Starting phenix.real_space_refine on Fri Aug 22 17:26:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9e_35268/08_2025/8i9e_35268.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9e_35268/08_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_35268/08_2025/8i9e_35268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9e_35268/08_2025/8i9e_35268.map" model { file = "/net/cci-nas-00/data/ceres_data/8i9e_35268/08_2025/8i9e_35268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9e_35268/08_2025/8i9e_35268.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.65, per 1000 atoms: 0.26 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: 0.59 Conformation dependent library (CDL) restraints added in 347.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.21 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: 0.91 Time building geometry restraints manager: 0.76 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: 1.530 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.660 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.680 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.004 0.001 ARG A 245 TYR 0.017 0.002 TYR A 183 PHE 0.012 0.002 PHE A 274 TRP 0.012 0.002 TRP A 478 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00837 ( 6599) covalent geometry : angle 0.74313 ( 8960) SS BOND : bond 0.00882 ( 5) SS BOND : angle 5.98368 ( 10) hydrogen bonds : bond 0.17042 ( 254) hydrogen bonds : angle 5.42719 ( 729) link_BETA1-4 : bond 0.00460 ( 6) link_BETA1-4 : angle 3.24740 ( 18) link_NAG-ASN : bond 0.00523 ( 7) link_NAG-ASN : angle 3.83100 ( 21) *********************** 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 : 0.243 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: 0.0722 time to fit residues: 9.7103 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 : 0.253 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3255 r_free = 0.3255 target = 0.115197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.084320 restraints weight = 9157.581| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.57 r_work: 0.2784 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 0.036 6617 Z= 0.119 Angle : 0.621 12.380 9009 Z= 0.300 Chirality : 0.045 0.294 966 Planarity : 0.004 0.037 1143 Dihedral : 8.309 57.564 1142 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.12 % Allowed : 18.45 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.30), residues: 756 helix: 0.34 (0.29), residues: 348 sheet: -1.18 (0.73), residues: 41 loop : -2.99 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 245 TYR 0.008 0.001 TYR A 158 PHE 0.011 0.001 PHE E 377 TRP 0.010 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6599) covalent geometry : angle 0.58149 ( 8960) SS BOND : bond 0.00350 ( 5) SS BOND : angle 2.15510 ( 10) hydrogen bonds : bond 0.05352 ( 254) hydrogen bonds : angle 4.11937 ( 729) link_BETA1-4 : bond 0.00483 ( 6) link_BETA1-4 : angle 2.56361 ( 18) link_NAG-ASN : bond 0.00517 ( 7) link_NAG-ASN : angle 3.65866 ( 21) *********************** 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 : 0.234 Fit side-chains REVERT: A 190 MET cc_start: 0.8630 (tmm) cc_final: 0.8387 (tmm) REVERT: A 416 LYS cc_start: 0.8505 (tppt) cc_final: 0.7593 (tptt) REVERT: A 480 MET cc_start: 0.8988 (mtp) cc_final: 0.8738 (mtm) REVERT: E 423 TYR cc_start: 0.8475 (t80) cc_final: 0.7900 (t80) REVERT: E 471 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7345 (mm-30) outliers start: 21 outliers final: 14 residues processed: 81 average time/residue: 0.0675 time to fit residues: 7.8705 Evaluate side-chains 73 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.0270 chunk 1 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.0470 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.121039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.090433 restraints weight = 9031.703| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.50 r_work: 0.2693 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1349 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= 0.109 Angle : 0.579 12.518 9009 Z= 0.278 Chirality : 0.044 0.293 966 Planarity : 0.003 0.032 1143 Dihedral : 6.876 57.312 1117 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.31), residues: 756 helix: 0.79 (0.29), residues: 354 sheet: -0.72 (0.75), residues: 41 loop : -2.66 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 245 TYR 0.008 0.001 TYR A 41 PHE 0.011 0.001 PHE A 315 TRP 0.010 0.001 TRP A 478 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 6599) covalent geometry : angle 0.53709 ( 8960) SS BOND : bond 0.01550 ( 5) SS BOND : angle 1.82129 ( 10) hydrogen bonds : bond 0.04582 ( 254) hydrogen bonds : angle 3.89299 ( 729) link_BETA1-4 : bond 0.00394 ( 6) link_BETA1-4 : angle 2.44097 ( 18) link_NAG-ASN : bond 0.00474 ( 7) link_NAG-ASN : angle 3.73862 ( 21) *********************** 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 90 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.250 Fit side-chains REVERT: A 190 MET cc_start: 0.8550 (tmm) cc_final: 0.8309 (tmm) REVERT: A 416 LYS cc_start: 0.8495 (tppt) cc_final: 0.7521 (tptt) REVERT: A 480 MET cc_start: 0.8870 (mtp) cc_final: 0.8643 (mtm) REVERT: A 489 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: A 494 ASP cc_start: 0.8026 (p0) cc_final: 0.7792 (p0) REVERT: E 423 TYR cc_start: 0.8442 (t80) cc_final: 0.7735 (t80) REVERT: E 471 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7219 (mm-30) outliers start: 19 outliers final: 15 residues processed: 86 average time/residue: 0.0679 time to fit residues: 8.4182 Evaluate side-chains 79 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 26 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.122561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.092258 restraints weight = 9145.281| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.48 r_work: 0.2835 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6617 Z= 0.106 Angle : 0.563 12.517 9009 Z= 0.268 Chirality : 0.043 0.288 966 Planarity : 0.003 0.031 1143 Dihedral : 6.352 57.718 1115 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.27 % Allowed : 19.49 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.31), residues: 756 helix: 1.04 (0.29), residues: 354 sheet: -0.49 (0.76), residues: 41 loop : -2.45 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 357 TYR 0.008 0.001 TYR A 41 PHE 0.010 0.001 PHE A 315 TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 6599) covalent geometry : angle 0.52161 ( 8960) SS BOND : bond 0.00660 ( 5) SS BOND : angle 1.61866 ( 10) hydrogen bonds : bond 0.04272 ( 254) hydrogen bonds : angle 3.76805 ( 729) link_BETA1-4 : bond 0.00418 ( 6) link_BETA1-4 : angle 2.34482 ( 18) link_NAG-ASN : bond 0.00459 ( 7) link_NAG-ASN : angle 3.73377 ( 21) *********************** 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 94 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.192 Fit side-chains REVERT: A 190 MET cc_start: 0.8604 (tmm) cc_final: 0.8353 (tmm) REVERT: A 416 LYS cc_start: 0.8444 (tppt) cc_final: 0.7500 (tptt) REVERT: A 480 MET cc_start: 0.8969 (mtp) cc_final: 0.8726 (mtm) REVERT: A 489 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: A 494 ASP cc_start: 0.8123 (p0) cc_final: 0.7869 (p0) REVERT: E 423 TYR cc_start: 0.8429 (t80) cc_final: 0.7723 (t80) REVERT: E 471 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7219 (mm-30) outliers start: 22 outliers final: 19 residues processed: 88 average time/residue: 0.0719 time to fit residues: 8.9016 Evaluate side-chains 86 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 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 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 18 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 49 optimal weight: 0.0970 chunk 70 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.122943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.092602 restraints weight = 9244.957| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.49 r_work: 0.2756 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6617 Z= 0.117 Angle : 0.564 12.556 9009 Z= 0.269 Chirality : 0.044 0.281 966 Planarity : 0.003 0.032 1143 Dihedral : 6.121 57.357 1112 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.57 % Allowed : 19.79 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.31), residues: 756 helix: 1.18 (0.29), residues: 354 sheet: -0.41 (0.76), residues: 41 loop : -2.30 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 245 TYR 0.010 0.001 TYR A 183 PHE 0.010 0.001 PHE A 327 TRP 0.009 0.001 TRP A 478 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6599) covalent geometry : angle 0.52272 ( 8960) SS BOND : bond 0.00606 ( 5) SS BOND : angle 1.70364 ( 10) hydrogen bonds : bond 0.04490 ( 254) hydrogen bonds : angle 3.72012 ( 729) link_BETA1-4 : bond 0.00399 ( 6) link_BETA1-4 : angle 2.28828 ( 18) link_NAG-ASN : bond 0.00446 ( 7) link_NAG-ASN : angle 3.73210 ( 21) *********************** 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 92 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.242 Fit side-chains REVERT: A 190 MET cc_start: 0.8466 (tmm) cc_final: 0.8176 (tmm) REVERT: A 416 LYS cc_start: 0.8436 (tppt) cc_final: 0.7467 (tptt) REVERT: A 480 MET cc_start: 0.8880 (mtp) cc_final: 0.8640 (mtm) REVERT: A 489 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: A 494 ASP cc_start: 0.8008 (p0) cc_final: 0.7766 (p0) REVERT: E 423 TYR cc_start: 0.8403 (t80) cc_final: 0.7734 (t80) REVERT: E 471 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7153 (mm-30) outliers start: 24 outliers final: 19 residues processed: 86 average time/residue: 0.0595 time to fit residues: 7.5589 Evaluate side-chains 85 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 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 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 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 41 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.122892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.092598 restraints weight = 9122.547| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.50 r_work: 0.2820 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1665 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= 0.121 Angle : 0.562 12.499 9009 Z= 0.268 Chirality : 0.044 0.283 966 Planarity : 0.003 0.033 1143 Dihedral : 5.992 57.421 1111 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.02 % Allowed : 20.68 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.31), residues: 756 helix: 1.23 (0.29), residues: 360 sheet: -0.26 (0.78), residues: 41 loop : -2.26 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 245 TYR 0.010 0.001 TYR A 183 PHE 0.010 0.001 PHE A 327 TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6599) covalent geometry : angle 0.52049 ( 8960) SS BOND : bond 0.00661 ( 5) SS BOND : angle 1.83081 ( 10) hydrogen bonds : bond 0.04512 ( 254) hydrogen bonds : angle 3.69158 ( 729) link_BETA1-4 : bond 0.00402 ( 6) link_BETA1-4 : angle 2.28613 ( 18) link_NAG-ASN : bond 0.00456 ( 7) link_NAG-ASN : angle 3.73550 ( 21) *********************** 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 94 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.172 Fit side-chains REVERT: A 82 MET cc_start: 0.8090 (mtt) cc_final: 0.7806 (mtt) REVERT: A 190 MET cc_start: 0.8563 (tmm) cc_final: 0.8266 (tmm) REVERT: A 416 LYS cc_start: 0.8450 (tppt) cc_final: 0.7500 (tptt) REVERT: A 480 MET cc_start: 0.8932 (mtp) cc_final: 0.8649 (mtm) REVERT: A 489 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: A 494 ASP cc_start: 0.8122 (p0) cc_final: 0.7879 (p0) REVERT: E 423 TYR cc_start: 0.8443 (t80) cc_final: 0.7869 (t80) REVERT: E 471 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7185 (mm-30) outliers start: 27 outliers final: 19 residues processed: 87 average time/residue: 0.0613 time to fit residues: 7.8984 Evaluate side-chains 86 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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 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 36 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 6 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.118025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.087325 restraints weight = 9191.245| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.47 r_work: 0.2699 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1700 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= 0.123 Angle : 0.563 12.492 9009 Z= 0.269 Chirality : 0.044 0.283 966 Planarity : 0.003 0.035 1143 Dihedral : 5.944 57.358 1111 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.57 % Allowed : 20.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.31), residues: 756 helix: 1.35 (0.29), residues: 354 sheet: -0.23 (0.78), residues: 41 loop : -2.09 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 245 TYR 0.010 0.001 TYR A 183 PHE 0.010 0.001 PHE A 327 TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6599) covalent geometry : angle 0.52153 ( 8960) SS BOND : bond 0.00569 ( 5) SS BOND : angle 1.80572 ( 10) hydrogen bonds : bond 0.04549 ( 254) hydrogen bonds : angle 3.67257 ( 729) link_BETA1-4 : bond 0.00390 ( 6) link_BETA1-4 : angle 2.27299 ( 18) link_NAG-ASN : bond 0.00454 ( 7) link_NAG-ASN : angle 3.72296 ( 21) *********************** 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 90 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.261 Fit side-chains REVERT: A 82 MET cc_start: 0.8044 (mtt) cc_final: 0.7722 (mtt) REVERT: A 190 MET cc_start: 0.8496 (tmm) cc_final: 0.8198 (tmm) REVERT: A 416 LYS cc_start: 0.8451 (tppt) cc_final: 0.7495 (tptt) REVERT: A 480 MET cc_start: 0.8842 (mtp) cc_final: 0.8573 (mtm) REVERT: A 489 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: A 494 ASP cc_start: 0.8019 (p0) cc_final: 0.7777 (p0) REVERT: E 423 TYR cc_start: 0.8448 (t80) cc_final: 0.7850 (t80) REVERT: E 471 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7170 (mm-30) outliers start: 24 outliers final: 20 residues processed: 84 average time/residue: 0.0624 time to fit residues: 7.7725 Evaluate side-chains 85 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 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 41 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 57 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.122719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.092408 restraints weight = 9100.474| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.45 r_work: 0.2752 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6617 Z= 0.102 Angle : 0.572 12.509 9009 Z= 0.274 Chirality : 0.044 0.284 966 Planarity : 0.003 0.033 1143 Dihedral : 5.859 57.840 1111 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.42 % Allowed : 21.43 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.31), residues: 756 helix: 1.37 (0.29), residues: 360 sheet: -0.16 (0.78), residues: 41 loop : -2.11 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 TYR 0.008 0.001 TYR A 183 PHE 0.010 0.001 PHE A 315 TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 6599) covalent geometry : angle 0.52411 ( 8960) SS BOND : bond 0.00549 ( 5) SS BOND : angle 3.33694 ( 10) hydrogen bonds : bond 0.04094 ( 254) hydrogen bonds : angle 3.61975 ( 729) link_BETA1-4 : bond 0.00423 ( 6) link_BETA1-4 : angle 2.23898 ( 18) link_NAG-ASN : bond 0.00463 ( 7) link_NAG-ASN : angle 3.70857 ( 21) *********************** 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 91 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.259 Fit side-chains REVERT: A 82 MET cc_start: 0.8004 (mtt) cc_final: 0.7652 (mtt) REVERT: A 190 MET cc_start: 0.8518 (tmm) cc_final: 0.8232 (tmm) REVERT: A 416 LYS cc_start: 0.8415 (tppt) cc_final: 0.7485 (tptt) REVERT: A 480 MET cc_start: 0.8864 (mtp) cc_final: 0.8607 (mtm) REVERT: A 489 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: A 494 ASP cc_start: 0.8024 (p0) cc_final: 0.7784 (p0) REVERT: E 423 TYR cc_start: 0.8458 (t80) cc_final: 0.7870 (t80) REVERT: E 471 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7138 (mm-30) outliers start: 23 outliers final: 18 residues processed: 85 average time/residue: 0.0679 time to fit residues: 8.4124 Evaluate side-chains 83 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER 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 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 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.0270 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.124308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.094013 restraints weight = 9203.596| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.50 r_work: 0.2730 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6617 Z= 0.097 Angle : 0.561 12.517 9009 Z= 0.268 Chirality : 0.043 0.281 966 Planarity : 0.003 0.037 1143 Dihedral : 5.540 57.941 1108 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.31), residues: 756 helix: 1.46 (0.29), residues: 360 sheet: -0.09 (0.79), residues: 41 loop : -2.03 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 TYR 0.011 0.001 TYR E 380 PHE 0.008 0.001 PHE A 315 TRP 0.008 0.001 TRP A 478 HIS 0.002 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 6599) covalent geometry : angle 0.51402 ( 8960) SS BOND : bond 0.00484 ( 5) SS BOND : angle 3.11504 ( 10) hydrogen bonds : bond 0.03924 ( 254) hydrogen bonds : angle 3.57031 ( 729) link_BETA1-4 : bond 0.00425 ( 6) link_BETA1-4 : angle 2.17965 ( 18) link_NAG-ASN : bond 0.00456 ( 7) link_NAG-ASN : angle 3.68963 ( 21) *********************** 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 87 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.221 Fit side-chains REVERT: A 82 MET cc_start: 0.7982 (mtt) cc_final: 0.7578 (mtt) REVERT: A 190 MET cc_start: 0.8456 (tmm) cc_final: 0.8177 (tmm) REVERT: A 416 LYS cc_start: 0.8397 (tppt) cc_final: 0.7452 (tptt) REVERT: A 480 MET cc_start: 0.8847 (mtp) cc_final: 0.8623 (mtm) REVERT: A 494 ASP cc_start: 0.7960 (p0) cc_final: 0.7711 (p0) REVERT: E 423 TYR cc_start: 0.8400 (t80) cc_final: 0.7881 (t80) REVERT: E 471 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7056 (mm-30) outliers start: 19 outliers final: 18 residues processed: 82 average time/residue: 0.0621 time to fit residues: 7.5536 Evaluate side-chains 83 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER 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 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 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 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.0970 chunk 67 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.122378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.091984 restraints weight = 9063.671| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.48 r_work: 0.2698 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1958 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= 0.114 Angle : 0.569 12.468 9009 Z= 0.272 Chirality : 0.044 0.281 966 Planarity : 0.003 0.037 1143 Dihedral : 5.522 57.654 1107 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.98 % Allowed : 21.88 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.31), residues: 756 helix: 1.39 (0.29), residues: 367 sheet: -0.06 (0.80), residues: 41 loop : -2.04 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 245 TYR 0.010 0.001 TYR A 183 PHE 0.009 0.001 PHE A 327 TRP 0.009 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6599) covalent geometry : angle 0.52273 ( 8960) SS BOND : bond 0.00519 ( 5) SS BOND : angle 3.07825 ( 10) hydrogen bonds : bond 0.04232 ( 254) hydrogen bonds : angle 3.58905 ( 729) link_BETA1-4 : bond 0.00398 ( 6) link_BETA1-4 : angle 2.18081 ( 18) link_NAG-ASN : bond 0.00443 ( 7) link_NAG-ASN : angle 3.68957 ( 21) ********************** 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 86 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.246 Fit side-chains REVERT: A 82 MET cc_start: 0.7960 (mtt) cc_final: 0.7563 (mtt) REVERT: A 87 GLU cc_start: 0.8560 (tp30) cc_final: 0.8086 (mm-30) REVERT: A 190 MET cc_start: 0.8436 (tmm) cc_final: 0.8152 (tmm) REVERT: A 416 LYS cc_start: 0.8409 (tppt) cc_final: 0.7442 (tptt) REVERT: A 480 MET cc_start: 0.8822 (mtp) cc_final: 0.8573 (mtm) REVERT: A 489 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.7679 (pm20) REVERT: A 494 ASP cc_start: 0.7961 (p0) cc_final: 0.7709 (p0) REVERT: E 423 TYR cc_start: 0.8376 (t80) cc_final: 0.7924 (t80) REVERT: E 471 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7126 (mm-30) outliers start: 20 outliers final: 18 residues processed: 81 average time/residue: 0.0632 time to fit residues: 7.5881 Evaluate side-chains 84 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER 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 445 THR Chi-restraints excluded: chain A residue 489 GLU 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 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 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 74 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.092475 restraints weight = 9158.819| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.52 r_work: 0.2702 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6617 Z= 0.105 Angle : 0.561 12.461 9009 Z= 0.269 Chirality : 0.044 0.283 966 Planarity : 0.003 0.037 1143 Dihedral : 5.475 57.833 1107 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.12 % Allowed : 21.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.31), residues: 756 helix: 1.47 (0.29), residues: 360 sheet: -0.06 (0.80), residues: 41 loop : -1.97 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 460 TYR 0.009 0.001 TYR A 183 PHE 0.008 0.001 PHE A 315 TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6599) covalent geometry : angle 0.51462 ( 8960) SS BOND : bond 0.00533 ( 5) SS BOND : angle 3.13955 ( 10) hydrogen bonds : bond 0.04060 ( 254) hydrogen bonds : angle 3.57164 ( 729) link_BETA1-4 : bond 0.00406 ( 6) link_BETA1-4 : angle 2.17888 ( 18) link_NAG-ASN : bond 0.00450 ( 7) link_NAG-ASN : angle 3.66359 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1862.30 seconds wall clock time: 32 minutes 37.23 seconds (1957.23 seconds total)