852_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u4o_63852/08_2026/9u4o_63852_neut.cif" } resolution = 2.77 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4202 2.51 5 N 1072 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6587 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4867 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 567} Conformer: "B" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 567} bond proxies already assigned to first conformer: 4982 Chain: "B" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1530 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 10, 'TRANS': 182} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 34 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 34 " occ=0.50 Time building chain proxies: 2.41, per 1000 atoms: 0.37 Number of scatterers: 6587 At special positions: 0 Unit cell: (77.469, 88.536, 123.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1276 8.00 N 1072 7.00 C 4202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=1.80 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 701 " - " ASN A 103 " " NAG A 702 " - " ASN A 90 " " NAG C 1 " - " ASN A 53 " " NAG D 1 " - " ASN A 546 " " NAG E 1 " - " ASN A 432 " " NAG F 1 " - " ASN A 322 " " NAG G 1 " - " ASN B 343 " Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 523.9 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 8 sheets defined 55.3% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.866A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP A 38 " --> pdb=" O AHIS A 34 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.528A pdb=" N PHE A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.545A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.759A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 170 removed outlier: 4.353A pdb=" N TRP A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 194 removed outlier: 3.782A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.882A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (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 282 removed outlier: 4.366A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.583A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.619A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.622A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.655A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 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 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.040A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.673A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.524A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.585A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.762A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.905A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.171A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.358A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.546A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.546A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.769A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 297 hydrogen bonds defined for protein. 841 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: 1.03 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1084 1.26 - 1.40: 1776 1.40 - 1.54: 3687 1.54 - 1.68: 164 1.68 - 1.81: 58 Bond restraints: 6769 Sorted by residual: bond pdb=" C ILE A 223 " pdb=" O ILE A 223 " ideal model delta sigma weight residual 1.236 1.120 0.116 1.09e-02 8.42e+03 1.14e+02 bond pdb=" C ASP A 213 " pdb=" O ASP A 213 " ideal model delta sigma weight residual 1.234 1.172 0.062 1.19e-02 7.06e+03 2.69e+01 bond pdb=" C LEU A 584 " pdb=" O LEU A 584 " ideal model delta sigma weight residual 1.237 1.180 0.056 1.16e-02 7.43e+03 2.36e+01 bond pdb=" C ALA B 419 " pdb=" O ALA B 419 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.21e-02 6.83e+03 1.99e+01 bond pdb=" CA TYR A 202 " pdb=" C TYR A 202 " ideal model delta sigma weight residual 1.524 1.470 0.055 1.24e-02 6.50e+03 1.94e+01 ... (remaining 6764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 8625 3.53 - 7.06: 526 7.06 - 10.59: 43 10.59 - 14.13: 7 14.13 - 17.66: 2 Bond angle restraints: 9203 Sorted by residual: angle pdb=" O ALA A 396 " pdb=" C ALA A 396 " pdb=" N ASN A 397 " ideal model delta sigma weight residual 122.12 130.18 -8.06 1.06e+00 8.90e-01 5.78e+01 angle pdb=" CA PHE A 588 " pdb=" C PHE A 588 " pdb=" O PHE A 588 " ideal model delta sigma weight residual 119.95 110.91 9.04 1.21e+00 6.83e-01 5.59e+01 angle pdb=" N LEU A 439 " pdb=" CA LEU A 439 " pdb=" C LEU A 439 " ideal model delta sigma weight residual 112.54 103.73 8.81 1.22e+00 6.72e-01 5.21e+01 angle pdb=" N VAL A 293 " pdb=" CA VAL A 293 " pdb=" CB VAL A 293 " ideal model delta sigma weight residual 112.26 103.38 8.88 1.29e+00 6.01e-01 4.74e+01 angle pdb=" N THR A 496 " pdb=" CA THR A 496 " pdb=" C THR A 496 " ideal model delta sigma weight residual 112.72 105.00 7.72 1.14e+00 7.69e-01 4.59e+01 ... (remaining 9198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.77: 3805 18.77 - 37.54: 258 37.54 - 56.31: 60 56.31 - 75.08: 38 75.08 - 93.85: 8 Dihedral angle restraints: 4169 sinusoidal: 1854 harmonic: 2315 Sorted by residual: dihedral pdb=" CD ARG B 355 " pdb=" NE ARG B 355 " pdb=" CZ ARG B 355 " pdb=" NH1 ARG B 355 " ideal model delta sinusoidal sigma weight residual 0.00 -60.89 60.89 1 1.00e+01 1.00e-02 4.93e+01 dihedral pdb=" CD ARG A 518 " pdb=" NE ARG A 518 " pdb=" CZ ARG A 518 " pdb=" NH1 ARG A 518 " ideal model delta sinusoidal sigma weight residual 0.00 60.79 -60.79 1 1.00e+01 1.00e-02 4.91e+01 dihedral pdb=" CD ARG A 192 " pdb=" NE ARG A 192 " pdb=" CZ ARG A 192 " pdb=" NH1 ARG A 192 " ideal model delta sinusoidal sigma weight residual 0.00 -51.72 51.72 1 1.00e+01 1.00e-02 3.65e+01 ... (remaining 4166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.222: 955 0.222 - 0.445: 42 0.445 - 0.667: 5 0.667 - 0.889: 0 0.889 - 1.111: 2 Chirality restraints: 1004 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.15e+01 chirality pdb=" C2 BMA E 3 " pdb=" C1 BMA E 3 " pdb=" C3 BMA E 3 " pdb=" O2 BMA E 3 " both_signs ideal model delta sigma weight residual False 2.47 1.36 1.11 2.00e-01 2.50e+01 3.09e+01 chirality pdb=" C2 BMA F 3 " pdb=" C1 BMA F 3 " pdb=" C3 BMA F 3 " pdb=" O2 BMA F 3 " both_signs ideal model delta sigma weight residual False 2.47 1.36 1.11 2.00e-01 2.50e+01 3.07e+01 ... (remaining 1001 not shown) Planarity restraints: 1182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.321 2.00e-02 2.50e+03 2.78e-01 9.65e+02 pdb=" C7 NAG G 1 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.145 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.495 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 355 " 0.979 9.50e-02 1.11e+02 4.39e-01 1.17e+02 pdb=" NE ARG B 355 " -0.056 2.00e-02 2.50e+03 pdb=" CZ ARG B 355 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 355 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 355 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 518 " 0.959 9.50e-02 1.11e+02 4.30e-01 1.12e+02 pdb=" NE ARG A 518 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 518 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 518 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 518 " 0.025 2.00e-02 2.50e+03 ... (remaining 1179 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 30 2.48 - 3.08: 4705 3.08 - 3.69: 9763 3.69 - 4.29: 15829 4.29 - 4.90: 24728 Nonbonded interactions: 55055 Sorted by model distance: nonbonded pdb=" CG2 THR A 276 " pdb=" CG2 THR A 445 " model vdw 1.874 3.880 nonbonded pdb=" O LEU A 162 " pdb=" CD1 LEU A 162 " model vdw 1.896 3.460 nonbonded pdb=" OD1 ASN B 440 " pdb=" CD1 LEU B 441 " model vdw 2.066 3.460 nonbonded pdb=" OE2 GLU A 22 " pdb=" N GLN A 89 " model vdw 2.216 3.120 nonbonded pdb=" CG ASN B 440 " pdb=" CD1 LEU B 441 " model vdw 2.242 3.690 ... (remaining 55050 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.920 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.830 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.232 6790 Z= 0.958 Angle : 1.964 42.063 9259 Z= 1.343 Chirality : 0.122 1.111 1004 Planarity : 0.030 0.439 1175 Dihedral : 14.906 93.846 2664 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.15 % Allowed : 10.52 % Favored : 88.33 % Cbeta Deviations : 1.35 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.25), residues: 787 helix: -2.63 (0.21), residues: 379 sheet: -0.60 (0.75), residues: 39 loop : -2.18 (0.27), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 161 TYR 0.028 0.002 TYR B 495 PHE 0.021 0.003 PHE A 588 TRP 0.022 0.004 TRP A 163 HIS 0.008 0.002 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.01310 / 0.95 ( 6769) covalent geometry : angle 1.89362 / 1.33 ( 9203) SS BOND : bond 0.08859 / 4.47 ( 7) SS BOND : angle 11.99736 / 6.22 ( 14) hydrogen bonds : bond 0.26809 / 17.41 ( 293) hydrogen bonds : angle 8.64747 / 6.01 ( 841) link_BETA1-4 : bond 0.02477 / 1.56 ( 7) link_BETA1-4 : angle 4.31393 / 2.34 ( 21) link_NAG-ASN : bond 0.00737 / 0.39 ( 7) link_NAG-ASN : angle 3.81139 / 2.49 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 383 MET cc_start: 0.8647 (mtp) cc_final: 0.8444 (mtp) outliers start: 8 outliers final: 0 residues processed: 144 average time/residue: 0.6392 time to fit residues: 96.2999 Evaluate side-chains 74 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 51 ASN A 239 HIS A 277 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS B 487 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.083080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.065828 restraints weight = 24911.893| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.41 r_work: 0.2727 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6790 Z= 0.164 Angle : 0.729 6.933 9259 Z= 0.368 Chirality : 0.046 0.155 1004 Planarity : 0.005 0.040 1175 Dihedral : 8.158 57.852 1147 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.31 % Allowed : 15.56 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.27), residues: 787 helix: -0.54 (0.25), residues: 397 sheet: -0.49 (0.69), residues: 43 loop : -1.65 (0.28), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 169 TYR 0.027 0.002 TYR A 385 PHE 0.019 0.002 PHE A 369 TRP 0.018 0.001 TRP A 478 HIS 0.004 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 6769) covalent geometry : angle 0.70558 / 0.36 ( 9203) SS BOND : bond 0.00740 / 0.41 ( 7) SS BOND : angle 2.05877 / 1.22 ( 14) hydrogen bonds : bond 0.06019 / 4.01 ( 293) hydrogen bonds : angle 5.32129 / 3.69 ( 841) link_BETA1-4 : bond 0.00619 / 0.31 ( 7) link_BETA1-4 : angle 2.76238 / 1.79 ( 21) link_NAG-ASN : bond 0.00499 / 0.34 ( 7) link_NAG-ASN : angle 2.36348 / 1.48 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.258 Fit side-chains REVERT: B 357 ARG cc_start: 0.8768 (mmm-85) cc_final: 0.8202 (ttt-90) REVERT: B 386 LYS cc_start: 0.9159 (tptt) cc_final: 0.8627 (tmmm) REVERT: B 516 GLU cc_start: 0.7633 (tt0) cc_final: 0.7327 (tt0) outliers start: 16 outliers final: 5 residues processed: 94 average time/residue: 0.5738 time to fit residues: 56.8111 Evaluate side-chains 67 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 338 ASN A 374 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 = 0.3104 r_free = 0.3104 target = 0.077800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.061265 restraints weight = 18228.763| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.92 r_work: 0.2645 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6790 Z= 0.184 Angle : 0.670 9.213 9259 Z= 0.338 Chirality : 0.045 0.145 1004 Planarity : 0.004 0.053 1175 Dihedral : 5.998 42.425 1147 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.31 % Allowed : 15.99 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.28), residues: 787 helix: 0.37 (0.26), residues: 398 sheet: -0.14 (0.65), residues: 54 loop : -1.50 (0.28), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 454 TYR 0.029 0.002 TYR A 385 PHE 0.022 0.002 PHE A 369 TRP 0.027 0.001 TRP A 478 HIS 0.005 0.002 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 6769) covalent geometry : angle 0.65184 / 0.33 ( 9203) SS BOND : bond 0.00789 / 0.43 ( 7) SS BOND : angle 1.90223 / 1.13 ( 14) hydrogen bonds : bond 0.05530 / 3.69 ( 293) hydrogen bonds : angle 4.78719 / 3.33 ( 841) link_BETA1-4 : bond 0.00653 / 0.36 ( 7) link_BETA1-4 : angle 2.48076 / 1.58 ( 21) link_NAG-ASN : bond 0.00264 / 0.16 ( 7) link_NAG-ASN : angle 1.77473 / 1.10 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.256 Fit side-chains REVERT: A 137 ASN cc_start: 0.7481 (m-40) cc_final: 0.6593 (p0) REVERT: B 357 ARG cc_start: 0.8888 (mmm-85) cc_final: 0.8622 (ttt-90) REVERT: B 386 LYS cc_start: 0.9189 (tptt) cc_final: 0.8684 (tmmm) REVERT: B 516 GLU cc_start: 0.7971 (tt0) cc_final: 0.7432 (pt0) outliers start: 16 outliers final: 6 residues processed: 80 average time/residue: 0.5569 time to fit residues: 47.0995 Evaluate side-chains 63 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 4.9990 chunk 18 optimal weight: 0.0980 chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.078766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.062440 restraints weight = 16222.616| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.80 r_work: 0.2673 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6790 Z= 0.125 Angle : 0.577 11.065 9259 Z= 0.288 Chirality : 0.042 0.140 1004 Planarity : 0.003 0.048 1175 Dihedral : 5.090 39.910 1147 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.73 % Allowed : 15.99 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.28), residues: 787 helix: 0.87 (0.26), residues: 399 sheet: 0.02 (0.75), residues: 44 loop : -1.28 (0.29), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.024 0.001 TYR B 369 PHE 0.019 0.001 PHE A 369 TRP 0.020 0.001 TRP A 478 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 6769) covalent geometry : angle 0.56375 / 0.28 ( 9203) SS BOND : bond 0.00663 / 0.36 ( 7) SS BOND : angle 1.34329 / 0.81 ( 14) hydrogen bonds : bond 0.04578 / 3.07 ( 293) hydrogen bonds : angle 4.55987 / 3.16 ( 841) link_BETA1-4 : bond 0.00534 / 0.31 ( 7) link_BETA1-4 : angle 1.97516 / 1.24 ( 21) link_NAG-ASN : bond 0.00255 / 0.17 ( 7) link_NAG-ASN : angle 1.59111 / 0.97 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.257 Fit side-chains REVERT: B 340 GLU cc_start: 0.8799 (tt0) cc_final: 0.8571 (pt0) REVERT: B 357 ARG cc_start: 0.8961 (mmm-85) cc_final: 0.8660 (ttt-90) REVERT: B 386 LYS cc_start: 0.9281 (tptt) cc_final: 0.8810 (tmmm) REVERT: B 516 GLU cc_start: 0.8191 (tt0) cc_final: 0.7621 (pt0) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.5790 time to fit residues: 47.0770 Evaluate side-chains 61 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 5 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 0.0970 chunk 18 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN A 526 GLN B 388 ASN B 477 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.079179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.061809 restraints weight = 24647.538| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.41 r_work: 0.2629 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6790 Z= 0.115 Angle : 0.566 8.062 9259 Z= 0.285 Chirality : 0.042 0.137 1004 Planarity : 0.003 0.047 1175 Dihedral : 4.759 38.769 1147 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.16 % Allowed : 15.71 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.29), residues: 787 helix: 1.16 (0.27), residues: 399 sheet: 0.33 (0.77), residues: 44 loop : -1.04 (0.29), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.022 0.001 TYR A 385 PHE 0.018 0.001 PHE A 369 TRP 0.018 0.001 TRP A 478 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 6769) covalent geometry : angle 0.55567 / 0.28 ( 9203) SS BOND : bond 0.00384 / 0.21 ( 7) SS BOND : angle 1.21665 / 0.70 ( 14) hydrogen bonds : bond 0.04285 / 2.87 ( 293) hydrogen bonds : angle 4.41966 / 3.05 ( 841) link_BETA1-4 : bond 0.00417 / 0.24 ( 7) link_BETA1-4 : angle 1.75629 / 1.11 ( 21) link_NAG-ASN : bond 0.00202 / 0.13 ( 7) link_NAG-ASN : angle 1.41172 / 0.88 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.206 Fit side-chains REVERT: A 137 ASN cc_start: 0.7448 (m110) cc_final: 0.6796 (p0) REVERT: B 357 ARG cc_start: 0.8946 (mmm-85) cc_final: 0.8668 (ttt-90) REVERT: B 386 LYS cc_start: 0.9303 (tptt) cc_final: 0.8826 (tmmm) REVERT: B 516 GLU cc_start: 0.8148 (tt0) cc_final: 0.7556 (pt0) outliers start: 15 outliers final: 10 residues processed: 77 average time/residue: 0.5098 time to fit residues: 41.2796 Evaluate side-chains 64 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 55 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 429 GLN A 522 GLN B 388 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.079402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.062437 restraints weight = 17822.593| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.04 r_work: 0.2693 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6790 Z= 0.116 Angle : 0.559 8.766 9259 Z= 0.280 Chirality : 0.042 0.147 1004 Planarity : 0.003 0.044 1175 Dihedral : 4.618 38.554 1147 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.16 % Allowed : 16.57 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.29), residues: 787 helix: 1.19 (0.27), residues: 407 sheet: 0.65 (0.80), residues: 42 loop : -0.93 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.021 0.001 TYR A 385 PHE 0.018 0.001 PHE A 369 TRP 0.017 0.001 TRP A 478 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 6769) covalent geometry : angle 0.54463 / 0.28 ( 9203) SS BOND : bond 0.00679 / 0.36 ( 7) SS BOND : angle 2.13044 / 1.16 ( 14) hydrogen bonds : bond 0.04226 / 2.83 ( 293) hydrogen bonds : angle 4.35972 / 3.01 ( 841) link_BETA1-4 : bond 0.00475 / 0.27 ( 7) link_BETA1-4 : angle 1.68441 / 1.06 ( 21) link_NAG-ASN : bond 0.00174 / 0.11 ( 7) link_NAG-ASN : angle 1.41642 / 0.87 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.264 Fit side-chains REVERT: A 137 ASN cc_start: 0.7476 (m-40) cc_final: 0.6811 (p0) REVERT: B 357 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8688 (ttt-90) REVERT: B 386 LYS cc_start: 0.9166 (tptt) cc_final: 0.8758 (tmmm) REVERT: B 516 GLU cc_start: 0.8352 (tt0) cc_final: 0.7901 (pt0) outliers start: 15 outliers final: 11 residues processed: 72 average time/residue: 0.4697 time to fit residues: 35.5708 Evaluate side-chains 67 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.077079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.060359 restraints weight = 17955.789| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.01 r_work: 0.2605 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6790 Z= 0.144 Angle : 0.574 8.523 9259 Z= 0.288 Chirality : 0.043 0.181 1004 Planarity : 0.004 0.044 1175 Dihedral : 4.505 37.234 1147 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.31 % Allowed : 16.43 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.29), residues: 787 helix: 1.24 (0.27), residues: 407 sheet: 0.74 (0.81), residues: 42 loop : -0.80 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.024 0.001 TYR A 385 PHE 0.021 0.001 PHE A 369 TRP 0.022 0.001 TRP A 478 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 6769) covalent geometry : angle 0.56233 / 0.28 ( 9203) SS BOND : bond 0.00378 / 0.21 ( 7) SS BOND : angle 1.83167 / 1.01 ( 14) hydrogen bonds : bond 0.04595 / 3.07 ( 293) hydrogen bonds : angle 4.28892 / 3.00 ( 841) link_BETA1-4 : bond 0.00482 / 0.28 ( 7) link_BETA1-4 : angle 1.61145 / 1.01 ( 21) link_NAG-ASN : bond 0.00196 / 0.11 ( 7) link_NAG-ASN : angle 1.44045 / 0.91 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.150 Fit side-chains REVERT: A 137 ASN cc_start: 0.7624 (m-40) cc_final: 0.6953 (p0) REVERT: A 455 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.9088 (tmm) REVERT: B 357 ARG cc_start: 0.8947 (mmm-85) cc_final: 0.8494 (ttt90) REVERT: B 386 LYS cc_start: 0.9262 (tptt) cc_final: 0.8892 (tmmm) REVERT: B 516 GLU cc_start: 0.8289 (tt0) cc_final: 0.7741 (pt0) outliers start: 16 outliers final: 11 residues processed: 74 average time/residue: 0.5016 time to fit residues: 38.9358 Evaluate side-chains 68 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 60 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.078421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.061695 restraints weight = 19669.513| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.07 r_work: 0.2682 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6790 Z= 0.112 Angle : 0.560 7.589 9259 Z= 0.282 Chirality : 0.042 0.185 1004 Planarity : 0.003 0.043 1175 Dihedral : 4.365 36.585 1147 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.87 % Allowed : 16.86 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.30), residues: 787 helix: 1.36 (0.27), residues: 407 sheet: 0.62 (0.81), residues: 42 loop : -0.68 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.025 0.001 TYR B 369 PHE 0.017 0.001 PHE A 369 TRP 0.016 0.001 TRP A 478 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 6769) covalent geometry : angle 0.55020 / 0.28 ( 9203) SS BOND : bond 0.00323 / 0.18 ( 7) SS BOND : angle 1.51882 / 0.84 ( 14) hydrogen bonds : bond 0.04152 / 2.79 ( 293) hydrogen bonds : angle 4.23121 / 2.95 ( 841) link_BETA1-4 : bond 0.00511 / 0.30 ( 7) link_BETA1-4 : angle 1.51276 / 0.96 ( 21) link_NAG-ASN : bond 0.00180 / 0.11 ( 7) link_NAG-ASN : angle 1.31929 / 0.82 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.236 Fit side-chains REVERT: A 137 ASN cc_start: 0.7414 (m-40) cc_final: 0.6697 (p0) REVERT: B 357 ARG cc_start: 0.8923 (mmm-85) cc_final: 0.8665 (ttt-90) REVERT: B 386 LYS cc_start: 0.9258 (tptt) cc_final: 0.8883 (tmmm) REVERT: B 516 GLU cc_start: 0.8288 (tt0) cc_final: 0.8001 (pt0) outliers start: 13 outliers final: 9 residues processed: 66 average time/residue: 0.5444 time to fit residues: 37.8261 Evaluate side-chains 64 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.077807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.061161 restraints weight = 17728.953| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.01 r_work: 0.2622 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6790 Z= 0.123 Angle : 0.550 6.879 9259 Z= 0.278 Chirality : 0.042 0.201 1004 Planarity : 0.003 0.044 1175 Dihedral : 4.305 38.787 1147 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.73 % Allowed : 17.44 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.30), residues: 787 helix: 1.50 (0.27), residues: 402 sheet: 0.69 (0.83), residues: 42 loop : -0.62 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.024 0.001 TYR B 369 PHE 0.019 0.001 PHE A 369 TRP 0.018 0.001 TRP A 478 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 6769) covalent geometry : angle 0.54007 / 0.28 ( 9203) SS BOND : bond 0.00336 / 0.18 ( 7) SS BOND : angle 1.44630 / 0.81 ( 14) hydrogen bonds : bond 0.04266 / 2.86 ( 293) hydrogen bonds : angle 4.20948 / 2.94 ( 841) link_BETA1-4 : bond 0.00484 / 0.28 ( 7) link_BETA1-4 : angle 1.51071 / 0.95 ( 21) link_NAG-ASN : bond 0.00161 / 0.09 ( 7) link_NAG-ASN : angle 1.34283 / 0.84 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.221 Fit side-chains REVERT: A 137 ASN cc_start: 0.7305 (m-40) cc_final: 0.6553 (p0) REVERT: B 357 ARG cc_start: 0.8944 (mmm-85) cc_final: 0.8702 (ttt-90) REVERT: B 386 LYS cc_start: 0.9262 (tptt) cc_final: 0.8844 (tmmm) REVERT: B 516 GLU cc_start: 0.8346 (tt0) cc_final: 0.7913 (pt0) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.4886 time to fit residues: 33.3872 Evaluate side-chains 61 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 0.0570 chunk 14 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 76 optimal weight: 0.0870 chunk 39 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 overall best weight: 0.3874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.078871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.061705 restraints weight = 22296.798| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.34 r_work: 0.2675 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6790 Z= 0.109 Angle : 0.566 11.949 9259 Z= 0.281 Chirality : 0.041 0.186 1004 Planarity : 0.003 0.040 1175 Dihedral : 4.217 37.997 1147 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.30 % Allowed : 18.16 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.30), residues: 787 helix: 1.60 (0.27), residues: 401 sheet: 0.61 (0.82), residues: 42 loop : -0.55 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.023 0.001 TYR B 369 PHE 0.017 0.001 PHE A 369 TRP 0.016 0.001 TRP A 478 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 6769) covalent geometry : angle 0.55773 / 0.28 ( 9203) SS BOND : bond 0.00297 / 0.16 ( 7) SS BOND : angle 1.33622 / 0.75 ( 14) hydrogen bonds : bond 0.03946 / 2.66 ( 293) hydrogen bonds : angle 4.15973 / 2.91 ( 841) link_BETA1-4 : bond 0.00496 / 0.29 ( 7) link_BETA1-4 : angle 1.44370 / 0.91 ( 21) link_NAG-ASN : bond 0.00157 / 0.09 ( 7) link_NAG-ASN : angle 1.27670 / 0.79 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.185 Fit side-chains REVERT: A 137 ASN cc_start: 0.7229 (m-40) cc_final: 0.6456 (p0) REVERT: B 357 ARG cc_start: 0.8965 (mmm-85) cc_final: 0.8714 (ttt-90) REVERT: B 386 LYS cc_start: 0.9283 (tptt) cc_final: 0.8835 (tmmm) REVERT: B 516 GLU cc_start: 0.8409 (tt0) cc_final: 0.8099 (pt0) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.5156 time to fit residues: 33.6136 Evaluate side-chains 60 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.0170 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.0050 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.7434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.061419 restraints weight = 15289.341| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.72 r_work: 0.2691 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6790 Z= 0.133 Angle : 0.571 9.833 9259 Z= 0.285 Chirality : 0.042 0.204 1004 Planarity : 0.004 0.040 1175 Dihedral : 4.237 37.643 1147 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.15 % Allowed : 18.59 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.30), residues: 787 helix: 1.62 (0.26), residues: 401 sheet: 0.77 (0.83), residues: 42 loop : -0.49 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.024 0.001 TYR A 385 PHE 0.019 0.001 PHE A 369 TRP 0.021 0.001 TRP A 478 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 6769) covalent geometry : angle 0.56226 / 0.28 ( 9203) SS BOND : bond 0.00356 / 0.20 ( 7) SS BOND : angle 1.45093 / 0.81 ( 14) hydrogen bonds : bond 0.04293 / 2.88 ( 293) hydrogen bonds : angle 4.17132 / 2.92 ( 841) link_BETA1-4 : bond 0.00460 / 0.27 ( 7) link_BETA1-4 : angle 1.47396 / 0.93 ( 21) link_NAG-ASN : bond 0.00182 / 0.10 ( 7) link_NAG-ASN : angle 1.34988 / 0.85 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2151.77 seconds wall clock time: 37 minutes 19.67 seconds (2239.67 seconds total)