Starting phenix.real_space_refine on Tue Mar 11 19:30:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo9_33341/03_2025/7xo9_33341.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo9_33341/03_2025/7xo9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xo9_33341/03_2025/7xo9_33341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo9_33341/03_2025/7xo9_33341.map" model { file = "/net/cci-nas-00/data/ceres_data/7xo9_33341/03_2025/7xo9_33341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo9_33341/03_2025/7xo9_33341.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.10, per 1000 atoms: 0.79 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: 1.55 Conformation dependent library (CDL) restraints added in 982.7 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: 0.77 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: 1.75 Time building geometry restraints manager: 1.85 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: 4.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.390 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.490 ------------------------------------------------------------------------------- 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 : 0.002 0.033 6666 Z= 0.148 Angle : 0.472 6.634 9060 Z= 0.252 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.000 TRP D 165 HIS 0.001 0.000 HIS D 535 PHE 0.005 0.001 PHE A 515 TYR 0.007 0.001 TYR A 369 ARG 0.002 0.000 ARG D 482 *********************** 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 : 0.668 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8069 (p0) cc_final: 0.7819 (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: 0.7561 (ttpp) REVERT: D 270 MET cc_start: 0.7896 (tpp) cc_final: 0.7637 (tpt) REVERT: D 294 THR cc_start: 0.6608 (p) cc_final: 0.6075 (p) REVERT: D 295 ASP cc_start: 0.6696 (p0) cc_final: 0.6268 (t0) REVERT: D 556 ASN cc_start: 0.7117 (m-40) cc_final: 0.6900 (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: 0.5932 (p90) outliers start: 0 outliers final: 2 residues processed: 200 average time/residue: 1.1644 time to fit residues: 244.4215 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 : 0.741 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.0980 chunk 31 optimal weight: 0.0070 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 45 optimal weight: 0.0060 chunk 70 optimal weight: 0.0970 overall best weight: 0.1212 ------------------------------------------------------------------------------- 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 373 HIS D 401 HIS D 505 HIS D 522 GLN D 524 GLN D 578 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.142990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128273 restraints weight = 9180.997| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.91 r_work: 0.3602 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6666 Z= 0.178 Angle : 0.544 9.952 9060 Z= 0.278 Chirality : 0.041 0.132 953 Planarity : 0.004 0.037 1172 Dihedral : 3.634 29.008 929 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.16 % Allowed : 19.25 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.29), residues: 789 helix: 0.43 (0.26), residues: 403 sheet: -0.84 (0.78), residues: 45 loop : -1.16 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 203 HIS 0.005 0.001 HIS D 374 PHE 0.021 0.002 PHE D 555 TYR 0.018 0.001 TYR A 369 ARG 0.006 0.001 ARG D 204 *********************** 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 182 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 331 ASN cc_start: 0.3695 (OUTLIER) cc_final: 0.3221 (p0) REVERT: A 405 ASN cc_start: 0.8541 (p0) cc_final: 0.8213 (p0) REVERT: D 37 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6991 (mt-10) REVERT: D 68 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7679 (ttmm) REVERT: D 295 ASP cc_start: 0.6833 (p0) cc_final: 0.6582 (m-30) REVERT: D 347 THR cc_start: 0.7964 (m) cc_final: 0.7688 (p) REVERT: D 376 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7831 (mtt) REVERT: D 518 ARG cc_start: 0.8339 (tmm160) cc_final: 0.8034 (ttp80) REVERT: D 555 PHE cc_start: 0.8356 (t80) cc_final: 0.7965 (t80) REVERT: D 556 ASN cc_start: 0.8111 (m-40) cc_final: 0.7581 (m-40) REVERT: D 613 TYR cc_start: 0.6834 (p90) cc_final: 0.6395 (p90) outliers start: 22 outliers final: 8 residues processed: 175 average time/residue: 1.1665 time to fit residues: 214.6837 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 : 0.659 ------------------------------------------------------------------------------- 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 68 LYS 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 376 MET 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 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 40 optimal weight: 0.0970 chunk 51 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 62 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN D 239 HIS D 305 GLN D 345 HIS D 373 HIS D 578 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.139236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124147 restraints weight = 9342.324| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.03 r_work: 0.3487 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6666 Z= 0.277 Angle : 0.572 8.336 9060 Z= 0.293 Chirality : 0.044 0.164 953 Planarity : 0.004 0.039 1172 Dihedral : 3.869 21.827 925 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.74 % Allowed : 20.26 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.30), residues: 789 helix: 0.57 (0.26), residues: 404 sheet: -0.77 (0.76), residues: 43 loop : -1.01 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 349 HIS 0.007 0.001 HIS D 374 PHE 0.015 0.002 PHE D 285 TYR 0.018 0.002 TYR A 396 ARG 0.005 0.001 ARG D 204 *********************** 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 181 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8472 (p0) cc_final: 0.8215 (p0) REVERT: A 408 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8250 (m) REVERT: D 75 GLU cc_start: 0.7570 (pt0) cc_final: 0.7330 (pt0) REVERT: D 114 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7565 (mmmt) REVERT: D 131 LYS cc_start: 0.7487 (ttmm) cc_final: 0.7136 (tppt) REVERT: D 295 ASP cc_start: 0.7035 (p0) cc_final: 0.6735 (t0) REVERT: D 347 THR cc_start: 0.8116 (m) cc_final: 0.7881 (p) REVERT: D 470 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8352 (ttpp) REVERT: D 518 ARG cc_start: 0.8345 (tmm160) cc_final: 0.8053 (ttp80) REVERT: D 541 LYS cc_start: 0.7590 (mttm) cc_final: 0.7372 (mttp) REVERT: D 556 ASN cc_start: 0.8167 (m-40) cc_final: 0.7840 (m-40) REVERT: D 589 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7442 (tp30) REVERT: D 613 TYR cc_start: 0.7347 (p90) cc_final: 0.6759 (p90) outliers start: 26 outliers final: 10 residues processed: 174 average time/residue: 1.1332 time to fit residues: 207.8941 Evaluate side-chains 158 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 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 212 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 589 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.2980 chunk 25 optimal weight: 0.1980 chunk 64 optimal weight: 0.4980 chunk 37 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 477 ASN D 96 GLN D 300 GLN D 330 ASN D 401 HIS D 578 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.138248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.123184 restraints weight = 9330.728| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.03 r_work: 0.3472 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6666 Z= 0.280 Angle : 0.584 11.253 9060 Z= 0.291 Chirality : 0.043 0.133 953 Planarity : 0.004 0.041 1172 Dihedral : 3.929 17.741 925 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.59 % Allowed : 20.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.30), residues: 789 helix: 0.72 (0.26), residues: 399 sheet: -0.81 (0.72), residues: 43 loop : -0.95 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 168 HIS 0.006 0.001 HIS D 374 PHE 0.018 0.002 PHE D 285 TYR 0.022 0.002 TYR D 50 ARG 0.004 0.000 ARG D 204 *********************** 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 173 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8410 (p0) cc_final: 0.8177 (p0) REVERT: A 408 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8262 (m) REVERT: D 75 GLU cc_start: 0.7606 (pt0) cc_final: 0.7357 (pt0) REVERT: D 81 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7831 (mm-40) REVERT: D 114 LYS cc_start: 0.7910 (mmmt) cc_final: 0.7531 (mmmt) REVERT: D 131 LYS cc_start: 0.7732 (ttmm) cc_final: 0.7531 (tppt) REVERT: D 249 MET cc_start: 0.7870 (mpp) cc_final: 0.7643 (mmt) REVERT: D 267 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8324 (mt) REVERT: D 470 LYS cc_start: 0.8667 (tppp) cc_final: 0.8386 (ttpp) REVERT: D 518 ARG cc_start: 0.8355 (tmm160) cc_final: 0.8071 (ttp80) REVERT: D 556 ASN cc_start: 0.8245 (m-40) cc_final: 0.7699 (m110) REVERT: D 613 TYR cc_start: 0.7508 (p90) cc_final: 0.6985 (p90) outliers start: 25 outliers final: 12 residues processed: 169 average time/residue: 1.1425 time to fit residues: 203.1611 Evaluate side-chains 161 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 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 267 LEU 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 411 SER Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 445 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 0.0970 chunk 25 optimal weight: 0.0070 chunk 24 optimal weight: 0.3980 chunk 40 optimal weight: 0.0370 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 0.0970 chunk 8 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 overall best weight: 0.0672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 210 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 = 0.3823 r_free = 0.3823 target = 0.141366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126153 restraints weight = 9298.395| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.03 r_work: 0.3506 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6666 Z= 0.145 Angle : 0.505 7.556 9060 Z= 0.255 Chirality : 0.040 0.126 953 Planarity : 0.004 0.041 1172 Dihedral : 3.495 12.684 925 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.16 % Allowed : 22.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.30), residues: 789 helix: 0.97 (0.27), residues: 399 sheet: -0.66 (0.75), residues: 43 loop : -0.83 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 168 HIS 0.005 0.001 HIS D 374 PHE 0.021 0.001 PHE D 285 TYR 0.019 0.001 TYR D 50 ARG 0.003 0.000 ARG D 204 *********************** 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 174 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8438 (p0) cc_final: 0.8125 (p0) REVERT: D 37 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7122 (mp0) REVERT: D 75 GLU cc_start: 0.7590 (pt0) cc_final: 0.7360 (pt0) REVERT: D 114 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7564 (mmmm) REVERT: D 160 GLU cc_start: 0.7309 (tt0) cc_final: 0.7104 (tt0) REVERT: D 257 SER cc_start: 0.8595 (t) cc_final: 0.8304 (p) REVERT: D 270 MET cc_start: 0.8260 (tpp) cc_final: 0.7901 (tpp) REVERT: D 435 GLU cc_start: 0.7492 (tp30) cc_final: 0.7275 (tp30) REVERT: D 518 ARG cc_start: 0.8335 (tmm160) cc_final: 0.8089 (ttp80) REVERT: D 556 ASN cc_start: 0.8195 (m-40) cc_final: 0.7676 (m110) REVERT: D 577 LYS cc_start: 0.8322 (mtpt) cc_final: 0.7981 (mtpp) REVERT: D 613 TYR cc_start: 0.7435 (p90) cc_final: 0.7000 (p90) outliers start: 15 outliers final: 7 residues processed: 170 average time/residue: 1.2310 time to fit residues: 219.2091 Evaluate side-chains 158 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 TYR 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 445 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 59 optimal weight: 0.0570 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 51 optimal weight: 0.0970 chunk 31 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 378 HIS D 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.137477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.122520 restraints weight = 9108.000| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.98 r_work: 0.3469 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6666 Z= 0.302 Angle : 0.571 7.585 9060 Z= 0.294 Chirality : 0.043 0.133 953 Planarity : 0.004 0.042 1172 Dihedral : 3.979 18.297 925 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.02 % Allowed : 23.42 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.30), residues: 789 helix: 0.89 (0.27), residues: 400 sheet: -0.67 (0.72), residues: 43 loop : -0.91 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 168 HIS 0.009 0.001 HIS D 374 PHE 0.024 0.002 PHE D 285 TYR 0.016 0.002 TYR A 369 ARG 0.006 0.000 ARG D 460 *********************** 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 172 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8385 (p0) cc_final: 0.8101 (p0) REVERT: D 37 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7359 (mp0) REVERT: D 43 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8601 (p) REVERT: D 75 GLU cc_start: 0.7563 (pt0) cc_final: 0.7288 (pt0) REVERT: D 114 LYS cc_start: 0.7910 (mmmt) cc_final: 0.7562 (mmmt) REVERT: D 142 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5829 (pp) REVERT: D 171 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: D 249 MET cc_start: 0.7931 (mmm) cc_final: 0.7690 (mmt) REVERT: D 335 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6891 (p0) REVERT: D 349 TRP cc_start: 0.8634 (m100) cc_final: 0.8332 (m100) REVERT: D 518 ARG cc_start: 0.8346 (tmm160) cc_final: 0.8080 (ttp80) REVERT: D 556 ASN cc_start: 0.8248 (m-40) cc_final: 0.7746 (m110) REVERT: D 577 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8081 (mtpp) REVERT: D 613 TYR cc_start: 0.7609 (p90) cc_final: 0.7125 (p90) outliers start: 21 outliers final: 7 residues processed: 169 average time/residue: 1.1222 time to fit residues: 200.0382 Evaluate side-chains 154 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 445 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 0.0060 chunk 64 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 42 optimal weight: 0.0070 overall best weight: 0.1614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 210 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 = 0.3803 r_free = 0.3803 target = 0.139908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.124756 restraints weight = 9146.313| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.99 r_work: 0.3487 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6666 Z= 0.184 Angle : 0.530 7.196 9060 Z= 0.268 Chirality : 0.041 0.129 953 Planarity : 0.004 0.042 1172 Dihedral : 3.762 14.066 925 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.59 % Allowed : 23.85 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.30), residues: 789 helix: 1.07 (0.27), residues: 399 sheet: -0.44 (0.73), residues: 43 loop : -0.83 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 168 HIS 0.005 0.001 HIS D 374 PHE 0.025 0.001 PHE D 285 TYR 0.020 0.001 TYR D 50 ARG 0.006 0.000 ARG D 559 *********************** 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 170 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 336 CYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6819 (m) REVERT: A 405 ASN cc_start: 0.8393 (p0) cc_final: 0.8079 (p0) REVERT: D 43 SER cc_start: 0.8900 (OUTLIER) cc_final: 0.8654 (p) REVERT: D 75 GLU cc_start: 0.7581 (pt0) cc_final: 0.7291 (pt0) REVERT: D 114 LYS cc_start: 0.7903 (mmmt) cc_final: 0.7679 (mmmm) REVERT: D 171 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7235 (pm20) REVERT: D 267 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8292 (mt) REVERT: D 349 TRP cc_start: 0.8575 (m100) cc_final: 0.8259 (m100) REVERT: D 518 ARG cc_start: 0.8363 (tmm160) cc_final: 0.8133 (ttp80) REVERT: D 556 ASN cc_start: 0.8227 (m-40) cc_final: 0.7728 (m110) REVERT: D 577 LYS cc_start: 0.8390 (mtpt) cc_final: 0.8069 (mtpp) REVERT: D 613 TYR cc_start: 0.7632 (p90) cc_final: 0.7101 (p90) outliers start: 18 outliers final: 9 residues processed: 166 average time/residue: 1.1805 time to fit residues: 205.6997 Evaluate side-chains 160 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 325 GLN 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 13 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 chunk 29 optimal weight: 0.0980 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 9 optimal weight: 0.0030 chunk 77 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN D 300 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.123469 restraints weight = 9099.649| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.98 r_work: 0.3467 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6666 Z= 0.242 Angle : 0.568 8.767 9060 Z= 0.286 Chirality : 0.042 0.154 953 Planarity : 0.004 0.042 1172 Dihedral : 3.865 15.409 925 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.73 % Allowed : 24.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.30), residues: 789 helix: 1.11 (0.27), residues: 396 sheet: -0.44 (0.73), residues: 43 loop : -0.83 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 168 HIS 0.006 0.001 HIS D 374 PHE 0.027 0.002 PHE D 285 TYR 0.017 0.002 TYR D 50 ARG 0.009 0.000 ARG D 559 *********************** 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 168 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 336 CYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6811 (m) REVERT: A 405 ASN cc_start: 0.8394 (p0) cc_final: 0.8074 (p0) REVERT: D 37 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7257 (mp0) REVERT: D 43 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8618 (p) REVERT: D 75 GLU cc_start: 0.7550 (pt0) cc_final: 0.7261 (pt0) REVERT: D 114 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7576 (mmmt) REVERT: D 152 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7445 (mmp) REVERT: D 267 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8372 (mt) REVERT: D 518 ARG cc_start: 0.8357 (tmm160) cc_final: 0.8079 (ttp80) REVERT: D 556 ASN cc_start: 0.8244 (m-40) cc_final: 0.7842 (m-40) REVERT: D 558 LEU cc_start: 0.7885 (mt) cc_final: 0.7524 (mp) REVERT: D 577 LYS cc_start: 0.8393 (mtpt) cc_final: 0.8070 (mtpp) REVERT: D 613 TYR cc_start: 0.7677 (p90) cc_final: 0.7087 (p90) outliers start: 19 outliers final: 10 residues processed: 166 average time/residue: 1.1795 time to fit residues: 206.7688 Evaluate side-chains 156 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 219 ARG Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 445 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 0.0670 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 4 optimal weight: 0.0980 chunk 23 optimal weight: 0.5980 chunk 62 optimal weight: 0.0980 overall best weight: 0.2918 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.138103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.123115 restraints weight = 9251.597| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.01 r_work: 0.3463 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6666 Z= 0.250 Angle : 0.571 8.299 9060 Z= 0.289 Chirality : 0.043 0.163 953 Planarity : 0.004 0.042 1172 Dihedral : 3.878 15.188 925 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.30 % Allowed : 25.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.30), residues: 789 helix: 1.10 (0.27), residues: 396 sheet: -0.45 (0.72), residues: 43 loop : -0.85 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 168 HIS 0.006 0.001 HIS D 374 PHE 0.027 0.002 PHE D 285 TYR 0.025 0.002 TYR D 50 ARG 0.006 0.000 ARG D 559 *********************** 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 164 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8398 (p0) cc_final: 0.8078 (p0) REVERT: D 37 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7264 (mp0) REVERT: D 43 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8616 (p) REVERT: D 75 GLU cc_start: 0.7561 (pt0) cc_final: 0.7285 (pt0) REVERT: D 114 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7664 (mmmt) REVERT: D 152 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7494 (mmp) REVERT: D 267 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8381 (mt) REVERT: D 518 ARG cc_start: 0.8365 (tmm160) cc_final: 0.8091 (ttp80) REVERT: D 556 ASN cc_start: 0.8234 (m-40) cc_final: 0.7797 (m-40) REVERT: D 577 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8090 (mtpp) REVERT: D 613 TYR cc_start: 0.7684 (p90) cc_final: 0.7444 (p90) outliers start: 16 outliers final: 9 residues processed: 161 average time/residue: 1.1309 time to fit residues: 191.8677 Evaluate side-chains 154 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 219 ARG Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 347 THR 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 73 optimal weight: 0.0870 chunk 21 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 61 optimal weight: 0.0870 overall best weight: 0.1672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 210 ASN D 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.139682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.124697 restraints weight = 9226.268| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.00 r_work: 0.3486 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6666 Z= 0.187 Angle : 0.545 6.550 9060 Z= 0.277 Chirality : 0.041 0.134 953 Planarity : 0.004 0.042 1172 Dihedral : 3.692 14.130 925 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.87 % Allowed : 25.86 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.30), residues: 789 helix: 1.17 (0.27), residues: 396 sheet: -0.41 (0.73), residues: 43 loop : -0.77 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D 168 HIS 0.006 0.001 HIS D 374 PHE 0.024 0.001 PHE D 285 TYR 0.018 0.001 TYR A 369 ARG 0.006 0.000 ARG D 559 ********************** 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 159 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8399 (p0) cc_final: 0.8083 (p0) REVERT: D 37 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7229 (mp0) REVERT: D 43 SER cc_start: 0.8881 (OUTLIER) cc_final: 0.8627 (p) REVERT: D 75 GLU cc_start: 0.7581 (pt0) cc_final: 0.7293 (pt0) REVERT: D 114 LYS cc_start: 0.7931 (mmmt) cc_final: 0.7643 (mmmt) REVERT: D 152 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7402 (mmp) REVERT: D 210 ASN cc_start: 0.7818 (m-40) cc_final: 0.7583 (m-40) REVERT: D 518 ARG cc_start: 0.8347 (tmm160) cc_final: 0.8112 (ttp80) REVERT: D 556 ASN cc_start: 0.8199 (m-40) cc_final: 0.7782 (m-40) REVERT: D 558 LEU cc_start: 0.7841 (mt) cc_final: 0.7612 (mp) REVERT: D 577 LYS cc_start: 0.8371 (mtpt) cc_final: 0.8035 (mtpp) REVERT: D 613 TYR cc_start: 0.7654 (p90) cc_final: 0.7362 (p90) outliers start: 13 outliers final: 7 residues processed: 157 average time/residue: 1.1382 time to fit residues: 188.1611 Evaluate side-chains 155 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 325 GLN 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 51 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 71 optimal weight: 0.0870 chunk 59 optimal weight: 0.0070 chunk 46 optimal weight: 0.2980 chunk 54 optimal weight: 0.2980 chunk 48 optimal weight: 0.1980 chunk 49 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 overall best weight: 0.1576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.139815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.124871 restraints weight = 9288.642| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.01 r_work: 0.3488 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6666 Z= 0.181 Angle : 0.545 6.784 9060 Z= 0.276 Chirality : 0.041 0.132 953 Planarity : 0.004 0.042 1172 Dihedral : 3.627 13.650 925 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.58 % Allowed : 26.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.30), residues: 789 helix: 1.19 (0.27), residues: 396 sheet: -0.33 (0.74), residues: 43 loop : -0.72 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 168 HIS 0.006 0.001 HIS D 374 PHE 0.024 0.001 PHE D 285 TYR 0.033 0.001 TYR D 50 ARG 0.008 0.000 ARG D 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5780.83 seconds wall clock time: 99 minutes 5.58 seconds (5945.58 seconds total)