Starting phenix.real_space_refine on Thu Jul 24 16:17:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9e_35268/07_2025/8i9e_35268.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9e_35268/07_2025/8i9e_35268.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/8i9e_35268/07_2025/8i9e_35268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9e_35268/07_2025/8i9e_35268.map" model { file = "/net/cci-nas-00/data/ceres_data/8i9e_35268/07_2025/8i9e_35268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9e_35268/07_2025/8i9e_35268.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= 0.000 sd= 0.002 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 33 5.16 5 C 4107 2.51 5 N 1050 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6421 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "E" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1369 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 8, 'TRANS': 158} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: "F" 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: "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: "H" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.28, per 1000 atoms: 1.13 Number of scatterers: 6421 At special positions: 0 Unit cell: (105.12, 87.6, 107.31, 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 33 16.00 O 1231 8.00 N 1050 7.00 C 4107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.02 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 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 B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 701 " - " ASN A 322 " " NAG B 1 " - " ASN A 53 " " NAG C 1 " - " ASN A 90 " " NAG D 1 " - " ASN A 103 " " NAG F 1 " - " ASN A 432 " " NAG G 1 " - " ASN A 546 " " NAG H 1 " - " ASN E 343 " Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 2.1 seconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 5 sheets defined 50.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 21 through 52 removed outlier: 3.560A pdb=" N LYS A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 80 removed outlier: 4.208A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.537A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 4.213A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 231 removed outlier: 4.089A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.951A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.862A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 305 through 319 removed outlier: 3.796A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.523A pdb=" N ASN A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 4.107A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.677A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.275A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 4.087A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.963A 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 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.163A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.665A 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: 3.813A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.912A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'E' and resid 339 through 344 removed outlier: 4.144A pdb=" N ASN E 343 " --> pdb=" O ASP E 339 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 344 " --> pdb=" O GLU E 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 339 through 344' Processing helix chain 'E' and resid 365 through 370 removed outlier: 4.227A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 370' Processing helix chain 'E' and resid 406 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.774A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.004A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 357 through 358 removed outlier: 3.609A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474 254 hydrogen bonds defined for protein. 729 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: 2.02 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2016 1.34 - 1.45: 1252 1.45 - 1.57: 3277 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 6599 Sorted by residual: bond pdb=" C ASN A 137 " pdb=" N PRO A 138 " ideal model delta sigma weight residual 1.334 1.314 0.020 8.40e-03 1.42e+04 5.68e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.23e+00 bond pdb=" CA ASN E 343 " pdb=" CB ASN E 343 " ideal model delta sigma weight residual 1.531 1.554 -0.023 1.51e-02 4.39e+03 2.40e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 ... (remaining 6594 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 8376 1.41 - 2.82: 498 2.82 - 4.23: 67 4.23 - 5.64: 14 5.64 - 7.05: 5 Bond angle restraints: 8960 Sorted by residual: angle pdb=" N CYS A 133 " pdb=" CA CYS A 133 " pdb=" C CYS A 133 " ideal model delta sigma weight residual 109.85 115.18 -5.33 1.58e+00 4.01e-01 1.14e+01 angle pdb=" N SER A 331 " pdb=" CA SER A 331 " pdb=" C SER A 331 " ideal model delta sigma weight residual 110.50 114.99 -4.49 1.41e+00 5.03e-01 1.02e+01 angle pdb=" N ASN A 149 " pdb=" CA ASN A 149 " pdb=" C ASN A 149 " ideal model delta sigma weight residual 113.02 109.81 3.21 1.20e+00 6.94e-01 7.18e+00 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 113.18 106.96 6.22 2.37e+00 1.78e-01 6.90e+00 angle pdb=" CA PRO A 146 " pdb=" C PRO A 146 " pdb=" O PRO A 146 " ideal model delta sigma weight residual 123.07 119.70 3.37 1.38e+00 5.25e-01 5.95e+00 ... (remaining 8955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 3494 17.38 - 34.76: 398 34.76 - 52.14: 118 52.14 - 69.52: 30 69.52 - 86.90: 6 Dihedral angle restraints: 4046 sinusoidal: 1803 harmonic: 2243 Sorted by residual: dihedral pdb=" CA VAL E 341 " pdb=" C VAL E 341 " pdb=" N PHE E 342 " pdb=" CA PHE E 342 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual -86.00 -46.70 -39.30 1 1.00e+01 1.00e-02 2.17e+01 dihedral pdb=" CA PHE E 490 " pdb=" C PHE E 490 " pdb=" N PRO E 491 " pdb=" CA PRO E 491 " ideal model delta harmonic sigma weight residual -180.00 -162.31 -17.69 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 4043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 872 0.085 - 0.170: 89 0.170 - 0.255: 3 0.255 - 0.339: 0 0.339 - 0.424: 2 Chirality restraints: 966 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" C4 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O4 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.29 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 963 not shown) Planarity restraints: 1150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 583 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 428 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C PHE A 428 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE A 428 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 429 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " -0.029 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO A 235 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.024 5.00e-02 4.00e+02 ... (remaining 1147 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1786 2.79 - 3.32: 5522 3.32 - 3.85: 9679 3.85 - 4.37: 11320 4.37 - 4.90: 20040 Nonbonded interactions: 48347 Sorted by model distance: nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR E 500 " model vdw 2.266 3.040 nonbonded pdb=" N ASP A 136 " pdb=" OD1 ASP A 136 " model vdw 2.304 3.120 nonbonded pdb=" N GLU A 430 " pdb=" OE1 GLU A 430 " model vdw 2.305 3.120 nonbonded pdb=" OG SER E 438 " pdb=" OD2 ASP E 442 " model vdw 2.315 3.040 nonbonded pdb=" O SER A 19 " pdb=" OG SER A 19 " model vdw 2.332 3.040 ... (remaining 48342 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 212.980 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 28.780 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 245.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.008 0.054 6617 Z= 0.353 Angle : 0.803 15.888 9009 Z= 0.421 Chirality : 0.054 0.424 966 Planarity : 0.004 0.050 1143 Dihedral : 16.266 86.905 2591 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 4.76 % Allowed : 16.37 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.37 (0.27), residues: 756 helix: -1.00 (0.26), residues: 353 sheet: -1.92 (0.70), residues: 41 loop : -3.68 (0.27), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 478 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.002 PHE A 274 TYR 0.017 0.002 TYR A 183 ARG 0.004 0.001 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 7) link_NAG-ASN : angle 3.83100 ( 21) link_BETA1-4 : bond 0.00460 ( 6) link_BETA1-4 : angle 3.24740 ( 18) hydrogen bonds : bond 0.17042 ( 254) hydrogen bonds : angle 5.42719 ( 729) SS BOND : bond 0.00882 ( 5) SS BOND : angle 5.98368 ( 10) covalent geometry : bond 0.00837 ( 6599) covalent geometry : angle 0.74313 ( 8960) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 416 LYS cc_start: 0.8423 (tppt) cc_final: 0.7528 (tptt) REVERT: E 353 TRP cc_start: 0.8192 (OUTLIER) cc_final: 0.7517 (p-90) REVERT: E 423 TYR cc_start: 0.8252 (t80) cc_final: 0.7702 (t80) REVERT: E 471 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7165 (tt0) outliers start: 32 outliers final: 20 residues processed: 96 average time/residue: 0.2285 time to fit residues: 30.8394 Evaluate side-chains 83 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 353 TRP Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 483 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 19 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 210 ASN A 239 HIS A 437 ASN A 472 GLN A 493 HIS A 505 HIS E 477 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.115105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.084258 restraints weight = 9030.234| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.55 r_work: 0.2784 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6617 Z= 0.122 Angle : 0.622 12.549 9009 Z= 0.301 Chirality : 0.045 0.296 966 Planarity : 0.004 0.038 1143 Dihedral : 8.303 57.617 1142 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.12 % Allowed : 18.60 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.89 (0.30), residues: 756 helix: 0.33 (0.29), residues: 348 sheet: -1.17 (0.74), residues: 41 loop : -2.99 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.011 0.001 PHE E 374 TYR 0.009 0.001 TYR A 158 ARG 0.002 0.000 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 7) link_NAG-ASN : angle 3.67969 ( 21) link_BETA1-4 : bond 0.00415 ( 6) link_BETA1-4 : angle 2.62605 ( 18) hydrogen bonds : bond 0.05418 ( 254) hydrogen bonds : angle 4.11663 ( 729) SS BOND : bond 0.00643 ( 5) SS BOND : angle 2.27495 ( 10) covalent geometry : bond 0.00265 ( 6599) covalent geometry : angle 0.58094 ( 8960) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 1.405 Fit side-chains REVERT: A 190 MET cc_start: 0.8632 (tmm) cc_final: 0.8388 (tmm) REVERT: A 416 LYS cc_start: 0.8504 (tppt) cc_final: 0.7593 (tptt) REVERT: A 480 MET cc_start: 0.8984 (mtp) cc_final: 0.8733 (mtm) REVERT: E 423 TYR cc_start: 0.8474 (t80) cc_final: 0.7903 (t80) REVERT: E 471 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7343 (mm-30) outliers start: 21 outliers final: 14 residues processed: 81 average time/residue: 0.2216 time to fit residues: 26.8721 Evaluate side-chains 74 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 483 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 0.0570 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 chunk 30 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 HIS A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.116573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.085480 restraints weight = 9132.243| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.57 r_work: 0.2803 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6617 Z= 0.111 Angle : 0.587 12.515 9009 Z= 0.281 Chirality : 0.044 0.291 966 Planarity : 0.004 0.033 1143 Dihedral : 6.937 57.231 1117 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.83 % Allowed : 18.90 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.30), residues: 756 helix: 0.76 (0.29), residues: 354 sheet: -0.76 (0.75), residues: 41 loop : -2.69 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.003 0.001 HIS A 374 PHE 0.011 0.001 PHE A 315 TYR 0.008 0.001 TYR A 183 ARG 0.001 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 7) link_NAG-ASN : angle 3.73920 ( 21) link_BETA1-4 : bond 0.00417 ( 6) link_BETA1-4 : angle 2.44883 ( 18) hydrogen bonds : bond 0.04703 ( 254) hydrogen bonds : angle 3.90764 ( 729) SS BOND : bond 0.00782 ( 5) SS BOND : angle 1.80296 ( 10) covalent geometry : bond 0.00245 ( 6599) covalent geometry : angle 0.54545 ( 8960) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.737 Fit side-chains REVERT: A 190 MET cc_start: 0.8636 (tmm) cc_final: 0.8386 (tmm) REVERT: A 416 LYS cc_start: 0.8528 (tppt) cc_final: 0.7592 (tptt) REVERT: A 480 MET cc_start: 0.8987 (mtp) cc_final: 0.8744 (mtm) REVERT: A 489 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: A 494 ASP cc_start: 0.8199 (p0) cc_final: 0.7951 (p0) REVERT: E 423 TYR cc_start: 0.8483 (t80) cc_final: 0.7847 (t80) REVERT: E 471 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7269 (mm-30) outliers start: 19 outliers final: 15 residues processed: 85 average time/residue: 0.2073 time to fit residues: 26.1842 Evaluate side-chains 77 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 483 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.0030 chunk 26 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.090772 restraints weight = 9178.498| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.55 r_work: 0.2806 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6617 Z= 0.107 Angle : 0.568 12.556 9009 Z= 0.270 Chirality : 0.043 0.290 966 Planarity : 0.003 0.031 1143 Dihedral : 6.324 57.716 1115 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.12 % Allowed : 20.09 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.92 (0.31), residues: 756 helix: 1.05 (0.29), residues: 354 sheet: -0.54 (0.75), residues: 41 loop : -2.45 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 417 PHE 0.010 0.001 PHE A 315 TYR 0.008 0.001 TYR A 41 ARG 0.002 0.000 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 7) link_NAG-ASN : angle 3.74025 ( 21) link_BETA1-4 : bond 0.00433 ( 6) link_BETA1-4 : angle 2.34897 ( 18) hydrogen bonds : bond 0.04300 ( 254) hydrogen bonds : angle 3.75876 ( 729) SS BOND : bond 0.00273 ( 5) SS BOND : angle 1.65186 ( 10) covalent geometry : bond 0.00240 ( 6599) covalent geometry : angle 0.52675 ( 8960) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.981 Fit side-chains REVERT: A 190 MET cc_start: 0.8591 (tmm) cc_final: 0.8348 (tmm) REVERT: A 416 LYS cc_start: 0.8438 (tppt) cc_final: 0.7490 (tptt) REVERT: A 480 MET cc_start: 0.8951 (mtp) cc_final: 0.8707 (mtm) REVERT: A 489 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.7718 (pm20) REVERT: A 494 ASP cc_start: 0.8135 (p0) cc_final: 0.7892 (p0) REVERT: E 423 TYR cc_start: 0.8432 (t80) cc_final: 0.7727 (t80) REVERT: E 471 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7156 (mm-30) outliers start: 21 outliers final: 18 residues processed: 88 average time/residue: 0.3390 time to fit residues: 42.4107 Evaluate side-chains 86 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 483 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 4 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 26 optimal weight: 0.0670 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.123109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.092949 restraints weight = 9066.897| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.46 r_work: 0.2780 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6617 Z= 0.112 Angle : 0.562 12.560 9009 Z= 0.267 Chirality : 0.044 0.285 966 Planarity : 0.003 0.031 1143 Dihedral : 6.112 57.528 1112 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.27 % Allowed : 20.68 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.31), residues: 756 helix: 1.19 (0.29), residues: 354 sheet: -0.40 (0.77), residues: 41 loop : -2.31 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 374 PHE 0.009 0.001 PHE A 315 TYR 0.009 0.001 TYR A 183 ARG 0.002 0.000 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 7) link_NAG-ASN : angle 3.73333 ( 21) link_BETA1-4 : bond 0.00397 ( 6) link_BETA1-4 : angle 2.29888 ( 18) hydrogen bonds : bond 0.04370 ( 254) hydrogen bonds : angle 3.70772 ( 729) SS BOND : bond 0.00518 ( 5) SS BOND : angle 1.68029 ( 10) covalent geometry : bond 0.00257 ( 6599) covalent geometry : angle 0.52046 ( 8960) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.937 Fit side-chains REVERT: A 190 MET cc_start: 0.8493 (tmm) cc_final: 0.8210 (tmm) REVERT: A 416 LYS cc_start: 0.8429 (tppt) cc_final: 0.7468 (tptt) REVERT: A 480 MET cc_start: 0.8890 (mtp) cc_final: 0.8654 (mtm) REVERT: A 489 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: A 494 ASP cc_start: 0.8014 (p0) cc_final: 0.7782 (p0) REVERT: E 423 TYR cc_start: 0.8411 (t80) cc_final: 0.7751 (t80) REVERT: E 471 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7130 (mm-30) outliers start: 22 outliers final: 17 residues processed: 84 average time/residue: 0.2432 time to fit residues: 29.9327 Evaluate side-chains 84 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 483 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 32 optimal weight: 8.9990 chunk 71 optimal weight: 0.0370 chunk 72 optimal weight: 3.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.122680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.092353 restraints weight = 9029.598| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.51 r_work: 0.2813 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6617 Z= 0.107 Angle : 0.554 12.540 9009 Z= 0.263 Chirality : 0.043 0.282 966 Planarity : 0.003 0.033 1143 Dihedral : 5.925 57.662 1111 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.02 % Allowed : 20.54 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.70 (0.31), residues: 756 helix: 1.15 (0.29), residues: 368 sheet: -0.54 (0.77), residues: 41 loop : -2.37 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 374 PHE 0.009 0.001 PHE A 315 TYR 0.009 0.001 TYR A 183 ARG 0.001 0.000 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 7) link_NAG-ASN : angle 3.72936 ( 21) link_BETA1-4 : bond 0.00415 ( 6) link_BETA1-4 : angle 2.26275 ( 18) hydrogen bonds : bond 0.04240 ( 254) hydrogen bonds : angle 3.67673 ( 729) SS BOND : bond 0.00628 ( 5) SS BOND : angle 1.75485 ( 10) covalent geometry : bond 0.00242 ( 6599) covalent geometry : angle 0.51189 ( 8960) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.786 Fit side-chains REVERT: A 190 MET cc_start: 0.8537 (tmm) cc_final: 0.8253 (tmm) REVERT: A 416 LYS cc_start: 0.8427 (tppt) cc_final: 0.7489 (tptt) REVERT: A 480 MET cc_start: 0.8911 (mtp) cc_final: 0.8669 (mtm) REVERT: A 489 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.7697 (pm20) REVERT: A 494 ASP cc_start: 0.8082 (p0) cc_final: 0.7851 (p0) REVERT: E 423 TYR cc_start: 0.8435 (t80) cc_final: 0.7773 (t80) REVERT: E 471 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7137 (mm-30) outliers start: 27 outliers final: 21 residues processed: 88 average time/residue: 0.1357 time to fit residues: 17.6170 Evaluate side-chains 88 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 483 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3292 r_free = 0.3292 target = 0.117986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.087249 restraints weight = 9118.735| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.46 r_work: 0.2692 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6617 Z= 0.122 Angle : 0.563 12.497 9009 Z= 0.268 Chirality : 0.044 0.282 966 Planarity : 0.003 0.034 1143 Dihedral : 5.885 57.400 1111 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.17 % Allowed : 20.83 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.31), residues: 756 helix: 1.36 (0.29), residues: 360 sheet: -0.56 (0.78), residues: 41 loop : -2.15 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.010 0.001 PHE A 327 TYR 0.010 0.001 TYR A 183 ARG 0.001 0.000 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 7) link_NAG-ASN : angle 3.72422 ( 21) link_BETA1-4 : bond 0.00390 ( 6) link_BETA1-4 : angle 2.24547 ( 18) hydrogen bonds : bond 0.04530 ( 254) hydrogen bonds : angle 3.68216 ( 729) SS BOND : bond 0.00469 ( 5) SS BOND : angle 1.76774 ( 10) covalent geometry : bond 0.00285 ( 6599) covalent geometry : angle 0.52193 ( 8960) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.688 Fit side-chains REVERT: A 190 MET cc_start: 0.8471 (tmm) cc_final: 0.8185 (tmm) REVERT: A 416 LYS cc_start: 0.8458 (tppt) cc_final: 0.7495 (tptt) REVERT: A 480 MET cc_start: 0.8837 (mtp) cc_final: 0.8571 (mtm) REVERT: A 489 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: A 494 ASP cc_start: 0.8026 (p0) cc_final: 0.7784 (p0) REVERT: E 423 TYR cc_start: 0.8396 (t80) cc_final: 0.7874 (t80) REVERT: E 471 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7130 (mm-30) outliers start: 28 outliers final: 23 residues processed: 89 average time/residue: 0.1351 time to fit residues: 17.6879 Evaluate side-chains 90 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 483 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.117275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.086699 restraints weight = 9090.549| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.44 r_work: 0.2751 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6617 Z= 0.123 Angle : 0.569 12.471 9009 Z= 0.270 Chirality : 0.044 0.284 966 Planarity : 0.003 0.034 1143 Dihedral : 5.861 57.405 1111 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.87 % Allowed : 21.28 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.31), residues: 756 helix: 1.41 (0.29), residues: 359 sheet: -0.55 (0.79), residues: 41 loop : -2.11 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.010 0.001 PHE A 327 TYR 0.010 0.001 TYR A 183 ARG 0.001 0.000 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 7) link_NAG-ASN : angle 3.71851 ( 21) link_BETA1-4 : bond 0.00411 ( 6) link_BETA1-4 : angle 2.25762 ( 18) hydrogen bonds : bond 0.04509 ( 254) hydrogen bonds : angle 3.68096 ( 729) SS BOND : bond 0.00585 ( 5) SS BOND : angle 1.90127 ( 10) covalent geometry : bond 0.00289 ( 6599) covalent geometry : angle 0.52823 ( 8960) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.745 Fit side-chains REVERT: A 190 MET cc_start: 0.8493 (tmm) cc_final: 0.8203 (tmm) REVERT: A 416 LYS cc_start: 0.8432 (tppt) cc_final: 0.7488 (tptt) REVERT: A 480 MET cc_start: 0.8846 (mtp) cc_final: 0.8574 (mtm) REVERT: A 489 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: A 494 ASP cc_start: 0.8025 (p0) cc_final: 0.7771 (p0) REVERT: E 423 TYR cc_start: 0.8478 (t80) cc_final: 0.7892 (t80) REVERT: E 471 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7108 (mm-30) outliers start: 26 outliers final: 22 residues processed: 87 average time/residue: 0.1465 time to fit residues: 18.5670 Evaluate side-chains 88 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 171 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 483 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 51 optimal weight: 0.0570 chunk 17 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 61 optimal weight: 0.0670 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 0.0060 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 overall best weight: 0.2652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.124800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.094582 restraints weight = 9149.855| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.49 r_work: 0.2824 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6617 Z= 0.093 Angle : 0.568 12.507 9009 Z= 0.270 Chirality : 0.043 0.285 966 Planarity : 0.003 0.033 1143 Dihedral : 5.674 58.429 1111 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.98 % Allowed : 22.47 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.31), residues: 756 helix: 1.52 (0.29), residues: 359 sheet: -0.55 (0.79), residues: 41 loop : -2.03 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.002 0.001 HIS A 374 PHE 0.010 0.001 PHE A 315 TYR 0.007 0.001 TYR A 41 ARG 0.002 0.000 ARG A 161 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 7) link_NAG-ASN : angle 3.66319 ( 21) link_BETA1-4 : bond 0.00449 ( 6) link_BETA1-4 : angle 2.20155 ( 18) hydrogen bonds : bond 0.03545 ( 254) hydrogen bonds : angle 3.57972 ( 729) SS BOND : bond 0.00472 ( 5) SS BOND : angle 3.17747 ( 10) covalent geometry : bond 0.00197 ( 6599) covalent geometry : angle 0.52097 ( 8960) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.680 Fit side-chains REVERT: A 190 MET cc_start: 0.8491 (tmm) cc_final: 0.8226 (tmm) REVERT: A 416 LYS cc_start: 0.8349 (tppt) cc_final: 0.7455 (tptt) REVERT: A 480 MET cc_start: 0.8899 (mtp) cc_final: 0.8674 (mtm) REVERT: E 423 TYR cc_start: 0.8478 (t80) cc_final: 0.7906 (t80) REVERT: E 471 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7043 (mm-30) outliers start: 20 outliers final: 19 residues processed: 86 average time/residue: 0.1382 time to fit residues: 17.4942 Evaluate side-chains 86 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 60 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.122878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.092657 restraints weight = 9197.466| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.46 r_work: 0.2704 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6617 Z= 0.126 Angle : 0.586 12.470 9009 Z= 0.280 Chirality : 0.045 0.282 966 Planarity : 0.003 0.034 1143 Dihedral : 5.661 57.357 1110 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.83 % Allowed : 22.32 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.31), residues: 756 helix: 1.42 (0.29), residues: 367 sheet: -0.50 (0.81), residues: 41 loop : -2.08 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.009 0.001 PHE A 315 TYR 0.010 0.001 TYR A 183 ARG 0.001 0.000 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 7) link_NAG-ASN : angle 3.67982 ( 21) link_BETA1-4 : bond 0.00402 ( 6) link_BETA1-4 : angle 2.16116 ( 18) hydrogen bonds : bond 0.04155 ( 254) hydrogen bonds : angle 3.61234 ( 729) SS BOND : bond 0.00405 ( 5) SS BOND : angle 3.57749 ( 10) covalent geometry : bond 0.00298 ( 6599) covalent geometry : angle 0.53840 ( 8960) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.672 Fit side-chains REVERT: A 190 MET cc_start: 0.8432 (tmm) cc_final: 0.8145 (tmm) REVERT: A 416 LYS cc_start: 0.8401 (tppt) cc_final: 0.7427 (tptt) REVERT: A 480 MET cc_start: 0.8812 (mtp) cc_final: 0.8562 (mtm) REVERT: E 423 TYR cc_start: 0.8396 (t80) cc_final: 0.7956 (t80) REVERT: E 471 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7114 (mm-30) outliers start: 19 outliers final: 18 residues processed: 79 average time/residue: 0.1388 time to fit residues: 16.1588 Evaluate side-chains 82 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 483 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 53 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 26 optimal weight: 0.0370 chunk 70 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 28 optimal weight: 0.0470 chunk 5 optimal weight: 0.6980 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.124093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.093838 restraints weight = 9303.224| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.52 r_work: 0.2725 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6617 Z= 0.092 Angle : 0.567 12.473 9009 Z= 0.270 Chirality : 0.043 0.284 966 Planarity : 0.003 0.036 1143 Dihedral : 5.447 58.332 1107 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.38 % Allowed : 22.62 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.31), residues: 756 helix: 1.55 (0.29), residues: 363 sheet: -0.44 (0.81), residues: 41 loop : -2.00 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.002 0.001 HIS A 374 PHE 0.010 0.001 PHE A 315 TYR 0.010 0.001 TYR E 380 ARG 0.001 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 7) link_NAG-ASN : angle 3.67663 ( 21) link_BETA1-4 : bond 0.00417 ( 6) link_BETA1-4 : angle 2.16030 ( 18) hydrogen bonds : bond 0.03750 ( 254) hydrogen bonds : angle 3.57909 ( 729) SS BOND : bond 0.00509 ( 5) SS BOND : angle 3.34530 ( 10) covalent geometry : bond 0.00194 ( 6599) covalent geometry : angle 0.51938 ( 8960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5109.39 seconds wall clock time: 94 minutes 19.90 seconds (5659.90 seconds total)