Starting phenix.real_space_refine on Fri Sep 11 01:35:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xo9_33341/09_2026/7xo9_33341.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo9_33341/09_2026/7xo9_33341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xo9_33341/09_2026/7xo9_33341.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xo9_33341/09_2026/7xo9_33341.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xo9_33341/09_2026/7xo9_33341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo9_33341/09_2026/7xo9_33341.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xo9_33341/09_2026/7xo9_33341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo9_33341/09_2026/7xo9_33341.map" } resolution = 3.0 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= 0.010 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 Cl 1 4.86 5 C 4154 2.51 5 N 1074 2.21 5 O 1216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6483 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1582 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.59, per 1000 atoms: 0.25 Number of scatterers: 6483 At special positions: 0 Unit cell: (97.232, 70.864, 117.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 37 16.00 O 1216 8.00 N 1074 7.00 C 4154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG D 903 " - " ASN D 546 " " NAG D 904 " - " ASN D 322 " " NAG D 905 " - " ASN D 90 " Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 379.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 902 " pdb="ZN ZN D 902 " - pdb=" NE2 HIS D 374 " 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 55.4% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.606A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.356A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.776A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.653A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.617A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.002A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 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: 3.616A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.649A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.988A 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 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.956A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.750A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (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 299 Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.504A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.867A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.671A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.919A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 449 through 466 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 485 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 531 removed outlier: 3.542A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.734A 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: 3.743A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.597A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.540A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.602A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.645A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.073A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.027A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2040 1.34 - 1.45: 1106 1.45 - 1.57: 3462 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6666 Sorted by residual: bond pdb=" N ASN D 322 " pdb=" CA ASN D 322 " ideal model delta sigma weight residual 1.453 1.481 -0.028 1.31e-02 5.83e+03 4.65e+00 bond pdb=" N SER D 19 " pdb=" CA SER D 19 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" C3 NAG D 904 " pdb=" O3 NAG D 904 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C3 NAG D 905 " pdb=" O3 NAG D 905 " ideal model delta sigma weight residual 1.403 1.429 -0.026 2.00e-02 2.50e+03 1.68e+00 ... (remaining 6661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 8884 1.33 - 2.65: 112 2.65 - 3.98: 53 3.98 - 5.31: 9 5.31 - 6.63: 2 Bond angle restraints: 9060 Sorted by residual: angle pdb=" C ASN D 322 " pdb=" CA ASN D 322 " pdb=" CB ASN D 322 " ideal model delta sigma weight residual 109.76 116.39 -6.63 1.99e+00 2.53e-01 1.11e+01 angle pdb=" C ASN D 322 " pdb=" N MET D 323 " pdb=" CA MET D 323 " ideal model delta sigma weight residual 120.87 126.40 -5.53 1.69e+00 3.50e-01 1.07e+01 angle pdb=" CA ASN D 322 " pdb=" C ASN D 322 " pdb=" O ASN D 322 " ideal model delta sigma weight residual 121.81 118.90 2.91 1.18e+00 7.18e-01 6.09e+00 angle pdb=" N ILE D 544 " pdb=" CA ILE D 544 " pdb=" C ILE D 544 " ideal model delta sigma weight residual 112.98 110.04 2.94 1.25e+00 6.40e-01 5.53e+00 angle pdb=" O PRO D 321 " pdb=" C PRO D 321 " pdb=" N ASN D 322 " ideal model delta sigma weight residual 123.06 120.18 2.88 1.23e+00 6.61e-01 5.48e+00 ... (remaining 9055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3584 17.84 - 35.69: 245 35.69 - 53.53: 43 53.53 - 71.37: 13 71.37 - 89.22: 6 Dihedral angle restraints: 3891 sinusoidal: 1563 harmonic: 2328 Sorted by residual: dihedral pdb=" CA LYS D 68 " pdb=" CB LYS D 68 " pdb=" CG LYS D 68 " pdb=" CD LYS D 68 " ideal model delta sinusoidal sigma weight residual 180.00 120.09 59.91 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LYS D 341 " pdb=" CA LYS D 341 " pdb=" CB LYS D 341 " pdb=" CG LYS D 341 " ideal model delta sinusoidal sigma weight residual -180.00 -121.74 -58.26 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB MET D 323 " pdb=" CG MET D 323 " pdb=" SD MET D 323 " pdb=" CE MET D 323 " ideal model delta sinusoidal sigma weight residual 180.00 122.17 57.83 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.249: 952 0.249 - 0.498: 0 0.498 - 0.747: 0 0.747 - 0.995: 0 0.995 - 1.244: 1 Chirality restraints: 953 Sorted by residual: chirality pdb=" C1 NAG D 905 " pdb=" ND2 ASN D 90 " pdb=" C2 NAG D 905 " pdb=" O5 NAG D 905 " both_signs ideal model delta sigma weight residual False -2.40 -1.16 -1.24 2.00e-01 2.50e+01 3.87e+01 chirality pdb=" C1 NAG D 903 " pdb=" ND2 ASN D 546 " pdb=" C2 NAG D 903 " pdb=" O5 NAG D 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ASN D 322 " pdb=" N ASN D 322 " pdb=" C ASN D 322 " pdb=" CB ASN D 322 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 950 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 905 " 0.245 2.00e-02 2.50e+03 2.10e-01 5.50e+02 pdb=" C7 NAG D 905 " -0.054 2.00e-02 2.50e+03 pdb=" C8 NAG D 905 " -0.028 2.00e-02 2.50e+03 pdb=" N2 NAG D 905 " -0.349 2.00e-02 2.50e+03 pdb=" O7 NAG D 905 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 903 " -0.247 2.00e-02 2.50e+03 2.08e-01 5.43e+02 pdb=" C7 NAG D 903 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG D 903 " -0.166 2.00e-02 2.50e+03 pdb=" N2 NAG D 903 " 0.353 2.00e-02 2.50e+03 pdb=" O7 NAG D 903 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 904 " 0.054 2.00e-02 2.50e+03 4.46e-02 2.48e+01 pdb=" C7 NAG D 904 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG D 904 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG D 904 " -0.070 2.00e-02 2.50e+03 pdb=" O7 NAG D 904 " -0.009 2.00e-02 2.50e+03 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 75 2.63 - 3.20: 6069 3.20 - 3.76: 10152 3.76 - 4.33: 14209 4.33 - 4.90: 23577 Nonbonded interactions: 54082 Sorted by model distance: nonbonded pdb=" O ALA D 501 " pdb=" OG SER D 507 " model vdw 2.059 3.040 nonbonded pdb=" O GLN D 388 " pdb=" NH1 ARG D 393 " model vdw 2.184 3.120 nonbonded pdb=" OE2 GLU D 402 " pdb="ZN ZN D 902 " model vdw 2.186 2.230 nonbonded pdb=" O TYR D 515 " pdb=" OG1 THR D 519 " model vdw 2.249 3.040 nonbonded pdb=" OG SER D 331 " pdb=" O ILE D 358 " model vdw 2.250 3.040 ... (remaining 54077 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: 13.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 0.155 6671 Z= 0.135 Angle : 0.561 19.811 9071 Z= 0.272 Chirality : 0.056 1.244 953 Planarity : 0.009 0.210 1172 Dihedral : 13.169 89.215 2394 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.27), residues: 789 helix: -0.48 (0.24), residues: 396 sheet: -1.57 (0.71), residues: 45 loop : -1.92 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 482 TYR 0.007 0.001 TYR A 369 PHE 0.005 0.001 PHE A 515 TRP 0.005 0.000 TRP D 165 HIS 0.001 0.000 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.12 ( 6666) covalent geometry : angle 0.47213 / 0.25 ( 9060) SS BOND : bond 0.00060 / 0.03 ( 1) SS BOND : angle 0.25074 / 0.15 ( 2) hydrogen bonds : bond 0.16039 / 9.41 ( 300) hydrogen bonds : angle 5.48091 / 3.74 ( 846) metal coordination : bond 0.15493 / 8.15 ( 1) link_NAG-ASN : bond 0.02086 / 1.07 ( 3) link_NAG-ASN : angle 9.60581 / 5.77 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8069 (p0) cc_final: 0.7817 (p0) REVERT: D 37 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6286 (mt-10) REVERT: D 94 LYS cc_start: 0.7854 (tttt) cc_final: 0.7563 (ttpp) REVERT: D 270 MET cc_start: 0.7896 (tpp) cc_final: 0.7638 (tpt) REVERT: D 294 THR cc_start: 0.6608 (p) cc_final: 0.6081 (p) REVERT: D 295 ASP cc_start: 0.6697 (p0) cc_final: 0.6268 (t0) REVERT: D 556 ASN cc_start: 0.7117 (m-40) cc_final: 0.6889 (m-40) REVERT: D 589 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6439 (tp30) REVERT: D 613 TYR cc_start: 0.6279 (p90) cc_final: 0.5933 (p90) outliers start: 0 outliers final: 2 residues processed: 200 average time/residue: 0.5479 time to fit residues: 115.2047 Evaluate side-chains 150 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.0970 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0470 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.0060 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.0970 chunk 74 optimal weight: 0.9980 overall best weight: 0.0688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN A 437 ASN A 439 ASN A 448 ASN A 460 ASN A 474 GLN A 481 ASN D 51 ASN D 96 GLN D 101 GLN D 149 ASN D 300 GLN D 401 HIS D 505 HIS D 522 GLN D 524 GLN D 578 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.146854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.132013 restraints weight = 9467.352| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.99 r_work: 0.3608 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6671 Z= 0.115 Angle : 0.551 10.383 9071 Z= 0.276 Chirality : 0.041 0.132 953 Planarity : 0.004 0.037 1172 Dihedral : 3.327 27.802 866 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.02 % Allowed : 18.97 % Favored : 78.02 % 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: -0.47 (0.29), residues: 789 helix: 0.48 (0.26), residues: 401 sheet: -0.89 (0.78), residues: 45 loop : -1.12 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 204 TYR 0.018 0.001 TYR A 369 PHE 0.022 0.002 PHE D 555 TRP 0.011 0.001 TRP D 203 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 6666) covalent geometry : angle 0.54178 / 0.27 ( 9060) SS BOND : bond 0.00106 / 0.06 ( 1) SS BOND : angle 0.35144 / 0.20 ( 2) hydrogen bonds : bond 0.04047 / 2.81 ( 300) hydrogen bonds : angle 4.58262 / 3.17 ( 846) metal coordination : bond 0.00386 / 0.20 ( 1) link_NAG-ASN : bond 0.00167 / 0.08 ( 3) link_NAG-ASN : angle 3.25849 / 1.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 331 ASN cc_start: 0.3590 (OUTLIER) cc_final: 0.3114 (p0) REVERT: D 37 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6963 (mt-10) REVERT: D 295 ASP cc_start: 0.6842 (p0) cc_final: 0.6611 (m-30) REVERT: D 363 LYS cc_start: 0.7708 (mptp) cc_final: 0.7472 (mptp) REVERT: D 518 ARG cc_start: 0.8353 (tmm160) cc_final: 0.8046 (ttp80) REVERT: D 555 PHE cc_start: 0.8345 (t80) cc_final: 0.8000 (t80) REVERT: D 556 ASN cc_start: 0.8079 (m-40) cc_final: 0.7771 (m-40) REVERT: D 613 TYR cc_start: 0.6703 (p90) cc_final: 0.6294 (p90) outliers start: 21 outliers final: 8 residues processed: 171 average time/residue: 0.5677 time to fit residues: 101.9595 Evaluate side-chains 157 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 445 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 0.0870 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 chunk 11 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 0.0870 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 GLN D 239 HIS D 345 HIS D 373 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.142724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127190 restraints weight = 9296.522| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.06 r_work: 0.3541 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6671 Z= 0.130 Angle : 0.534 8.742 9071 Z= 0.269 Chirality : 0.041 0.138 953 Planarity : 0.004 0.036 1172 Dihedral : 3.411 17.770 862 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.30 % Allowed : 20.26 % Favored : 76.44 % 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: -0.12 (0.30), residues: 789 helix: 0.73 (0.26), residues: 404 sheet: -0.72 (0.76), residues: 45 loop : -0.92 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 204 TYR 0.022 0.001 TYR D 50 PHE 0.014 0.002 PHE D 555 TRP 0.008 0.001 TRP D 168 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 6666) covalent geometry : angle 0.52602 / 0.27 ( 9060) SS BOND : bond 0.00996 / 0.52 ( 1) SS BOND : angle 0.21087 / 0.11 ( 2) hydrogen bonds : bond 0.04363 / 2.99 ( 300) hydrogen bonds : angle 4.46009 / 3.09 ( 846) metal coordination : bond 0.00115 / 0.06 ( 1) link_NAG-ASN : bond 0.00065 / 0.03 ( 3) link_NAG-ASN : angle 3.02778 / 1.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8534 (p0) cc_final: 0.8237 (p0) REVERT: D 37 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7206 (mt-10) REVERT: D 68 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7602 (ttmm) REVERT: D 114 LYS cc_start: 0.7988 (mmmt) cc_final: 0.7584 (mmmt) REVERT: D 131 LYS cc_start: 0.7289 (tppt) cc_final: 0.7085 (tttp) REVERT: D 295 ASP cc_start: 0.7004 (p0) cc_final: 0.6795 (m-30) REVERT: D 347 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.8015 (p) REVERT: D 416 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7564 (ptpt) REVERT: D 435 GLU cc_start: 0.7430 (tp30) cc_final: 0.7200 (tp30) REVERT: D 518 ARG cc_start: 0.8357 (tmm160) cc_final: 0.8031 (ppt90) REVERT: D 541 LYS cc_start: 0.7507 (mttm) cc_final: 0.7293 (mttp) REVERT: D 555 PHE cc_start: 0.8409 (t80) cc_final: 0.8177 (t80) REVERT: D 556 ASN cc_start: 0.8087 (m-40) cc_final: 0.7829 (m-40) REVERT: D 558 LEU cc_start: 0.7727 (mt) cc_final: 0.7282 (mp) REVERT: D 613 TYR cc_start: 0.7100 (p90) cc_final: 0.6594 (p90) outliers start: 23 outliers final: 9 residues processed: 170 average time/residue: 0.5220 time to fit residues: 93.2715 Evaluate side-chains 160 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 445 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 68 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 chunk 2 optimal weight: 0.0980 chunk 61 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 overall best weight: 0.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN D 330 ASN D 345 HIS D 373 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.141238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.125897 restraints weight = 9374.540| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.07 r_work: 0.3513 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6671 Z= 0.134 Angle : 0.537 10.211 9071 Z= 0.269 Chirality : 0.041 0.135 953 Planarity : 0.004 0.043 1172 Dihedral : 3.513 13.956 862 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.88 % Allowed : 20.40 % Favored : 75.72 % 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: 0.13 (0.30), residues: 789 helix: 0.92 (0.27), residues: 398 sheet: -0.59 (0.75), residues: 43 loop : -0.74 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 204 TYR 0.019 0.001 TYR D 50 PHE 0.017 0.002 PHE D 285 TRP 0.010 0.001 TRP D 168 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 6666) covalent geometry : angle 0.52970 / 0.27 ( 9060) SS BOND : bond 0.00336 / 0.18 ( 1) SS BOND : angle 0.33338 / 0.18 ( 2) hydrogen bonds : bond 0.04507 / 3.11 ( 300) hydrogen bonds : angle 4.45038 / 3.09 ( 846) metal coordination : bond 0.00225 / 0.12 ( 1) link_NAG-ASN : bond 0.00078 / 0.04 ( 3) link_NAG-ASN : angle 2.86112 / 1.66 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8433 (p0) cc_final: 0.8159 (p0) REVERT: A 408 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8276 (m) REVERT: D 37 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7237 (mt-10) REVERT: D 43 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8640 (p) REVERT: D 114 LYS cc_start: 0.7920 (mmmt) cc_final: 0.7605 (mmmm) REVERT: D 157 ASP cc_start: 0.7449 (t0) cc_final: 0.7174 (t70) REVERT: D 295 ASP cc_start: 0.6937 (p0) cc_final: 0.6732 (t0) REVERT: D 347 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.8130 (p) REVERT: D 416 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7553 (ptpt) REVERT: D 470 LYS cc_start: 0.8573 (tppp) cc_final: 0.8209 (ttpp) REVERT: D 518 ARG cc_start: 0.8324 (tmm160) cc_final: 0.8063 (ttp80) REVERT: D 541 LYS cc_start: 0.7538 (mttm) cc_final: 0.7238 (mttp) REVERT: D 556 ASN cc_start: 0.8104 (m-40) cc_final: 0.7805 (m110) REVERT: D 558 LEU cc_start: 0.7725 (mt) cc_final: 0.7306 (mp) REVERT: D 579 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.8019 (ptp) REVERT: D 613 TYR cc_start: 0.7265 (p90) cc_final: 0.6685 (p90) outliers start: 27 outliers final: 10 residues processed: 175 average time/residue: 0.5052 time to fit residues: 92.9200 Evaluate side-chains 165 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 60 optimal weight: 0.0770 chunk 50 optimal weight: 0.4980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 ASN D 96 GLN D 378 HIS D 401 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.137393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.122464 restraints weight = 9415.202| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.05 r_work: 0.3460 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6671 Z= 0.203 Angle : 0.593 9.769 9071 Z= 0.301 Chirality : 0.044 0.135 953 Planarity : 0.004 0.042 1172 Dihedral : 4.095 19.616 862 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.31 % Allowed : 20.69 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.30), residues: 789 helix: 0.84 (0.27), residues: 400 sheet: -0.61 (0.73), residues: 43 loop : -0.87 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 559 TYR 0.025 0.002 TYR D 50 PHE 0.024 0.002 PHE D 285 TRP 0.015 0.002 TRP D 349 HIS 0.009 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.20 ( 6666) covalent geometry : angle 0.58462 / 0.30 ( 9060) SS BOND : bond 0.00478 / 0.25 ( 1) SS BOND : angle 0.66280 / 0.39 ( 2) hydrogen bonds : bond 0.05350 / 3.66 ( 300) hydrogen bonds : angle 4.54894 / 3.17 ( 846) metal coordination : bond 0.00407 / 0.21 ( 1) link_NAG-ASN : bond 0.00210 / 0.10 ( 3) link_NAG-ASN : angle 3.23056 / 1.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.6176 (mt) REVERT: A 405 ASN cc_start: 0.8398 (p0) cc_final: 0.8149 (p0) REVERT: A 408 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8290 (m) REVERT: D 37 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7364 (mt-10) REVERT: D 43 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8573 (p) REVERT: D 81 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7904 (mm-40) REVERT: D 114 LYS cc_start: 0.7897 (mmmt) cc_final: 0.7573 (mmmm) REVERT: D 142 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6330 (pp) REVERT: D 157 ASP cc_start: 0.7364 (t0) cc_final: 0.7079 (t70) REVERT: D 363 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7752 (mmtt) REVERT: D 406 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7651 (mm-30) REVERT: D 518 ARG cc_start: 0.8323 (tmm160) cc_final: 0.8028 (ttp80) REVERT: D 556 ASN cc_start: 0.8210 (m-40) cc_final: 0.7619 (m110) REVERT: D 613 TYR cc_start: 0.7561 (p90) cc_final: 0.7019 (p90) outliers start: 30 outliers final: 13 residues processed: 170 average time/residue: 0.5056 time to fit residues: 90.5090 Evaluate side-chains 161 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 445 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0040 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 60 optimal weight: 0.5980 chunk 48 optimal weight: 0.0870 chunk 77 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 210 ASN D 287 GLN D 401 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122037 restraints weight = 9289.384| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.99 r_work: 0.3460 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6671 Z= 0.195 Angle : 0.581 9.001 9071 Z= 0.294 Chirality : 0.043 0.137 953 Planarity : 0.004 0.042 1172 Dihedral : 4.115 18.260 862 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.59 % Allowed : 21.26 % Favored : 75.14 % 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 (0.30), residues: 789 helix: 0.83 (0.26), residues: 400 sheet: -0.71 (0.72), residues: 43 loop : -0.91 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 460 TYR 0.016 0.002 TYR A 369 PHE 0.024 0.002 PHE D 285 TRP 0.016 0.002 TRP D 168 HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 ( 6666) covalent geometry : angle 0.57269 / 0.29 ( 9060) SS BOND : bond 0.00407 / 0.21 ( 1) SS BOND : angle 0.71717 / 0.41 ( 2) hydrogen bonds : bond 0.05173 / 3.56 ( 300) hydrogen bonds : angle 4.50484 / 3.14 ( 846) metal coordination : bond 0.00339 / 0.18 ( 1) link_NAG-ASN : bond 0.00206 / 0.10 ( 3) link_NAG-ASN : angle 3.16209 / 1.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8416 (p0) cc_final: 0.8127 (p0) REVERT: A 408 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8308 (m) REVERT: D 114 LYS cc_start: 0.7913 (mmmt) cc_final: 0.7678 (mmmm) REVERT: D 142 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.6088 (pp) REVERT: D 157 ASP cc_start: 0.7301 (t0) cc_final: 0.7026 (t70) REVERT: D 349 TRP cc_start: 0.8644 (m100) cc_final: 0.8343 (m100) REVERT: D 363 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7733 (mmtt) REVERT: D 406 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7599 (mm-30) REVERT: D 416 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7467 (ptpt) REVERT: D 458 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7846 (ttmm) REVERT: D 518 ARG cc_start: 0.8356 (tmm160) cc_final: 0.8030 (ttp80) REVERT: D 541 LYS cc_start: 0.7622 (mttt) cc_final: 0.7397 (mttp) REVERT: D 556 ASN cc_start: 0.8240 (m-40) cc_final: 0.7716 (m110) REVERT: D 577 LYS cc_start: 0.8401 (mtpt) cc_final: 0.8069 (mtpp) REVERT: D 613 TYR cc_start: 0.7557 (p90) cc_final: 0.7082 (p90) outliers start: 25 outliers final: 14 residues processed: 174 average time/residue: 0.5165 time to fit residues: 94.6283 Evaluate side-chains 162 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 458 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.136941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.122236 restraints weight = 9127.622| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.98 r_work: 0.3466 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6671 Z= 0.180 Angle : 0.566 8.051 9071 Z= 0.286 Chirality : 0.043 0.134 953 Planarity : 0.004 0.042 1172 Dihedral : 4.052 17.431 862 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.30 % Allowed : 22.99 % Favored : 73.71 % 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: 0.01 (0.30), residues: 789 helix: 0.88 (0.27), residues: 400 sheet: -0.67 (0.72), residues: 43 loop : -0.90 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 460 TYR 0.019 0.002 TYR D 50 PHE 0.025 0.002 PHE D 285 TRP 0.019 0.002 TRP D 168 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 6666) covalent geometry : angle 0.55920 / 0.28 ( 9060) SS BOND : bond 0.00536 / 0.28 ( 1) SS BOND : angle 0.67748 / 0.39 ( 2) hydrogen bonds : bond 0.05088 / 3.51 ( 300) hydrogen bonds : angle 4.49040 / 3.12 ( 846) metal coordination : bond 0.00402 / 0.21 ( 1) link_NAG-ASN : bond 0.00131 / 0.07 ( 3) link_NAG-ASN : angle 2.77370 / 1.55 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8411 (p0) cc_final: 0.8103 (p0) REVERT: A 408 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8278 (m) REVERT: D 37 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7363 (mp0) REVERT: D 43 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8588 (p) REVERT: D 114 LYS cc_start: 0.7889 (mmmt) cc_final: 0.7588 (mmmt) REVERT: D 157 ASP cc_start: 0.7273 (t0) cc_final: 0.6996 (t70) REVERT: D 323 MET cc_start: 0.8419 (mmm) cc_final: 0.8128 (mmt) REVERT: D 349 TRP cc_start: 0.8592 (m100) cc_final: 0.8343 (m100) REVERT: D 363 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7773 (mmtt) REVERT: D 406 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7616 (mm-30) REVERT: D 416 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7459 (ptpt) REVERT: D 518 ARG cc_start: 0.8334 (tmm160) cc_final: 0.8044 (ttp80) REVERT: D 541 LYS cc_start: 0.7579 (mttt) cc_final: 0.7317 (mttp) REVERT: D 556 ASN cc_start: 0.8298 (m-40) cc_final: 0.7812 (m-40) REVERT: D 577 LYS cc_start: 0.8398 (mtpt) cc_final: 0.8080 (mtpp) REVERT: D 613 TYR cc_start: 0.7586 (p90) cc_final: 0.7080 (p90) outliers start: 23 outliers final: 14 residues processed: 170 average time/residue: 0.4924 time to fit residues: 88.2856 Evaluate side-chains 166 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 476 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 0.0870 chunk 66 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 7 optimal weight: 0.0970 chunk 75 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.137296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.122547 restraints weight = 9098.173| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.97 r_work: 0.3454 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6671 Z= 0.160 Angle : 0.557 6.838 9071 Z= 0.282 Chirality : 0.042 0.142 953 Planarity : 0.004 0.042 1172 Dihedral : 3.995 16.434 862 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.59 % Allowed : 23.99 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.30), residues: 789 helix: 0.93 (0.27), residues: 400 sheet: -0.60 (0.73), residues: 43 loop : -0.88 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 559 TYR 0.017 0.001 TYR A 369 PHE 0.025 0.002 PHE D 285 TRP 0.024 0.001 TRP D 168 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 6666) covalent geometry : angle 0.55056 / 0.28 ( 9060) SS BOND : bond 0.00328 / 0.17 ( 1) SS BOND : angle 0.65687 / 0.38 ( 2) hydrogen bonds : bond 0.04913 / 3.38 ( 300) hydrogen bonds : angle 4.46377 / 3.10 ( 846) metal coordination : bond 0.00307 / 0.16 ( 1) link_NAG-ASN : bond 0.00094 / 0.05 ( 3) link_NAG-ASN : angle 2.71934 / 1.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8398 (p0) cc_final: 0.8098 (p0) REVERT: A 408 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8291 (m) REVERT: D 37 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7134 (mp0) REVERT: D 43 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8604 (p) REVERT: D 114 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7582 (mmmt) REVERT: D 157 ASP cc_start: 0.7259 (t0) cc_final: 0.6977 (t70) REVERT: D 323 MET cc_start: 0.8394 (mmm) cc_final: 0.8188 (mmt) REVERT: D 363 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7784 (mmtt) REVERT: D 406 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7490 (mm-30) REVERT: D 416 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7446 (ptpt) REVERT: D 518 ARG cc_start: 0.8327 (tmm160) cc_final: 0.8026 (ttp80) REVERT: D 541 LYS cc_start: 0.7564 (mttt) cc_final: 0.7321 (mttp) REVERT: D 556 ASN cc_start: 0.8280 (m-40) cc_final: 0.7853 (m-40) REVERT: D 577 LYS cc_start: 0.8419 (mtpt) cc_final: 0.8090 (mtpp) REVERT: D 613 TYR cc_start: 0.7586 (p90) cc_final: 0.7057 (p90) outliers start: 18 outliers final: 11 residues processed: 175 average time/residue: 0.4846 time to fit residues: 89.4297 Evaluate side-chains 166 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 476 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 401 HIS D 493 HIS D 508 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.133020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118663 restraints weight = 9291.441| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.95 r_work: 0.3397 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 6671 Z= 0.382 Angle : 0.725 10.348 9071 Z= 0.368 Chirality : 0.052 0.250 953 Planarity : 0.005 0.057 1172 Dihedral : 4.815 23.736 862 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.16 % Allowed : 22.70 % Favored : 74.14 % 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: 789 helix: 0.56 (0.26), residues: 391 sheet: -1.02 (0.69), residues: 44 loop : -1.16 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 559 TYR 0.020 0.002 TYR D 385 PHE 0.029 0.003 PHE D 285 TRP 0.027 0.003 TRP D 168 HIS 0.009 0.002 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00913 / 0.38 ( 6666) covalent geometry : angle 0.71799 / 0.37 ( 9060) SS BOND : bond 0.00489 / 0.26 ( 1) SS BOND : angle 2.13209 / 1.24 ( 2) hydrogen bonds : bond 0.06560 / 4.44 ( 300) hydrogen bonds : angle 4.74253 / 3.29 ( 846) metal coordination : bond 0.00832 / 0.44 ( 1) link_NAG-ASN : bond 0.00384 / 0.20 ( 3) link_NAG-ASN : angle 3.23559 / 1.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8397 (p0) cc_final: 0.8132 (p0) REVERT: A 408 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8267 (m) REVERT: D 37 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7431 (mt-10) REVERT: D 114 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7686 (mmmt) REVERT: D 122 THR cc_start: 0.8628 (t) cc_final: 0.8289 (p) REVERT: D 157 ASP cc_start: 0.7238 (t0) cc_final: 0.6978 (t0) REVERT: D 256 ILE cc_start: 0.8144 (mm) cc_final: 0.7941 (mt) REVERT: D 335 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6927 (p0) REVERT: D 363 LYS cc_start: 0.8347 (mmtt) cc_final: 0.8089 (mmtt) REVERT: D 406 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7514 (mm-30) REVERT: D 416 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7426 (ptpt) REVERT: D 435 GLU cc_start: 0.7532 (tp30) cc_final: 0.7284 (tp30) REVERT: D 458 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7743 (ttmm) REVERT: D 518 ARG cc_start: 0.8328 (tmm160) cc_final: 0.8054 (ttp80) REVERT: D 541 LYS cc_start: 0.7740 (mttt) cc_final: 0.7459 (mttp) REVERT: D 556 ASN cc_start: 0.8300 (m-40) cc_final: 0.7889 (m-40) REVERT: D 613 TYR cc_start: 0.7649 (p90) cc_final: 0.7237 (p90) outliers start: 22 outliers final: 12 residues processed: 171 average time/residue: 0.5600 time to fit residues: 100.8134 Evaluate side-chains 164 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 458 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 52 optimal weight: 0.4980 chunk 55 optimal weight: 0.3980 chunk 4 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 65.122 > 50:) chunk 22 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 0.2980 chunk 56 optimal weight: 0.4980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 448 ASN D 210 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121499 restraints weight = 9179.063| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.97 r_work: 0.3436 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6671 Z= 0.189 Angle : 0.610 8.262 9071 Z= 0.309 Chirality : 0.044 0.167 953 Planarity : 0.005 0.051 1172 Dihedral : 4.325 18.772 862 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.30 % Allowed : 24.71 % Favored : 72.99 % 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: -0.21 (0.30), residues: 789 helix: 0.82 (0.27), residues: 389 sheet: -0.87 (0.71), residues: 44 loop : -1.10 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 559 TYR 0.029 0.002 TYR D 50 PHE 0.023 0.002 PHE D 285 TRP 0.041 0.002 TRP D 168 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 ( 6666) covalent geometry : angle 0.60198 / 0.31 ( 9060) SS BOND : bond 0.00498 / 0.26 ( 1) SS BOND : angle 1.25164 / 0.73 ( 2) hydrogen bonds : bond 0.05313 / 3.63 ( 300) hydrogen bonds : angle 4.59266 / 3.19 ( 846) metal coordination : bond 0.00383 / 0.20 ( 1) link_NAG-ASN : bond 0.00173 / 0.09 ( 3) link_NAG-ASN : angle 3.05118 / 1.71 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8403 (p0) cc_final: 0.8081 (p0) REVERT: A 408 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8271 (m) REVERT: D 114 LYS cc_start: 0.7922 (mmmt) cc_final: 0.7638 (mmmt) REVERT: D 157 ASP cc_start: 0.7228 (t0) cc_final: 0.6948 (t0) REVERT: D 323 MET cc_start: 0.8508 (mmm) cc_final: 0.8208 (mmt) REVERT: D 363 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7877 (mmtt) REVERT: D 406 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7488 (mm-30) REVERT: D 416 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7419 (ptpt) REVERT: D 518 ARG cc_start: 0.8364 (tmm160) cc_final: 0.8049 (ttp80) REVERT: D 541 LYS cc_start: 0.7626 (mttt) cc_final: 0.7362 (mttp) REVERT: D 556 ASN cc_start: 0.8265 (m-40) cc_final: 0.7829 (m-40) REVERT: D 613 TYR cc_start: 0.7609 (p90) cc_final: 0.7121 (p90) outliers start: 16 outliers final: 9 residues processed: 168 average time/residue: 0.4988 time to fit residues: 88.7187 Evaluate side-chains 158 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 445 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 0.0980 chunk 16 optimal weight: 0.4980 chunk 51 optimal weight: 0.2980 chunk 55 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 20 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 38 optimal weight: 0.0270 chunk 40 optimal weight: 0.0770 overall best weight: 0.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123882 restraints weight = 9245.626| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.96 r_work: 0.3498 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6671 Z= 0.115 Angle : 0.556 8.113 9071 Z= 0.281 Chirality : 0.041 0.132 953 Planarity : 0.004 0.044 1172 Dihedral : 3.849 14.976 862 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.29 % Allowed : 26.15 % Favored : 72.56 % 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: 0.06 (0.30), residues: 789 helix: 1.02 (0.27), residues: 390 sheet: -0.78 (0.72), residues: 44 loop : -0.93 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 559 TYR 0.018 0.001 TYR A 369 PHE 0.022 0.001 PHE D 285 TRP 0.052 0.002 TRP D 168 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 6666) covalent geometry : angle 0.55043 / 0.28 ( 9060) SS BOND : bond 0.00067 / 0.04 ( 1) SS BOND : angle 0.38314 / 0.23 ( 2) hydrogen bonds : bond 0.04383 / 3.03 ( 300) hydrogen bonds : angle 4.43875 / 3.08 ( 846) metal coordination : bond 0.00061 / 0.03 ( 1) link_NAG-ASN : bond 0.00198 / 0.09 ( 3) link_NAG-ASN : angle 2.65738 / 1.50 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2742.37 seconds wall clock time: 47 minutes 33.35 seconds (2853.35 seconds total)