Starting phenix.real_space_refine on Tue Feb 3 19:08:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo6_33338/02_2026/7xo6_33338.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo6_33338/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xo6_33338/02_2026/7xo6_33338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo6_33338/02_2026/7xo6_33338.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xo6_33338/02_2026/7xo6_33338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo6_33338/02_2026/7xo6_33338.map" } 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-2.0-5952/lib/python3.9/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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.20, per 1000 atoms: 0.19 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: 0.57 Conformation dependent library (CDL) restraints added in 167.0 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: 0.19 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: 0.68 Time building geometry restraints manager: 0.71 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: 3624 17.64 - 35.29: 251 35.29 - 52.93: 50 52.93 - 70.57: 15 70.57 - 88.22: 8 Dihedral angle restraints: 3948 sinusoidal: 1635 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 3945 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: 9.550 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.000 Find NCS groups from input model: 0.020 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:8.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 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 : 13.228 88.216 2462 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 covalent geometry : bond 0.00277 ( 6618) covalent geometry : angle 0.55572 ( 8987) hydrogen bonds : bond 0.18089 ( 295) hydrogen bonds : angle 5.95613 ( 831) link_BETA1-4 : bond 0.03569 ( 1) link_BETA1-4 : angle 9.30574 ( 3) link_NAG-ASN : bond 0.02268 ( 3) link_NAG-ASN : angle 9.63156 ( 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 : 0.245 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 212 average time/residue: 0.4667 time to fit residues: 103.9351 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 : 0.145 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.133421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.122895 restraints weight = 9305.224| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.65 r_work: 0.3667 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2576 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= 0.186 Angle : 0.595 7.638 8999 Z= 0.296 Chirality : 0.045 0.172 946 Planarity : 0.004 0.043 1160 Dihedral : 4.735 41.570 949 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.21 % Allowed : 20.15 % 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 are not related in a simple way. whole: -0.22 (0.29), residues: 780 helix: 0.87 (0.27), residues: 387 sheet: -0.15 (0.68), residues: 41 loop : -1.31 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 95 TYR 0.023 0.002 TYR D 202 PHE 0.015 0.002 PHE D 72 TRP 0.014 0.002 TRP D 203 HIS 0.005 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 6618) covalent geometry : angle 0.57396 ( 8987) hydrogen bonds : bond 0.04632 ( 295) hydrogen bonds : angle 4.52831 ( 831) link_BETA1-4 : bond 0.00851 ( 1) link_BETA1-4 : angle 3.36049 ( 3) link_NAG-ASN : bond 0.00695 ( 3) link_NAG-ASN : angle 4.66193 ( 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 180 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.184 Fit side-chains REVERT: D 206 ASP cc_start: 0.7581 (t0) cc_final: 0.6611 (t0) REVERT: D 249 MET cc_start: 0.8399 (mmm) cc_final: 0.7993 (mpp) REVERT: D 369 PHE cc_start: 0.8048 (t80) cc_final: 0.7771 (t80) REVERT: D 497 TYR cc_start: 0.8448 (m-80) cc_final: 0.8233 (m-80) REVERT: D 517 THR cc_start: 0.7904 (p) cc_final: 0.7623 (p) REVERT: A 355 ARG cc_start: 0.8088 (tpp-160) cc_final: 0.7830 (ttt90) REVERT: A 365 TYR cc_start: 0.7132 (m-80) cc_final: 0.6899 (m-80) REVERT: A 477 ASN cc_start: 0.7820 (t0) cc_final: 0.7416 (t0) outliers start: 22 outliers final: 8 residues processed: 167 average time/residue: 0.5240 time to fit residues: 91.6671 Evaluate side-chains 166 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 427 ASP 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: 0.4980 chunk 75 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 11 optimal weight: 0.0020 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 71 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 42 optimal weight: 0.0670 chunk 54 optimal weight: 0.5980 overall best weight: 0.2526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN D 98 GLN D 524 GLN D 531 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.133402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.122835 restraints weight = 9186.304| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.66 r_work: 0.3666 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6622 Z= 0.137 Angle : 0.543 9.312 8999 Z= 0.269 Chirality : 0.042 0.140 946 Planarity : 0.004 0.048 1160 Dihedral : 4.412 36.910 945 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.07 % Allowed : 22.48 % Favored : 74.45 % 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 are not related in a simple way. whole: 0.17 (0.29), residues: 780 helix: 1.08 (0.26), residues: 396 sheet: 0.09 (0.70), residues: 43 loop : -1.03 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 357 TYR 0.020 0.002 TYR D 202 PHE 0.014 0.001 PHE D 83 TRP 0.013 0.001 TRP D 163 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6618) covalent geometry : angle 0.53049 ( 8987) hydrogen bonds : bond 0.04190 ( 295) hydrogen bonds : angle 4.30795 ( 831) link_BETA1-4 : bond 0.00368 ( 1) link_BETA1-4 : angle 2.18659 ( 3) link_NAG-ASN : bond 0.00199 ( 3) link_NAG-ASN : angle 3.48080 ( 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 176 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.183 Fit side-chains REVERT: D 183 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7957 (t80) REVERT: D 323 MET cc_start: 0.8005 (mmm) cc_final: 0.7783 (mmt) REVERT: D 369 PHE cc_start: 0.8068 (t80) cc_final: 0.7722 (t80) REVERT: D 497 TYR cc_start: 0.8461 (m-80) cc_final: 0.8231 (m-80) REVERT: D 517 THR cc_start: 0.7820 (p) cc_final: 0.7505 (p) REVERT: A 355 ARG cc_start: 0.8087 (tpp-160) cc_final: 0.7775 (ttt90) REVERT: A 477 ASN cc_start: 0.7875 (t0) cc_final: 0.7604 (t160) REVERT: A 496 SER cc_start: 0.7140 (OUTLIER) cc_final: 0.6917 (p) outliers start: 21 outliers final: 6 residues processed: 162 average time/residue: 0.5493 time to fit residues: 93.1637 Evaluate side-chains 156 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 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 469 SER Chi-restraints excluded: chain A residue 496 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.4980 chunk 34 optimal weight: 0.0980 chunk 55 optimal weight: 0.3980 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 58 optimal weight: 0.0040 overall best weight: 0.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN D 531 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 = 0.3913 r_free = 0.3913 target = 0.137231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.126705 restraints weight = 9290.462| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.70 r_work: 0.3672 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6622 Z= 0.105 Angle : 0.497 7.502 8999 Z= 0.247 Chirality : 0.040 0.136 946 Planarity : 0.004 0.042 1160 Dihedral : 4.093 34.957 945 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.34 % Allowed : 23.07 % Favored : 74.60 % 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: 0.58 (0.30), residues: 780 helix: 1.47 (0.27), residues: 388 sheet: 0.17 (0.72), residues: 43 loop : -0.83 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.022 0.001 TYR D 202 PHE 0.013 0.001 PHE D 83 TRP 0.012 0.001 TRP D 163 HIS 0.003 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 6618) covalent geometry : angle 0.48897 ( 8987) hydrogen bonds : bond 0.03659 ( 295) hydrogen bonds : angle 4.14451 ( 831) link_BETA1-4 : bond 0.00370 ( 1) link_BETA1-4 : angle 1.64396 ( 3) link_NAG-ASN : bond 0.00169 ( 3) link_NAG-ASN : angle 2.77976 ( 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 169 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.165 Fit side-chains REVERT: D 176 LEU cc_start: 0.8526 (mt) cc_final: 0.8324 (mt) REVERT: D 183 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.7892 (t80) REVERT: D 323 MET cc_start: 0.7994 (mmm) cc_final: 0.7791 (mmt) REVERT: D 369 PHE cc_start: 0.8022 (t80) cc_final: 0.7702 (t80) REVERT: D 497 TYR cc_start: 0.8441 (m-80) cc_final: 0.8227 (m-80) REVERT: D 517 THR cc_start: 0.7667 (p) cc_final: 0.7368 (p) REVERT: A 477 ASN cc_start: 0.7860 (t0) cc_final: 0.7592 (t160) outliers start: 16 outliers final: 10 residues processed: 159 average time/residue: 0.5308 time to fit residues: 88.5268 Evaluate side-chains 155 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 501 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 56 optimal weight: 0.0970 chunk 17 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 50 optimal weight: 0.0980 chunk 52 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 0.0970 chunk 14 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 overall best weight: 0.0976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 GLN D 102 GLN D 524 GLN D 531 GLN D 578 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.137374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.126800 restraints weight = 9372.890| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.71 r_work: 0.3694 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6622 Z= 0.097 Angle : 0.487 7.068 8999 Z= 0.242 Chirality : 0.039 0.133 946 Planarity : 0.004 0.039 1160 Dihedral : 3.881 33.120 945 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.92 % Allowed : 23.50 % Favored : 73.58 % 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: 0.84 (0.30), residues: 780 helix: 1.70 (0.27), residues: 382 sheet: 0.24 (0.73), residues: 43 loop : -0.66 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 498 TYR 0.022 0.001 TYR D 202 PHE 0.013 0.001 PHE D 83 TRP 0.011 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 6618) covalent geometry : angle 0.48043 ( 8987) hydrogen bonds : bond 0.03445 ( 295) hydrogen bonds : angle 4.02797 ( 831) link_BETA1-4 : bond 0.00474 ( 1) link_BETA1-4 : angle 1.27096 ( 3) link_NAG-ASN : bond 0.00147 ( 3) link_NAG-ASN : angle 2.41170 ( 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 170 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: D 176 LEU cc_start: 0.8429 (mt) cc_final: 0.8169 (mt) REVERT: D 183 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7883 (t80) REVERT: D 323 MET cc_start: 0.8002 (mmm) cc_final: 0.7629 (mmm) REVERT: D 369 PHE cc_start: 0.7990 (t80) cc_final: 0.7630 (t80) REVERT: D 497 TYR cc_start: 0.8437 (m-80) cc_final: 0.8232 (m-80) REVERT: D 517 THR cc_start: 0.7564 (p) cc_final: 0.7215 (p) REVERT: A 496 SER cc_start: 0.7140 (OUTLIER) cc_final: 0.6901 (p) outliers start: 20 outliers final: 9 residues processed: 162 average time/residue: 0.4789 time to fit residues: 81.4600 Evaluate side-chains 157 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 ILE 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 485 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 501 TYR 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: 0.9980 chunk 65 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 21 optimal weight: 0.0970 chunk 53 optimal weight: 0.0370 chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 GLN D 102 GLN D 472 GLN D 531 GLN D 578 ASN D 598 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.135601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.125050 restraints weight = 9267.611| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.70 r_work: 0.3638 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6622 Z= 0.146 Angle : 0.527 7.278 8999 Z= 0.263 Chirality : 0.041 0.131 946 Planarity : 0.004 0.041 1160 Dihedral : 4.133 31.633 945 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.77 % Allowed : 24.67 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.30), residues: 780 helix: 1.61 (0.27), residues: 389 sheet: 0.31 (0.73), residues: 43 loop : -0.65 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 498 TYR 0.023 0.002 TYR D 202 PHE 0.009 0.001 PHE D 523 TRP 0.011 0.001 TRP D 163 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6618) covalent geometry : angle 0.52014 ( 8987) hydrogen bonds : bond 0.04013 ( 295) hydrogen bonds : angle 4.17621 ( 831) link_BETA1-4 : bond 0.00225 ( 1) link_BETA1-4 : angle 1.09024 ( 3) link_NAG-ASN : bond 0.00254 ( 3) link_NAG-ASN : angle 2.72764 ( 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 168 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.244 Fit side-chains REVERT: D 183 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7686 (t80) REVERT: D 323 MET cc_start: 0.8031 (mmm) cc_final: 0.7610 (mmm) REVERT: D 369 PHE cc_start: 0.7997 (t80) cc_final: 0.7644 (t80) REVERT: D 517 THR cc_start: 0.7808 (p) cc_final: 0.7479 (p) REVERT: A 355 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7826 (ttt90) REVERT: A 396 TYR cc_start: 0.7569 (m-80) cc_final: 0.7311 (m-80) REVERT: A 477 ASN cc_start: 0.7866 (t0) cc_final: 0.7605 (t160) REVERT: A 496 SER cc_start: 0.7135 (OUTLIER) cc_final: 0.6907 (p) outliers start: 19 outliers final: 7 residues processed: 157 average time/residue: 0.4885 time to fit residues: 80.5886 Evaluate side-chains 157 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 421 ILE Chi-restraints excluded: chain D residue 430 GLU 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 496 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 0.0670 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 45 optimal weight: 0.1980 chunk 25 optimal weight: 0.0670 chunk 17 optimal weight: 0.2980 chunk 18 optimal weight: 0.4980 chunk 67 optimal weight: 0.4980 chunk 74 optimal weight: 0.4980 chunk 72 optimal weight: 0.5980 overall best weight: 0.2256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 GLN D 531 GLN D 598 GLN ** 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 = 0.3891 r_free = 0.3891 target = 0.135474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.124932 restraints weight = 9247.878| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.71 r_work: 0.3646 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6622 Z= 0.126 Angle : 0.528 11.287 8999 Z= 0.260 Chirality : 0.040 0.131 946 Planarity : 0.004 0.042 1160 Dihedral : 4.110 30.560 945 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.48 % Allowed : 24.67 % Favored : 72.85 % 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 are not related in a simple way. whole: 0.83 (0.31), residues: 780 helix: 1.60 (0.27), residues: 395 sheet: 0.31 (0.73), residues: 43 loop : -0.66 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 498 TYR 0.024 0.001 TYR D 202 PHE 0.011 0.001 PHE D 83 TRP 0.011 0.001 TRP D 163 HIS 0.004 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6618) covalent geometry : angle 0.52201 ( 8987) hydrogen bonds : bond 0.03836 ( 295) hydrogen bonds : angle 4.15878 ( 831) link_BETA1-4 : bond 0.00238 ( 1) link_BETA1-4 : angle 1.21465 ( 3) link_NAG-ASN : bond 0.00192 ( 3) link_NAG-ASN : angle 2.58492 ( 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 169 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: D 102 GLN cc_start: 0.7701 (mp10) cc_final: 0.7466 (mp10) REVERT: D 183 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.7764 (t80) REVERT: D 369 PHE cc_start: 0.7956 (t80) cc_final: 0.7555 (t80) REVERT: D 517 THR cc_start: 0.7762 (p) cc_final: 0.7429 (p) REVERT: A 355 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7822 (ttt90) REVERT: A 396 TYR cc_start: 0.7560 (m-80) cc_final: 0.7324 (m-80) REVERT: A 477 ASN cc_start: 0.7861 (t0) cc_final: 0.7598 (t160) outliers start: 17 outliers final: 9 residues processed: 159 average time/residue: 0.4707 time to fit residues: 78.3986 Evaluate side-chains 159 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 421 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0270 chunk 62 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 chunk 34 optimal weight: 0.2980 chunk 41 optimal weight: 0.1980 chunk 12 optimal weight: 0.1980 chunk 14 optimal weight: 0.3980 chunk 43 optimal weight: 0.0970 overall best weight: 0.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 531 GLN D 578 ASN D 598 GLN ** 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 = 0.3908 r_free = 0.3908 target = 0.137185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.126646 restraints weight = 9312.971| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.70 r_work: 0.3667 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6622 Z= 0.103 Angle : 0.518 10.111 8999 Z= 0.254 Chirality : 0.039 0.130 946 Planarity : 0.004 0.043 1160 Dihedral : 3.901 28.988 945 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.61 % Allowed : 26.13 % 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: 1.00 (0.31), residues: 780 helix: 1.75 (0.27), residues: 395 sheet: 0.32 (0.72), residues: 43 loop : -0.56 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 498 TYR 0.024 0.001 TYR D 202 PHE 0.009 0.001 PHE D 327 TRP 0.011 0.001 TRP D 163 HIS 0.003 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 6618) covalent geometry : angle 0.51289 ( 8987) hydrogen bonds : bond 0.03540 ( 295) hydrogen bonds : angle 4.10706 ( 831) link_BETA1-4 : bond 0.00369 ( 1) link_BETA1-4 : angle 1.15818 ( 3) link_NAG-ASN : bond 0.00146 ( 3) link_NAG-ASN : angle 2.29708 ( 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 159 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.174 Fit side-chains REVERT: D 102 GLN cc_start: 0.7726 (mp10) cc_final: 0.7488 (mp10) REVERT: D 183 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7847 (t80) REVERT: D 369 PHE cc_start: 0.7922 (t80) cc_final: 0.7500 (t80) REVERT: D 517 THR cc_start: 0.7617 (p) cc_final: 0.7290 (p) REVERT: A 477 ASN cc_start: 0.7868 (t0) cc_final: 0.7604 (t160) outliers start: 11 outliers final: 8 residues processed: 154 average time/residue: 0.5239 time to fit residues: 84.3379 Evaluate side-chains 155 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 421 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 602 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 58 optimal weight: 0.0570 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 overall best weight: 0.2298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 531 GLN D 578 ASN D 598 GLN ** 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 = 0.3896 r_free = 0.3896 target = 0.136007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.125481 restraints weight = 9353.904| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.70 r_work: 0.3646 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6622 Z= 0.128 Angle : 0.531 9.595 8999 Z= 0.262 Chirality : 0.040 0.130 946 Planarity : 0.004 0.051 1160 Dihedral : 3.982 26.940 945 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.46 % Allowed : 25.84 % 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: 0.93 (0.31), residues: 780 helix: 1.69 (0.27), residues: 389 sheet: 0.30 (0.71), residues: 43 loop : -0.56 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 577 TYR 0.024 0.001 TYR D 202 PHE 0.011 0.001 PHE D 83 TRP 0.011 0.001 TRP D 163 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6618) covalent geometry : angle 0.52569 ( 8987) hydrogen bonds : bond 0.03829 ( 295) hydrogen bonds : angle 4.17374 ( 831) link_BETA1-4 : bond 0.00260 ( 1) link_BETA1-4 : angle 0.95747 ( 3) link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 2.33434 ( 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 160 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.163 Fit side-chains REVERT: D 102 GLN cc_start: 0.7759 (mp10) cc_final: 0.7553 (mp10) REVERT: D 183 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.7780 (t80) REVERT: D 369 PHE cc_start: 0.7900 (t80) cc_final: 0.7540 (t80) REVERT: D 517 THR cc_start: 0.7757 (p) cc_final: 0.7427 (p) REVERT: A 355 ARG cc_start: 0.8111 (tpp-160) cc_final: 0.7840 (ttt90) REVERT: A 365 TYR cc_start: 0.7417 (m-80) cc_final: 0.7181 (m-80) REVERT: A 396 TYR cc_start: 0.7635 (m-80) cc_final: 0.7411 (m-80) outliers start: 10 outliers final: 9 residues processed: 156 average time/residue: 0.5010 time to fit residues: 81.9851 Evaluate side-chains 157 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 421 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 574 VAL Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain A residue 367 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 0.0470 chunk 16 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 50 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 71 optimal weight: 0.0770 chunk 27 optimal weight: 0.3980 chunk 42 optimal weight: 0.0570 overall best weight: 0.1354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 531 GLN D 578 ASN D 598 GLN ** 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 = 0.3904 r_free = 0.3904 target = 0.136298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.125763 restraints weight = 9155.881| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.69 r_work: 0.3678 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6622 Z= 0.108 Angle : 0.528 9.626 8999 Z= 0.261 Chirality : 0.039 0.129 946 Planarity : 0.004 0.055 1160 Dihedral : 3.853 22.330 945 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.75 % Allowed : 26.13 % Favored : 72.12 % 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: 0.95 (0.31), residues: 780 helix: 1.72 (0.27), residues: 389 sheet: 0.30 (0.71), residues: 43 loop : -0.57 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 577 TYR 0.023 0.001 TYR D 202 PHE 0.008 0.001 PHE D 327 TRP 0.011 0.001 TRP D 163 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 6618) covalent geometry : angle 0.52385 ( 8987) hydrogen bonds : bond 0.03641 ( 295) hydrogen bonds : angle 4.15477 ( 831) link_BETA1-4 : bond 0.00374 ( 1) link_BETA1-4 : angle 1.04248 ( 3) link_NAG-ASN : bond 0.00432 ( 3) link_NAG-ASN : angle 2.18862 ( 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 157 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.246 Fit side-chains REVERT: D 183 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7768 (t80) REVERT: D 517 THR cc_start: 0.7682 (p) cc_final: 0.7339 (p) REVERT: A 365 TYR cc_start: 0.7425 (m-80) cc_final: 0.7183 (m-80) outliers start: 12 outliers final: 8 residues processed: 153 average time/residue: 0.4726 time to fit residues: 76.0701 Evaluate side-chains 154 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 421 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 574 VAL Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain A residue 367 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 42 optimal weight: 0.0570 chunk 53 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 64 optimal weight: 0.0970 chunk 14 optimal weight: 0.5980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 531 GLN D 578 ASN D 598 GLN ** 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 = 0.3863 r_free = 0.3863 target = 0.133088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.122689 restraints weight = 9168.790| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.67 r_work: 0.3628 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6622 Z= 0.166 Angle : 0.569 8.928 8999 Z= 0.283 Chirality : 0.042 0.133 946 Planarity : 0.004 0.064 1160 Dihedral : 4.162 22.263 945 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.04 % Allowed : 25.26 % 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: 0.65 (0.30), residues: 780 helix: 1.35 (0.27), residues: 395 sheet: 0.28 (0.71), residues: 43 loop : -0.61 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.023 0.002 TYR D 202 PHE 0.010 0.001 PHE D 83 TRP 0.010 0.001 TRP D 163 HIS 0.006 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6618) covalent geometry : angle 0.56378 ( 8987) hydrogen bonds : bond 0.04275 ( 295) hydrogen bonds : angle 4.28010 ( 831) link_BETA1-4 : bond 0.00221 ( 1) link_BETA1-4 : angle 0.93081 ( 3) link_NAG-ASN : bond 0.00324 ( 3) link_NAG-ASN : angle 2.56636 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2769.15 seconds wall clock time: 47 minutes 46.73 seconds (2866.73 seconds total)