Starting phenix.real_space_refine on Tue Mar 3 15:21:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo9_33341/03_2026/7xo9_33341.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo9_33341/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xo9_33341/03_2026/7xo9_33341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo9_33341/03_2026/7xo9_33341.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xo9_33341/03_2026/7xo9_33341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo9_33341/03_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-dev-5986/lib/python3.9/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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.69, per 1000 atoms: 0.26 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: 0.85 Conformation dependent library (CDL) restraints added in 183.2 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: 0.21 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: 1.06 Time building geometry restraints manager: 1.03 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: 3643 17.84 - 35.69: 249 35.69 - 53.53: 43 53.53 - 71.37: 13 71.37 - 89.22: 6 Dihedral angle restraints: 3954 sinusoidal: 1626 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 3951 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: 10.480 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.940 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:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 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 : 13.058 89.215 2457 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 covalent geometry : bond 0.00226 ( 6666) covalent geometry : angle 0.47213 ( 9060) SS BOND : bond 0.00060 ( 1) SS BOND : angle 0.25074 ( 2) hydrogen bonds : bond 0.16039 ( 300) hydrogen bonds : angle 5.48091 ( 846) metal coordination : bond 0.15493 ( 1) link_NAG-ASN : bond 0.02086 ( 3) link_NAG-ASN : angle 9.60581 ( 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 : 0.217 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: 0.5560 time to fit residues: 116.4441 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 : 0.209 ------------------------------------------------------------------------------- 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: 0.7980 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3906 r_free = 0.3906 target = 0.146767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.131918 restraints weight = 9447.573| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.99 r_work: 0.3615 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6671 Z= 0.114 Angle : 0.544 10.159 9071 Z= 0.273 Chirality : 0.041 0.134 953 Planarity : 0.004 0.036 1172 Dihedral : 3.599 29.455 929 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.87 % Allowed : 19.40 % Favored : 77.73 % 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: 400 sheet: -0.88 (0.78), residues: 45 loop : -1.13 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 204 TYR 0.020 0.001 TYR A 369 PHE 0.023 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 covalent geometry : bond 0.00240 ( 6666) covalent geometry : angle 0.53349 ( 9060) SS BOND : bond 0.00075 ( 1) SS BOND : angle 0.39149 ( 2) hydrogen bonds : bond 0.04052 ( 300) hydrogen bonds : angle 4.56709 ( 846) metal coordination : bond 0.00161 ( 1) link_NAG-ASN : bond 0.00257 ( 3) link_NAG-ASN : angle 3.36390 ( 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 175 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 331 ASN cc_start: 0.3563 (OUTLIER) cc_final: 0.3094 (p0) REVERT: D 37 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6983 (mt-10) REVERT: D 363 LYS cc_start: 0.7699 (mptp) cc_final: 0.7460 (mptp) REVERT: D 518 ARG cc_start: 0.8349 (tmm160) cc_final: 0.8044 (ttp80) REVERT: D 555 PHE cc_start: 0.8330 (t80) cc_final: 0.7955 (t80) REVERT: D 556 ASN cc_start: 0.8083 (m-40) cc_final: 0.7764 (m-40) REVERT: D 613 TYR cc_start: 0.6711 (p90) cc_final: 0.6298 (p90) outliers start: 20 outliers final: 7 residues processed: 169 average time/residue: 0.5614 time to fit residues: 99.5099 Evaluate side-chains 152 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 0.0060 chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 59 optimal weight: 0.0030 chunk 65 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 0.0770 overall best weight: 0.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 ASN 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 = 0.3850 r_free = 0.3850 target = 0.142058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.127034 restraints weight = 9346.513| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.02 r_work: 0.3550 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6671 Z= 0.125 Angle : 0.528 8.713 9071 Z= 0.265 Chirality : 0.041 0.137 953 Planarity : 0.004 0.036 1172 Dihedral : 3.447 16.413 925 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.30 % Allowed : 20.83 % Favored : 75.86 % 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: 0.77 (0.26), residues: 403 sheet: -0.71 (0.76), residues: 45 loop : -0.89 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 204 TYR 0.023 0.001 TYR D 50 PHE 0.014 0.001 PHE D 285 TRP 0.007 0.001 TRP D 168 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6666) covalent geometry : angle 0.51917 ( 9060) SS BOND : bond 0.00698 ( 1) SS BOND : angle 0.25259 ( 2) hydrogen bonds : bond 0.04287 ( 300) hydrogen bonds : angle 4.45585 ( 846) metal coordination : bond 0.00121 ( 1) link_NAG-ASN : bond 0.00079 ( 3) link_NAG-ASN : angle 3.09583 ( 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 175 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8528 (p0) cc_final: 0.8221 (p0) REVERT: D 37 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7165 (mt-10) REVERT: D 68 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7658 (ttmm) REVERT: D 101 GLN cc_start: 0.7527 (tt0) cc_final: 0.7288 (tt0) REVERT: D 114 LYS cc_start: 0.8028 (mmmt) cc_final: 0.7601 (mmmt) REVERT: D 181 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7115 (mt-10) REVERT: D 347 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7977 (p) REVERT: D 416 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7543 (ptpt) REVERT: D 435 GLU cc_start: 0.7439 (tp30) cc_final: 0.7213 (tp30) REVERT: D 518 ARG cc_start: 0.8346 (tmm160) cc_final: 0.8046 (ppt90) REVERT: D 541 LYS cc_start: 0.7473 (mttm) cc_final: 0.7272 (mttp) REVERT: D 555 PHE cc_start: 0.8389 (t80) cc_final: 0.8183 (t80) REVERT: D 556 ASN cc_start: 0.8065 (m-40) cc_final: 0.7751 (m-40) REVERT: D 558 LEU cc_start: 0.7660 (mt) cc_final: 0.7236 (mp) REVERT: D 613 TYR cc_start: 0.7022 (p90) cc_final: 0.6521 (p90) outliers start: 23 outliers final: 9 residues processed: 168 average time/residue: 0.5473 time to fit residues: 96.5476 Evaluate side-chains 164 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 212 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 295 ASP 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: 0.0070 chunk 8 optimal weight: 0.5980 chunk 50 optimal weight: 0.0670 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 2 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 overall best weight: 0.2334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN D 81 GLN D 96 GLN D 330 ASN D 345 HIS D 373 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125370 restraints weight = 9397.085| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.06 r_work: 0.3511 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6671 Z= 0.139 Angle : 0.550 11.075 9071 Z= 0.273 Chirality : 0.042 0.129 953 Planarity : 0.004 0.042 1172 Dihedral : 3.565 14.585 925 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.88 % Allowed : 19.83 % Favored : 76.29 % 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: 0.10 (0.30), residues: 789 helix: 0.88 (0.26), residues: 399 sheet: -0.63 (0.75), residues: 43 loop : -0.74 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 559 TYR 0.018 0.001 TYR D 50 PHE 0.016 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 covalent geometry : bond 0.00321 ( 6666) covalent geometry : angle 0.54207 ( 9060) SS BOND : bond 0.00334 ( 1) SS BOND : angle 0.34203 ( 2) hydrogen bonds : bond 0.04581 ( 300) hydrogen bonds : angle 4.39276 ( 846) metal coordination : bond 0.00257 ( 1) link_NAG-ASN : bond 0.00061 ( 3) link_NAG-ASN : angle 2.94578 ( 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 183 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8416 (p0) cc_final: 0.8141 (p0) REVERT: D 37 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7253 (mt-10) REVERT: D 43 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8630 (p) REVERT: D 68 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7660 (ttmm) REVERT: D 77 SER cc_start: 0.8659 (t) cc_final: 0.8417 (m) REVERT: D 114 LYS cc_start: 0.7926 (mmmt) cc_final: 0.7620 (mmmm) REVERT: D 157 ASP cc_start: 0.7412 (t0) cc_final: 0.7143 (t70) REVERT: D 295 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.6522 (t0) REVERT: D 347 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8143 (p) REVERT: D 518 ARG cc_start: 0.8299 (tmm160) cc_final: 0.8041 (ttp80) REVERT: D 556 ASN cc_start: 0.8095 (m-40) cc_final: 0.7804 (m110) REVERT: D 613 TYR cc_start: 0.7302 (p90) cc_final: 0.6731 (p90) outliers start: 27 outliers final: 11 residues processed: 171 average time/residue: 0.5060 time to fit residues: 91.0121 Evaluate side-chains 167 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 347 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9990 chunk 25 optimal weight: 0.0270 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 75 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN D 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.137149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122142 restraints weight = 9425.400| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.04 r_work: 0.3461 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6671 Z= 0.200 Angle : 0.591 8.901 9071 Z= 0.301 Chirality : 0.044 0.141 953 Planarity : 0.004 0.039 1172 Dihedral : 4.096 20.739 925 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.02 % Allowed : 20.40 % Favored : 75.57 % 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: 0.83 (0.27), residues: 400 sheet: -0.67 (0.73), residues: 43 loop : -0.85 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 460 TYR 0.016 0.002 TYR D 50 PHE 0.022 0.002 PHE D 285 TRP 0.015 0.002 TRP D 477 HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 6666) covalent geometry : angle 0.58210 ( 9060) SS BOND : bond 0.00456 ( 1) SS BOND : angle 0.55237 ( 2) hydrogen bonds : bond 0.05267 ( 300) hydrogen bonds : angle 4.48159 ( 846) metal coordination : bond 0.00403 ( 1) link_NAG-ASN : bond 0.00248 ( 3) link_NAG-ASN : angle 3.23428 ( 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 182 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8394 (p0) cc_final: 0.8147 (p0) REVERT: A 408 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8256 (m) REVERT: D 37 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7350 (mt-10) REVERT: D 43 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8581 (p) REVERT: D 114 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7602 (mmmm) REVERT: D 157 ASP cc_start: 0.7368 (t0) cc_final: 0.7084 (t70) REVERT: D 295 ASP cc_start: 0.6879 (OUTLIER) cc_final: 0.6639 (t0) REVERT: D 349 TRP cc_start: 0.8706 (m100) cc_final: 0.8361 (m100) REVERT: D 363 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7753 (mmtt) REVERT: D 470 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8326 (ttpp) REVERT: D 518 ARG cc_start: 0.8331 (tmm160) cc_final: 0.8056 (ttp80) REVERT: D 556 ASN cc_start: 0.8249 (m-40) cc_final: 0.7718 (m110) REVERT: D 613 TYR cc_start: 0.7531 (p90) cc_final: 0.6980 (p90) outliers start: 28 outliers final: 10 residues processed: 174 average time/residue: 0.5418 time to fit residues: 98.8536 Evaluate side-chains 164 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 254 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 470 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 210 ASN D 287 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 = 0.3753 r_free = 0.3753 target = 0.136050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121099 restraints weight = 9375.720| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.02 r_work: 0.3448 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6671 Z= 0.211 Angle : 0.593 10.222 9071 Z= 0.300 Chirality : 0.044 0.141 953 Planarity : 0.004 0.043 1172 Dihedral : 4.193 18.323 925 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.74 % Allowed : 20.69 % Favored : 75.57 % 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: 0.82 (0.26), residues: 399 sheet: -0.73 (0.71), residues: 43 loop : -0.94 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 204 TYR 0.016 0.002 TYR A 369 PHE 0.024 0.002 PHE D 285 TRP 0.015 0.002 TRP D 168 HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 6666) covalent geometry : angle 0.58470 ( 9060) SS BOND : bond 0.00436 ( 1) SS BOND : angle 0.90708 ( 2) hydrogen bonds : bond 0.05286 ( 300) hydrogen bonds : angle 4.47614 ( 846) metal coordination : bond 0.00569 ( 1) link_NAG-ASN : bond 0.00228 ( 3) link_NAG-ASN : angle 3.21093 ( 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 184 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8411 (p0) cc_final: 0.8115 (p0) REVERT: A 408 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8262 (m) REVERT: D 114 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7645 (mmmm) REVERT: D 142 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5759 (pp) REVERT: D 157 ASP cc_start: 0.7323 (t0) cc_final: 0.7043 (t70) REVERT: D 295 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6684 (t0) REVERT: D 349 TRP cc_start: 0.8613 (m100) cc_final: 0.8358 (m100) REVERT: D 363 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7901 (mmtp) REVERT: D 406 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7608 (mm-30) REVERT: D 458 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7860 (ttmm) REVERT: D 518 ARG cc_start: 0.8323 (tmm160) cc_final: 0.8007 (ttp80) REVERT: D 556 ASN cc_start: 0.8300 (m-40) cc_final: 0.7801 (m-40) REVERT: D 577 LYS cc_start: 0.8395 (mtpt) cc_final: 0.8194 (mtpt) REVERT: D 613 TYR cc_start: 0.7557 (p90) cc_final: 0.6998 (p90) outliers start: 26 outliers final: 13 residues processed: 178 average time/residue: 0.5502 time to fit residues: 102.5667 Evaluate side-chains 167 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 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 295 ASP 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: 0.9990 chunk 22 optimal weight: 0.0980 chunk 15 optimal weight: 0.2980 chunk 52 optimal weight: 0.3980 chunk 55 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 71 optimal weight: 0.0870 chunk 16 optimal weight: 0.4980 overall best weight: 0.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.137870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122860 restraints weight = 9217.817| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.01 r_work: 0.3475 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6671 Z= 0.137 Angle : 0.545 7.278 9071 Z= 0.275 Chirality : 0.041 0.130 953 Planarity : 0.004 0.042 1172 Dihedral : 3.877 14.929 925 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.59 % Allowed : 22.56 % Favored : 73.85 % 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: 0.14 (0.30), residues: 789 helix: 1.01 (0.27), residues: 398 sheet: -0.50 (0.73), residues: 43 loop : -0.87 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 559 TYR 0.017 0.001 TYR A 369 PHE 0.026 0.001 PHE D 285 TRP 0.020 0.001 TRP D 168 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6666) covalent geometry : angle 0.53914 ( 9060) SS BOND : bond 0.00233 ( 1) SS BOND : angle 0.34053 ( 2) hydrogen bonds : bond 0.04645 ( 300) hydrogen bonds : angle 4.42653 ( 846) metal coordination : bond 0.00190 ( 1) link_NAG-ASN : bond 0.00109 ( 3) link_NAG-ASN : angle 2.54162 ( 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 182 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8397 (p0) cc_final: 0.8092 (p0) REVERT: A 408 SER cc_start: 0.8586 (OUTLIER) cc_final: 0.8301 (m) REVERT: D 37 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7205 (mp0) REVERT: D 43 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8617 (p) REVERT: D 114 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7545 (mmmm) REVERT: D 157 ASP cc_start: 0.7290 (t0) cc_final: 0.6987 (t70) REVERT: D 295 ASP cc_start: 0.6897 (OUTLIER) cc_final: 0.6658 (t0) REVERT: D 335 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6687 (p0) REVERT: D 349 TRP cc_start: 0.8575 (m100) cc_final: 0.8331 (m100) REVERT: D 363 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7833 (mmtt) REVERT: D 458 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7898 (ttmm) REVERT: D 518 ARG cc_start: 0.8378 (tmm160) cc_final: 0.8109 (ttp80) REVERT: D 531 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: D 556 ASN cc_start: 0.8266 (m-40) cc_final: 0.7809 (m-40) REVERT: D 577 LYS cc_start: 0.8392 (mtpt) cc_final: 0.8068 (mtpm) REVERT: D 613 TYR cc_start: 0.7506 (p90) cc_final: 0.7075 (p90) outliers start: 25 outliers final: 12 residues processed: 174 average time/residue: 0.5193 time to fit residues: 95.1411 Evaluate side-chains 175 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 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 295 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 531 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 14 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 46 optimal weight: 0.0060 chunk 7 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121368 restraints weight = 9116.998| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.97 r_work: 0.3436 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6671 Z= 0.206 Angle : 0.594 8.684 9071 Z= 0.301 Chirality : 0.044 0.186 953 Planarity : 0.005 0.043 1172 Dihedral : 4.145 18.015 925 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.45 % Allowed : 22.70 % Favored : 73.85 % 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: -0.02 (0.30), residues: 789 helix: 0.94 (0.27), residues: 394 sheet: -0.68 (0.72), residues: 44 loop : -0.99 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 559 TYR 0.024 0.002 TYR D 50 PHE 0.027 0.002 PHE D 285 TRP 0.024 0.002 TRP D 168 HIS 0.009 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 6666) covalent geometry : angle 0.58732 ( 9060) SS BOND : bond 0.00422 ( 1) SS BOND : angle 0.98940 ( 2) hydrogen bonds : bond 0.05360 ( 300) hydrogen bonds : angle 4.50297 ( 846) metal coordination : bond 0.00421 ( 1) link_NAG-ASN : bond 0.00123 ( 3) link_NAG-ASN : angle 2.82949 ( 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: 24 poor density : 154 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 341 VAL cc_start: 0.7734 (m) cc_final: 0.7456 (p) REVERT: A 405 ASN cc_start: 0.8406 (p0) cc_final: 0.8098 (p0) REVERT: A 408 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.8270 (m) REVERT: D 37 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7336 (mp0) REVERT: D 114 LYS cc_start: 0.7907 (mmmt) cc_final: 0.7589 (mmmt) REVERT: D 142 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.6100 (pp) REVERT: D 157 ASP cc_start: 0.7335 (t0) cc_final: 0.7041 (t70) REVERT: D 295 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6720 (t0) REVERT: D 335 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6725 (p0) REVERT: D 363 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7942 (mmtt) REVERT: D 406 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7483 (mm-30) REVERT: D 458 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7816 (ttmm) REVERT: D 518 ARG cc_start: 0.8357 (tmm160) cc_final: 0.8027 (ttp80) REVERT: D 556 ASN cc_start: 0.8296 (m-40) cc_final: 0.7889 (m-40) REVERT: D 577 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8124 (mtpp) REVERT: D 613 TYR cc_start: 0.7609 (p90) cc_final: 0.7098 (p90) outliers start: 24 outliers final: 14 residues processed: 172 average time/residue: 0.5290 time to fit residues: 95.6754 Evaluate side-chains 163 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 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 283 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 458 LYS 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: 0.9980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.0980 chunk 27 optimal weight: 0.2980 chunk 73 optimal weight: 0.0980 chunk 60 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 overall best weight: 0.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.138067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.123148 restraints weight = 9318.324| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.01 r_work: 0.3463 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6671 Z= 0.128 Angle : 0.551 7.166 9071 Z= 0.278 Chirality : 0.041 0.134 953 Planarity : 0.004 0.043 1172 Dihedral : 3.836 14.212 925 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.59 % Allowed : 25.00 % Favored : 72.41 % 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: 0.16 (0.30), residues: 789 helix: 1.04 (0.27), residues: 396 sheet: -0.45 (0.72), residues: 43 loop : -0.87 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 559 TYR 0.024 0.001 TYR D 50 PHE 0.026 0.001 PHE D 285 TRP 0.034 0.001 TRP D 168 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6666) covalent geometry : angle 0.54526 ( 9060) SS BOND : bond 0.00436 ( 1) SS BOND : angle 0.55503 ( 2) hydrogen bonds : bond 0.04599 ( 300) hydrogen bonds : angle 4.41822 ( 846) metal coordination : bond 0.00167 ( 1) link_NAG-ASN : bond 0.00163 ( 3) link_NAG-ASN : angle 2.48998 ( 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 167 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8395 (p0) cc_final: 0.8081 (p0) REVERT: A 408 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8295 (m) REVERT: D 43 SER cc_start: 0.8900 (OUTLIER) cc_final: 0.8643 (p) REVERT: D 114 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7654 (mmmt) REVERT: D 157 ASP cc_start: 0.7300 (t0) cc_final: 0.7004 (t70) REVERT: D 295 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6684 (t0) REVERT: D 406 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7569 (mm-30) REVERT: D 518 ARG cc_start: 0.8347 (tmm160) cc_final: 0.8053 (ttp80) REVERT: D 556 ASN cc_start: 0.8257 (m-40) cc_final: 0.7828 (m-40) REVERT: D 577 LYS cc_start: 0.8396 (mtpt) cc_final: 0.8061 (mtpp) REVERT: D 613 TYR cc_start: 0.7606 (p90) cc_final: 0.7108 (p90) outliers start: 18 outliers final: 9 residues processed: 161 average time/residue: 0.5174 time to fit residues: 87.5849 Evaluate side-chains 159 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 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 283 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 476 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.1980 chunk 73 optimal weight: 0.4980 chunk 52 optimal weight: 0.0170 chunk 55 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 0.0060 chunk 53 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 overall best weight: 0.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.138319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.123345 restraints weight = 9202.335| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.98 r_work: 0.3461 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6671 Z= 0.140 Angle : 0.566 7.325 9071 Z= 0.286 Chirality : 0.042 0.155 953 Planarity : 0.004 0.042 1172 Dihedral : 3.834 14.494 925 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.87 % Allowed : 26.29 % Favored : 71.84 % 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 (0.30), residues: 789 helix: 1.01 (0.26), residues: 396 sheet: -0.57 (0.71), residues: 43 loop : -0.80 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 559 TYR 0.023 0.001 TYR D 50 PHE 0.025 0.001 PHE D 285 TRP 0.048 0.002 TRP D 168 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6666) covalent geometry : angle 0.56079 ( 9060) SS BOND : bond 0.00183 ( 1) SS BOND : angle 0.53933 ( 2) hydrogen bonds : bond 0.04757 ( 300) hydrogen bonds : angle 4.41245 ( 846) metal coordination : bond 0.00244 ( 1) link_NAG-ASN : bond 0.00111 ( 3) link_NAG-ASN : angle 2.51522 ( 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 166 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8387 (p0) cc_final: 0.8076 (p0) REVERT: A 408 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8299 (m) REVERT: D 37 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7258 (mp0) REVERT: D 43 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8639 (p) REVERT: D 114 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7663 (mmmt) REVERT: D 157 ASP cc_start: 0.7313 (t0) cc_final: 0.7007 (t70) REVERT: D 295 ASP cc_start: 0.6912 (OUTLIER) cc_final: 0.6699 (t0) REVERT: D 360 MET cc_start: 0.8804 (ttm) cc_final: 0.8592 (ttp) REVERT: D 363 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7880 (mmtt) REVERT: D 406 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7620 (mm-30) REVERT: D 518 ARG cc_start: 0.8352 (tmm160) cc_final: 0.8084 (ttp80) REVERT: D 556 ASN cc_start: 0.8208 (m-40) cc_final: 0.7804 (m-40) REVERT: D 558 LEU cc_start: 0.7912 (mt) cc_final: 0.7560 (mp) REVERT: D 577 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8082 (mtpp) REVERT: D 613 TYR cc_start: 0.7622 (p90) cc_final: 0.7118 (p90) outliers start: 13 outliers final: 10 residues processed: 163 average time/residue: 0.4949 time to fit residues: 85.2415 Evaluate side-chains 162 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 248 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 476 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 0.0970 chunk 16 optimal weight: 0.0470 chunk 51 optimal weight: 0.6980 chunk 55 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 14 optimal weight: 0.0770 chunk 20 optimal weight: 0.0970 chunk 26 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 38 optimal weight: 0.0010 chunk 40 optimal weight: 0.1980 overall best weight: 0.0638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN D 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.126751 restraints weight = 9235.139| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.01 r_work: 0.3509 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6671 Z= 0.109 Angle : 0.531 5.907 9071 Z= 0.269 Chirality : 0.040 0.134 953 Planarity : 0.004 0.043 1172 Dihedral : 3.525 13.250 925 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.87 % Allowed : 26.15 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.30), residues: 789 helix: 1.10 (0.27), residues: 397 sheet: -0.48 (0.72), residues: 43 loop : -0.67 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 559 TYR 0.030 0.001 TYR D 50 PHE 0.021 0.001 PHE D 285 TRP 0.056 0.001 TRP D 168 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 6666) covalent geometry : angle 0.52718 ( 9060) SS BOND : bond 0.00064 ( 1) SS BOND : angle 0.12380 ( 2) hydrogen bonds : bond 0.04086 ( 300) hydrogen bonds : angle 4.34437 ( 846) metal coordination : bond 0.00079 ( 1) link_NAG-ASN : bond 0.00219 ( 3) link_NAG-ASN : angle 2.05820 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2849.76 seconds wall clock time: 49 minutes 10.76 seconds (2950.76 seconds total)