Starting phenix.real_space_refine on Thu Jul 2 03:50:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xo6_33338/07_2026/7xo6_33338.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo6_33338/07_2026/7xo6_33338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xo6_33338/07_2026/7xo6_33338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo6_33338/07_2026/7xo6_33338.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xo6_33338/07_2026/7xo6_33338.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xo6_33338/07_2026/7xo6_33338.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xo6_33338/07_2026/7xo6_33338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo6_33338/07_2026/7xo6_33338.cif" } resolution = 2.6 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4112 2.51 5 N 1076 2.21 5 O 1214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6440 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4824 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 25, 'TRANS': 566} Chain breaks: 1 Chain: "A" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} 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 chiralities: 2 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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 chiralities: 1 Time building chain proxies: 1.10, per 1000 atoms: 0.17 Number of scatterers: 6440 At special positions: 0 Unit cell: (97.232, 74.984, 121.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1214 8.00 N 1076 7.00 C 4112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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-ASN " NAG A1301 " - " ASN A 343 " " NAG B 1 " - " ASN D 53 " " NAG D 902 " - " ASN D 546 " Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 206.1 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1486 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 56.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'D' and resid 22 through 53 removed outlier: 4.023A pdb=" N ASP D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.671A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.705A pdb=" N ALA D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.964A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 250 removed outlier: 3.769A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.521A pdb=" N ARG D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.626A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.653A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.637A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.516A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.468A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.719A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.514A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.514A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.808A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.705A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.265A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.858A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.935A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.798A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.595A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 831 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: 0.74 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1188 1.33 - 1.45: 1836 1.45 - 1.57: 3536 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6618 Sorted by residual: bond pdb=" CA SER A 349 " pdb=" CB SER A 349 " ideal model delta sigma weight residual 1.529 1.458 0.071 1.61e-02 3.86e+03 1.93e+01 bond pdb=" C ALA A 348 " pdb=" N SER A 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.31e-02 5.83e+03 6.32e+00 bond pdb=" CA ALA A 348 " pdb=" CB ALA A 348 " ideal model delta sigma weight residual 1.529 1.489 0.040 1.66e-02 3.63e+03 5.69e+00 bond pdb=" C PRO A 373 " pdb=" O PRO A 373 " ideal model delta sigma weight residual 1.235 1.206 0.029 1.30e-02 5.92e+03 4.91e+00 bond pdb=" CA ALA A 348 " pdb=" C ALA A 348 " ideal model delta sigma weight residual 1.526 1.498 0.029 1.37e-02 5.33e+03 4.38e+00 ... (remaining 6613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 8894 2.40 - 4.79: 80 4.79 - 7.19: 8 7.19 - 9.58: 3 9.58 - 11.98: 2 Bond angle restraints: 8987 Sorted by residual: angle pdb=" N PRO D 289 " pdb=" CA PRO D 289 " pdb=" C PRO D 289 " ideal model delta sigma weight residual 112.47 121.13 -8.66 2.06e+00 2.36e-01 1.77e+01 angle pdb=" C3 NAG B 1 " pdb=" C2 NAG B 1 " pdb=" N2 NAG B 1 " ideal model delta sigma weight residual 110.74 98.76 11.98 3.00e+00 1.11e-01 1.59e+01 angle pdb=" CA SER A 349 " pdb=" C SER A 349 " pdb=" O SER A 349 " ideal model delta sigma weight residual 121.87 117.48 4.39 1.16e+00 7.43e-01 1.43e+01 angle pdb=" CB LEU A 518 " pdb=" CG LEU A 518 " pdb=" CD2 LEU A 518 " ideal model delta sigma weight residual 110.70 120.82 -10.12 3.00e+00 1.11e-01 1.14e+01 angle pdb=" CB LEU A 518 " pdb=" CG LEU A 518 " pdb=" CD1 LEU A 518 " ideal model delta sigma weight residual 110.70 120.26 -9.56 3.00e+00 1.11e-01 1.02e+01 ... (remaining 8982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3551 17.64 - 35.29: 243 35.29 - 52.93: 47 52.93 - 70.57: 15 70.57 - 88.22: 8 Dihedral angle restraints: 3864 sinusoidal: 1551 harmonic: 2313 Sorted by residual: dihedral pdb=" C ASP A 339 " pdb=" N ASP A 339 " pdb=" CA ASP A 339 " pdb=" CB ASP A 339 " ideal model delta harmonic sigma weight residual -122.60 -131.92 9.32 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" C GLN D 287 " pdb=" N GLN D 287 " pdb=" CA GLN D 287 " pdb=" CB GLN D 287 " ideal model delta harmonic sigma weight residual -122.60 -131.90 9.30 0 2.50e+00 1.60e-01 1.38e+01 dihedral pdb=" N PRO D 289 " pdb=" C PRO D 289 " pdb=" CA PRO D 289 " pdb=" CB PRO D 289 " ideal model delta harmonic sigma weight residual 115.10 124.08 -8.98 0 2.50e+00 1.60e-01 1.29e+01 ... (remaining 3861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 941 0.338 - 0.675: 3 0.675 - 1.013: 0 1.013 - 1.350: 1 1.350 - 1.688: 1 Chirality restraints: 946 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.19e+01 chirality pdb=" CG LEU A 518 " pdb=" CB LEU A 518 " pdb=" CD1 LEU A 518 " pdb=" CD2 LEU A 518 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.12e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.69e+01 ... (remaining 943 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.266 2.00e-02 2.50e+03 2.22e-01 6.14e+02 pdb=" C7 NAG A1301 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.369 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.189 2.00e-02 2.50e+03 1.53e-01 2.92e+02 pdb=" C7 NAG B 2 " -0.054 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.140 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.240 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 902 " 0.159 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C7 NAG D 902 " -0.044 2.00e-02 2.50e+03 pdb=" C8 NAG D 902 " 0.117 2.00e-02 2.50e+03 pdb=" N2 NAG D 902 " -0.218 2.00e-02 2.50e+03 pdb=" O7 NAG D 902 " -0.014 2.00e-02 2.50e+03 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 80 2.64 - 3.21: 5947 3.21 - 3.77: 10011 3.77 - 4.34: 13887 4.34 - 4.90: 23217 Nonbonded interactions: 53142 Sorted by model distance: nonbonded pdb=" OH TYR D 279 " pdb=" OD1 ASN D 290 " model vdw 2.075 3.040 nonbonded pdb=" OG1 THR D 365 " pdb=" OD1 ASN D 368 " model vdw 2.146 3.040 nonbonded pdb=" OD2 ASP D 494 " pdb=" OG1 THR D 496 " model vdw 2.156 3.040 nonbonded pdb=" NH1 ARG D 177 " pdb=" O GLU D 495 " model vdw 2.221 3.120 nonbonded pdb=" O ALA D 212 " pdb=" ND2 ASN D 216 " model vdw 2.269 3.120 ... (remaining 53137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.570 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.370 Find NCS groups from input model: 0.030 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:5.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 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 : 0.003 0.071 6622 Z= 0.159 Angle : 0.656 18.487 8999 Z= 0.308 Chirality : 0.080 1.688 946 Planarity : 0.009 0.222 1160 Dihedral : 13.254 88.216 2378 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % 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 are not related in a simple way. whole: -1.43 (0.28), residues: 780 helix: -0.11 (0.25), residues: 385 sheet: -0.50 (0.74), residues: 41 loop : -1.95 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 357 TYR 0.005 0.000 TYR A 495 PHE 0.016 0.001 PHE A 374 TRP 0.006 0.000 TRP D 163 HIS 0.002 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.16 ( 6618) covalent geometry : angle 0.55572 / 0.29 ( 8987) hydrogen bonds : bond 0.18089 / 11.44 ( 295) hydrogen bonds : angle 5.95613 / 4.39 ( 831) link_BETA1-4 : bond 0.03569 / 1.88 ( 1) link_BETA1-4 : angle 9.30574 / 4.90 ( 3) link_NAG-ASN : bond 0.02268 / 1.12 ( 3) link_NAG-ASN : angle 9.63156 / 4.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.141 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 212 average time/residue: 0.3807 time to fit residues: 85.0725 Evaluate side-chains 156 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 421 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 31 ASN D 86 GLN D 101 GLN D 197 ASN D 221 GLN D 265 HIS D 368 ASN D 373 HIS D 378 HIS D 524 GLN D 552 GLN D 562 ASN D 598 GLN D 599 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.133692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.123061 restraints weight = 9232.846| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.66 r_work: 0.3668 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6622 Z= 0.176 Angle : 0.590 7.368 8999 Z= 0.291 Chirality : 0.045 0.158 946 Planarity : 0.004 0.045 1160 Dihedral : 3.843 21.429 865 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.36 % Allowed : 19.56 % Favored : 77.08 % 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 are not related in a simple way. whole: -0.23 (0.29), residues: 780 helix: 0.86 (0.26), residues: 387 sheet: -0.16 (0.68), residues: 41 loop : -1.30 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 95 TYR 0.025 0.002 TYR D 202 PHE 0.015 0.002 PHE D 512 TRP 0.014 0.002 TRP D 163 HIS 0.006 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 6618) covalent geometry : angle 0.57195 / 0.29 ( 8987) hydrogen bonds : bond 0.04782 / 3.17 ( 295) hydrogen bonds : angle 4.52027 / 3.32 ( 831) link_BETA1-4 : bond 0.01254 / 0.66 ( 1) link_BETA1-4 : angle 2.82781 / 1.49 ( 3) link_NAG-ASN : bond 0.00256 / 0.12 ( 3) link_NAG-ASN : angle 4.36469 / 2.23 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.147 Fit side-chains REVERT: D 206 ASP cc_start: 0.7612 (t0) cc_final: 0.6613 (t0) REVERT: D 249 MET cc_start: 0.8433 (mmm) cc_final: 0.7890 (mpp) REVERT: D 369 PHE cc_start: 0.8052 (t80) cc_final: 0.7792 (t80) REVERT: D 517 THR cc_start: 0.7878 (p) cc_final: 0.7610 (p) REVERT: A 355 ARG cc_start: 0.8101 (tpp-160) cc_final: 0.7818 (ttt90) REVERT: A 365 TYR cc_start: 0.7171 (m-80) cc_final: 0.6965 (m-80) REVERT: A 477 ASN cc_start: 0.7858 (t0) cc_final: 0.7449 (t0) outliers start: 23 outliers final: 6 residues processed: 169 average time/residue: 0.4223 time to fit residues: 74.9186 Evaluate side-chains 160 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 154 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.0030 chunk 75 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 11 optimal weight: 0.0670 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.0170 chunk 71 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 42 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 overall best weight: 0.1366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 89 GLN D 531 GLN D 578 ASN A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 450 ASN A 505 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.135112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.124606 restraints weight = 9190.068| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.66 r_work: 0.3690 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6622 Z= 0.107 Angle : 0.518 9.475 8999 Z= 0.254 Chirality : 0.040 0.141 946 Planarity : 0.004 0.042 1160 Dihedral : 3.618 24.227 861 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.92 % Allowed : 22.77 % Favored : 74.31 % 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 are not related in a simple way. whole: 0.33 (0.30), residues: 780 helix: 1.29 (0.26), residues: 387 sheet: 0.06 (0.70), residues: 43 loop : -0.97 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 95 TYR 0.018 0.001 TYR D 202 PHE 0.014 0.001 PHE D 83 TRP 0.012 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 6618) covalent geometry : angle 0.50579 / 0.25 ( 8987) hydrogen bonds : bond 0.03822 / 2.54 ( 295) hydrogen bonds : angle 4.25526 / 3.13 ( 831) link_BETA1-4 : bond 0.00496 / 0.26 ( 1) link_BETA1-4 : angle 2.06239 / 1.08 ( 3) link_NAG-ASN : bond 0.00196 / 0.10 ( 3) link_NAG-ASN : angle 3.33655 / 1.72 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.222 Fit side-chains REVERT: D 183 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.7997 (t80) REVERT: D 323 MET cc_start: 0.7934 (mmm) cc_final: 0.7725 (mmt) REVERT: D 369 PHE cc_start: 0.7982 (t80) cc_final: 0.7668 (t80) REVERT: D 517 THR cc_start: 0.7724 (p) cc_final: 0.7409 (p) REVERT: A 355 ARG cc_start: 0.8074 (tpp-160) cc_final: 0.7790 (ttt90) REVERT: A 477 ASN cc_start: 0.7860 (t0) cc_final: 0.7588 (t160) outliers start: 20 outliers final: 8 residues processed: 155 average time/residue: 0.4262 time to fit residues: 69.4583 Evaluate side-chains 152 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 494 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 1 optimal weight: 0.0970 chunk 47 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 98 GLN D 175 GLN D 374 HIS D 531 GLN D 578 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.132226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.121967 restraints weight = 9224.500| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.66 r_work: 0.3623 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6622 Z= 0.262 Angle : 0.622 7.447 8999 Z= 0.312 Chirality : 0.046 0.148 946 Planarity : 0.005 0.048 1160 Dihedral : 4.296 24.290 861 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.21 % Allowed : 23.07 % Favored : 73.72 % 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 are not related in a simple way. whole: 0.05 (0.29), residues: 780 helix: 0.93 (0.26), residues: 390 sheet: 0.04 (0.72), residues: 43 loop : -0.99 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 357 TYR 0.023 0.002 TYR D 385 PHE 0.014 0.002 PHE D 603 TRP 0.014 0.002 TRP A 436 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.26 ( 6618) covalent geometry : angle 0.61083 / 0.31 ( 8987) hydrogen bonds : bond 0.05152 / 3.46 ( 295) hydrogen bonds : angle 4.54819 / 3.35 ( 831) link_BETA1-4 : bond 0.00259 / 0.14 ( 1) link_BETA1-4 : angle 1.40528 / 0.74 ( 3) link_NAG-ASN : bond 0.00390 / 0.20 ( 3) link_NAG-ASN : angle 3.74892 / 1.93 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.225 Fit side-chains REVERT: D 183 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7528 (t80) REVERT: D 376 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8195 (mmt) REVERT: D 441 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7932 (tptm) REVERT: D 609 GLU cc_start: 0.7482 (mp0) cc_final: 0.7258 (mp0) REVERT: A 355 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7763 (ttt90) REVERT: A 477 ASN cc_start: 0.7892 (t0) cc_final: 0.7629 (t160) REVERT: A 496 SER cc_start: 0.7304 (OUTLIER) cc_final: 0.7077 (p) REVERT: A 498 ARG cc_start: 0.8730 (mtt90) cc_final: 0.8452 (mtt90) outliers start: 22 outliers final: 7 residues processed: 162 average time/residue: 0.4194 time to fit residues: 71.3905 Evaluate side-chains 165 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 441 LYS Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 496 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 56 optimal weight: 0.2980 chunk 17 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 74 optimal weight: 0.0870 chunk 14 optimal weight: 0.5980 chunk 68 optimal weight: 0.0570 overall best weight: 0.1876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 175 GLN D 578 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.134228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.123994 restraints weight = 9296.578| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.66 r_work: 0.3640 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6622 Z= 0.121 Angle : 0.541 7.864 8999 Z= 0.266 Chirality : 0.041 0.135 946 Planarity : 0.004 0.046 1160 Dihedral : 4.002 22.346 861 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.50 % Allowed : 23.80 % Favored : 72.70 % 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 are not related in a simple way. whole: 0.41 (0.30), residues: 780 helix: 1.31 (0.27), residues: 379 sheet: 0.12 (0.72), residues: 43 loop : -0.83 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 357 TYR 0.023 0.001 TYR D 202 PHE 0.011 0.001 PHE D 83 TRP 0.013 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6618) covalent geometry : angle 0.53162 / 0.26 ( 8987) hydrogen bonds : bond 0.04070 / 2.74 ( 295) hydrogen bonds : angle 4.30556 / 3.19 ( 831) link_BETA1-4 : bond 0.00241 / 0.13 ( 1) link_BETA1-4 : angle 1.54574 / 0.81 ( 3) link_NAG-ASN : bond 0.00220 / 0.11 ( 3) link_NAG-ASN : angle 3.12511 / 1.61 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.184 Fit side-chains REVERT: D 183 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7693 (t80) REVERT: A 355 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7778 (ttt90) REVERT: A 396 TYR cc_start: 0.7565 (m-80) cc_final: 0.7353 (m-80) REVERT: A 477 ASN cc_start: 0.7843 (t0) cc_final: 0.7582 (t160) REVERT: A 498 ARG cc_start: 0.8704 (mtt90) cc_final: 0.8441 (mtt90) outliers start: 24 outliers final: 10 residues processed: 166 average time/residue: 0.4200 time to fit residues: 73.1868 Evaluate side-chains 166 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 494 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 21 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 60 optimal weight: 0.0050 chunk 67 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 102 GLN D 175 GLN D 472 GLN D 578 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.133497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.123312 restraints weight = 9257.343| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.67 r_work: 0.3632 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6622 Z= 0.154 Angle : 0.555 7.863 8999 Z= 0.273 Chirality : 0.042 0.132 946 Planarity : 0.004 0.047 1160 Dihedral : 4.001 21.688 861 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.50 % Allowed : 24.82 % Favored : 71.68 % 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 are not related in a simple way. whole: 0.45 (0.30), residues: 780 helix: 1.33 (0.27), residues: 379 sheet: 0.18 (0.72), residues: 43 loop : -0.80 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 577 TYR 0.023 0.002 TYR D 202 PHE 0.016 0.001 PHE D 327 TRP 0.014 0.001 TRP D 163 HIS 0.004 0.001 HIS D 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 6618) covalent geometry : angle 0.54647 / 0.27 ( 8987) hydrogen bonds : bond 0.04255 / 2.87 ( 295) hydrogen bonds : angle 4.27076 / 3.17 ( 831) link_BETA1-4 : bond 0.00363 / 0.19 ( 1) link_BETA1-4 : angle 1.26772 / 0.66 ( 3) link_NAG-ASN : bond 0.00228 / 0.12 ( 3) link_NAG-ASN : angle 3.02232 / 1.56 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.184 Fit side-chains REVERT: D 98 GLN cc_start: 0.8040 (tt0) cc_final: 0.7760 (tt0) REVERT: D 102 GLN cc_start: 0.7843 (mp10) cc_final: 0.7621 (mp10) REVERT: D 183 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7717 (t80) REVERT: A 355 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7832 (ttt90) REVERT: A 498 ARG cc_start: 0.8719 (mtt90) cc_final: 0.8395 (mtt90) outliers start: 24 outliers final: 10 residues processed: 169 average time/residue: 0.4261 time to fit residues: 75.5371 Evaluate side-chains 165 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 494 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 45 optimal weight: 0.0670 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 67 optimal weight: 0.0870 chunk 74 optimal weight: 0.0570 chunk 72 optimal weight: 0.3980 overall best weight: 0.1614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 101 GLN D 175 GLN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.135074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.124849 restraints weight = 9274.461| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.67 r_work: 0.3642 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6622 Z= 0.113 Angle : 0.532 7.648 8999 Z= 0.261 Chirality : 0.040 0.130 946 Planarity : 0.004 0.042 1160 Dihedral : 3.855 21.036 861 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.04 % Allowed : 25.69 % Favored : 72.26 % 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 are not related in a simple way. whole: 0.70 (0.30), residues: 780 helix: 1.52 (0.27), residues: 388 sheet: 0.22 (0.72), residues: 43 loop : -0.70 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 577 TYR 0.024 0.001 TYR D 202 PHE 0.014 0.001 PHE D 327 TRP 0.013 0.001 TRP D 163 HIS 0.004 0.001 HIS D 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6618) covalent geometry : angle 0.52426 / 0.26 ( 8987) hydrogen bonds : bond 0.03805 / 2.56 ( 295) hydrogen bonds : angle 4.21657 / 3.14 ( 831) link_BETA1-4 : bond 0.00355 / 0.19 ( 1) link_BETA1-4 : angle 1.31270 / 0.68 ( 3) link_NAG-ASN : bond 0.00180 / 0.09 ( 3) link_NAG-ASN : angle 2.75001 / 1.42 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: D 102 GLN cc_start: 0.7854 (mp10) cc_final: 0.7604 (mp10) REVERT: D 183 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7776 (t80) REVERT: D 323 MET cc_start: 0.8011 (mmm) cc_final: 0.7771 (mmt) REVERT: D 327 PHE cc_start: 0.7995 (t80) cc_final: 0.7325 (t80) REVERT: D 517 THR cc_start: 0.7741 (p) cc_final: 0.7379 (p) REVERT: A 355 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7846 (ttt90) REVERT: A 498 ARG cc_start: 0.8702 (mtt90) cc_final: 0.8370 (mtt90) outliers start: 14 outliers final: 7 residues processed: 165 average time/residue: 0.4480 time to fit residues: 77.4677 Evaluate side-chains 160 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 367 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 43 optimal weight: 0.5980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 101 GLN D 175 GLN D 578 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.132411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.122119 restraints weight = 9282.800| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.66 r_work: 0.3607 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6622 Z= 0.189 Angle : 0.598 10.958 8999 Z= 0.292 Chirality : 0.043 0.131 946 Planarity : 0.004 0.045 1160 Dihedral : 4.091 23.784 861 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.48 % Allowed : 26.42 % Favored : 71.09 % 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 are not related in a simple way. whole: 0.46 (0.30), residues: 780 helix: 1.23 (0.26), residues: 394 sheet: 0.17 (0.73), residues: 43 loop : -0.74 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 577 TYR 0.024 0.002 TYR D 202 PHE 0.018 0.002 PHE D 327 TRP 0.013 0.002 TRP D 163 HIS 0.004 0.001 HIS D 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 6618) covalent geometry : angle 0.59081 / 0.29 ( 8987) hydrogen bonds : bond 0.04497 / 3.03 ( 295) hydrogen bonds : angle 4.38076 / 3.26 ( 831) link_BETA1-4 : bond 0.00247 / 0.13 ( 1) link_BETA1-4 : angle 0.96103 / 0.50 ( 3) link_NAG-ASN : bond 0.00303 / 0.15 ( 3) link_NAG-ASN : angle 3.01372 / 1.56 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: D 102 GLN cc_start: 0.7930 (mp10) cc_final: 0.7706 (mp10) REVERT: D 183 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7635 (t80) REVERT: D 297 MET cc_start: 0.8401 (mtm) cc_final: 0.8197 (mtp) REVERT: D 441 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7955 (tptm) REVERT: D 609 GLU cc_start: 0.7453 (mp0) cc_final: 0.7226 (mp0) REVERT: A 355 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7826 (ttt90) REVERT: A 365 TYR cc_start: 0.7370 (m-80) cc_final: 0.7132 (m-80) REVERT: A 466 ARG cc_start: 0.7903 (mtp85) cc_final: 0.7435 (mtm110) REVERT: A 498 ARG cc_start: 0.8725 (mtt90) cc_final: 0.8377 (mtt90) outliers start: 17 outliers final: 9 residues processed: 164 average time/residue: 0.4323 time to fit residues: 74.4664 Evaluate side-chains 166 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 441 LYS Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 494 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 27 optimal weight: 0.0980 chunk 58 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 31 ASN D 175 GLN D 220 ASN D 578 ASN A 477 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.133363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.123024 restraints weight = 9335.763| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.68 r_work: 0.3623 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6622 Z= 0.175 Angle : 0.592 10.255 8999 Z= 0.289 Chirality : 0.043 0.134 946 Planarity : 0.005 0.044 1160 Dihedral : 4.146 23.826 861 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.34 % Allowed : 27.15 % Favored : 70.51 % 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 are not related in a simple way. whole: 0.48 (0.30), residues: 780 helix: 1.24 (0.26), residues: 394 sheet: 0.22 (0.74), residues: 43 loop : -0.73 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 577 TYR 0.025 0.002 TYR D 202 PHE 0.017 0.001 PHE D 327 TRP 0.012 0.001 TRP D 163 HIS 0.005 0.001 HIS D 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 6618) covalent geometry : angle 0.58490 / 0.29 ( 8987) hydrogen bonds : bond 0.04380 / 2.95 ( 295) hydrogen bonds : angle 4.36674 / 3.24 ( 831) link_BETA1-4 : bond 0.00360 / 0.19 ( 1) link_BETA1-4 : angle 0.99222 / 0.52 ( 3) link_NAG-ASN : bond 0.00259 / 0.13 ( 3) link_NAG-ASN : angle 2.96212 / 1.53 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: D 102 GLN cc_start: 0.7953 (mp10) cc_final: 0.7714 (mp10) REVERT: D 183 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7660 (t80) REVERT: D 323 MET cc_start: 0.7986 (mmm) cc_final: 0.7732 (mmt) REVERT: D 441 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7989 (tptm) REVERT: D 609 GLU cc_start: 0.7506 (mp0) cc_final: 0.7275 (mp0) REVERT: A 355 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7800 (ttt90) REVERT: A 365 TYR cc_start: 0.7431 (m-80) cc_final: 0.7192 (m-80) REVERT: A 466 ARG cc_start: 0.7903 (mtp85) cc_final: 0.7439 (mtm110) REVERT: A 498 ARG cc_start: 0.8735 (mtt90) cc_final: 0.8399 (mtt90) outliers start: 16 outliers final: 10 residues processed: 155 average time/residue: 0.4679 time to fit residues: 76.0017 Evaluate side-chains 159 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 441 LYS Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 71 optimal weight: 0.0670 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 175 GLN D 578 ASN A 477 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.133176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.122973 restraints weight = 9182.680| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.66 r_work: 0.3628 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6622 Z= 0.153 Angle : 0.580 10.248 8999 Z= 0.283 Chirality : 0.042 0.134 946 Planarity : 0.004 0.049 1160 Dihedral : 4.094 23.405 861 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.77 % Allowed : 27.15 % Favored : 70.07 % 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 are not related in a simple way. whole: 0.57 (0.30), residues: 780 helix: 1.32 (0.27), residues: 394 sheet: 0.22 (0.74), residues: 43 loop : -0.68 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 577 TYR 0.024 0.002 TYR D 202 PHE 0.023 0.001 PHE D 327 TRP 0.012 0.001 TRP D 163 HIS 0.004 0.001 HIS D 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 6618) covalent geometry : angle 0.57266 / 0.28 ( 8987) hydrogen bonds : bond 0.04228 / 2.85 ( 295) hydrogen bonds : angle 4.32786 / 3.20 ( 831) link_BETA1-4 : bond 0.00300 / 0.16 ( 1) link_BETA1-4 : angle 0.90261 / 0.47 ( 3) link_NAG-ASN : bond 0.00240 / 0.12 ( 3) link_NAG-ASN : angle 2.91697 / 1.51 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: D 102 GLN cc_start: 0.7954 (mp10) cc_final: 0.7715 (mp10) REVERT: D 183 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7746 (t80) REVERT: D 323 MET cc_start: 0.8055 (mmm) cc_final: 0.7807 (mmt) REVERT: D 609 GLU cc_start: 0.7503 (mp0) cc_final: 0.7288 (mp0) REVERT: A 355 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7786 (ttt90) REVERT: A 466 ARG cc_start: 0.7889 (mtp85) cc_final: 0.7384 (mtm110) REVERT: A 498 ARG cc_start: 0.8730 (mtt90) cc_final: 0.8395 (mtt90) outliers start: 19 outliers final: 9 residues processed: 158 average time/residue: 0.4377 time to fit residues: 72.6115 Evaluate side-chains 161 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 42 optimal weight: 0.4980 chunk 53 optimal weight: 0.0070 chunk 33 optimal weight: 0.9980 chunk 57 optimal weight: 0.0870 chunk 3 optimal weight: 0.1980 chunk 56 optimal weight: 0.2980 chunk 64 optimal weight: 0.0070 chunk 14 optimal weight: 0.9980 overall best weight: 0.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 101 GLN D 175 GLN D 578 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.134594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.124242 restraints weight = 9187.760| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.67 r_work: 0.3645 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6622 Z= 0.111 Angle : 0.556 10.593 8999 Z= 0.269 Chirality : 0.040 0.130 946 Planarity : 0.005 0.063 1160 Dihedral : 3.909 22.469 861 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.61 % Allowed : 28.03 % Favored : 70.36 % 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 are not related in a simple way. whole: 0.77 (0.30), residues: 780 helix: 1.50 (0.27), residues: 394 sheet: 0.29 (0.72), residues: 43 loop : -0.61 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 577 TYR 0.024 0.001 TYR D 202 PHE 0.021 0.001 PHE D 327 TRP 0.013 0.001 TRP D 163 HIS 0.003 0.001 HIS D 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 6618) covalent geometry : angle 0.54948 / 0.27 ( 8987) hydrogen bonds : bond 0.03697 / 2.48 ( 295) hydrogen bonds : angle 4.24838 / 3.15 ( 831) link_BETA1-4 : bond 0.00335 / 0.18 ( 1) link_BETA1-4 : angle 1.04809 / 0.54 ( 3) link_NAG-ASN : bond 0.00166 / 0.09 ( 3) link_NAG-ASN : angle 2.64804 / 1.36 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2404.10 seconds wall clock time: 41 minutes 39.07 seconds (2499.07 seconds total)