Starting phenix.real_space_refine on Tue Feb 11 21:31:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9l_25761/02_2025/7t9l_25761.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9l_25761/02_2025/7t9l_25761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t9l_25761/02_2025/7t9l_25761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9l_25761/02_2025/7t9l_25761.map" model { file = "/net/cci-nas-00/data/ceres_data/7t9l_25761/02_2025/7t9l_25761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9l_25761/02_2025/7t9l_25761.cif" } resolution = 2.66 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= -0.001 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4203 2.51 5 N 1084 2.21 5 O 1243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6567 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.03, per 1000 atoms: 0.77 Number of scatterers: 6567 At special positions: 0 Unit cell: (78, 86, 122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1243 8.00 N 1084 7.00 C 4203 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 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 A1301 " - " ASN A 343 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG D 706 " - " ASN D 546 " Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 867.5 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 56.4% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.680A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.679A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 52 Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.206A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.622A pdb=" N SER D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 Proline residue: D 178 - end of helix removed outlier: 3.809A 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 220 through 252 removed outlier: 4.532A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix 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 removed outlier: 3.767A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.500A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.721A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 4.352A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.518A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.389A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.826A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.344A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.000A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 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 358 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 Processing sheet with id=AA4, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.972A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.218A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 315 hydrogen bonds defined for protein. 906 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: 1.79 Time building geometry restraints manager: 1.75 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: 2050 1.34 - 1.46: 1710 1.46 - 1.58: 2934 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6752 Sorted by residual: bond pdb=" CG LEU D 558 " pdb=" CD1 LEU D 558 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.55e+00 bond pdb=" C1 NAG D 706 " pdb=" O5 NAG D 706 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.80e+00 bond pdb=" C1 NAG D 705 " pdb=" O5 NAG D 705 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.05e+00 bond pdb=" C1 NAG D 702 " pdb=" O5 NAG D 702 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.90e+00 ... (remaining 6747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 8952 2.65 - 5.31: 188 5.31 - 7.96: 25 7.96 - 10.62: 8 10.62 - 13.27: 3 Bond angle restraints: 9176 Sorted by residual: angle pdb=" CB LYS D 534 " pdb=" CG LYS D 534 " pdb=" CD LYS D 534 " ideal model delta sigma weight residual 111.30 121.60 -10.30 2.30e+00 1.89e-01 2.00e+01 angle pdb=" CB MET D 152 " pdb=" CG MET D 152 " pdb=" SD MET D 152 " ideal model delta sigma weight residual 112.70 125.97 -13.27 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C SER A 359 " pdb=" N ASN A 360 " pdb=" CA ASN A 360 " ideal model delta sigma weight residual 122.46 128.55 -6.09 1.41e+00 5.03e-01 1.86e+01 angle pdb=" CB MET D 323 " pdb=" CG MET D 323 " pdb=" SD MET D 323 " ideal model delta sigma weight residual 112.70 125.10 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CB LYS D 600 " pdb=" CG LYS D 600 " pdb=" CD LYS D 600 " ideal model delta sigma weight residual 111.30 119.94 -8.64 2.30e+00 1.89e-01 1.41e+01 ... (remaining 9171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3669 17.94 - 35.89: 337 35.89 - 53.83: 57 53.83 - 71.78: 12 71.78 - 89.72: 6 Dihedral angle restraints: 4081 sinusoidal: 1740 harmonic: 2341 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 38.00 55.00 1 1.00e+01 1.00e-02 4.09e+01 dihedral pdb=" CA GLN D 139 " pdb=" C GLN D 139 " pdb=" N GLU D 140 " pdb=" CA GLU D 140 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ALA D 396 " pdb=" C ALA D 396 " pdb=" N ASN D 397 " pdb=" CA ASN D 397 " ideal model delta harmonic sigma weight residual 180.00 159.15 20.85 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 4078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 644 0.048 - 0.095: 230 0.095 - 0.143: 85 0.143 - 0.191: 14 0.191 - 0.239: 7 Chirality restraints: 980 Sorted by residual: chirality pdb=" CG LEU D 267 " pdb=" CB LEU D 267 " pdb=" CD1 LEU D 267 " pdb=" CD2 LEU D 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB VAL D 581 " pdb=" CA VAL D 581 " pdb=" CG1 VAL D 581 " pdb=" CG2 VAL D 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE A 332 " pdb=" CA ILE A 332 " pdb=" CG1 ILE A 332 " pdb=" CG2 ILE A 332 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 977 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 68 " 0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C LYS D 68 " -0.077 2.00e-02 2.50e+03 pdb=" O LYS D 68 " 0.029 2.00e-02 2.50e+03 pdb=" N TRP D 69 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 241 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C HIS D 241 " 0.058 2.00e-02 2.50e+03 pdb=" O HIS D 241 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA D 242 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 240 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C LEU D 240 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU D 240 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS D 241 " -0.019 2.00e-02 2.50e+03 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1755 2.80 - 3.33: 5984 3.33 - 3.85: 11578 3.85 - 4.38: 13246 4.38 - 4.90: 22673 Nonbonded interactions: 55236 Sorted by model distance: nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR D 217 " pdb=" OD2 ASP D 225 " model vdw 2.329 3.040 nonbonded pdb=" NZ LYS D 475 " pdb=" OE1 GLU D 495 " model vdw 2.333 3.120 nonbonded pdb=" OG SER D 170 " pdb=" NZ LYS D 174 " model vdw 2.341 3.120 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.360 3.120 ... (remaining 55231 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: 3.670 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: 0.240 Check model and map are aligned: 0.000 Set scattering table: 0.070 Process input model: 18.680 Find NCS groups from input model: 0.060 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:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.006 0.078 6752 Z= 0.389 Angle : 0.956 13.272 9176 Z= 0.497 Chirality : 0.058 0.239 980 Planarity : 0.009 0.076 1179 Dihedral : 14.116 89.721 2559 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.14 % Allowed : 2.42 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.53 (0.26), residues: 792 helix: -1.05 (0.22), residues: 393 sheet: 0.51 (0.73), residues: 44 loop : -1.02 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 594 HIS 0.009 0.002 HIS D 401 PHE 0.038 0.003 PHE A 347 TYR 0.029 0.002 TYR D 385 ARG 0.016 0.001 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8386 (tp) cc_final: 0.8131 (tt) REVERT: D 110 GLU cc_start: 0.8260 (tp30) cc_final: 0.7953 (tp30) REVERT: D 114 LYS cc_start: 0.9112 (ttpp) cc_final: 0.8730 (tppt) REVERT: D 291 ILE cc_start: 0.8288 (mt) cc_final: 0.7977 (mm) REVERT: D 366 MET cc_start: 0.8645 (ttp) cc_final: 0.8381 (ttp) REVERT: D 435 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7390 (mm-30) REVERT: D 471 ASP cc_start: 0.8816 (p0) cc_final: 0.8580 (p0) REVERT: D 472 GLN cc_start: 0.8345 (mm110) cc_final: 0.7917 (mm-40) REVERT: D 579 MET cc_start: 0.8879 (mtm) cc_final: 0.8645 (ttm) REVERT: D 582 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7712 (mmm160) outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 1.3838 time to fit residues: 267.9440 Evaluate side-chains 119 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.0770 chunk 59 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN D 175 GLN D 374 HIS D 472 GLN D 598 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.107198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.081300 restraints weight = 11871.311| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.83 r_work: 0.3010 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6752 Z= 0.201 Angle : 0.620 10.053 9176 Z= 0.315 Chirality : 0.044 0.170 980 Planarity : 0.005 0.041 1179 Dihedral : 6.627 129.165 1015 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.28 % Allowed : 14.96 % Favored : 82.76 % 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: 0.10 (0.29), residues: 792 helix: 0.50 (0.26), residues: 387 sheet: 0.13 (0.74), residues: 49 loop : -0.29 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 165 HIS 0.004 0.001 HIS D 241 PHE 0.014 0.001 PHE D 592 TYR 0.016 0.001 TYR D 41 ARG 0.008 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8512 (tp) cc_final: 0.8257 (tt) REVERT: A 444 LYS cc_start: 0.8897 (mttt) cc_final: 0.8505 (mttp) REVERT: D 114 LYS cc_start: 0.9276 (ttpp) cc_final: 0.8931 (tppt) REVERT: D 287 GLN cc_start: 0.9163 (mm-40) cc_final: 0.8848 (tm-30) REVERT: D 297 MET cc_start: 0.9194 (mtm) cc_final: 0.8925 (mtp) REVERT: D 472 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7759 (mm-40) REVERT: D 579 MET cc_start: 0.9100 (mtm) cc_final: 0.8843 (ttm) REVERT: D 597 ASP cc_start: 0.8973 (t0) cc_final: 0.8761 (t0) outliers start: 16 outliers final: 4 residues processed: 129 average time/residue: 1.2842 time to fit residues: 174.1443 Evaluate side-chains 113 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 359 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 ASN D 175 GLN D 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.103874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.077579 restraints weight = 12045.109| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.83 r_work: 0.2921 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6752 Z= 0.252 Angle : 0.643 17.827 9176 Z= 0.327 Chirality : 0.045 0.338 980 Planarity : 0.004 0.039 1179 Dihedral : 4.960 54.039 1013 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.71 % Allowed : 18.23 % Favored : 79.06 % 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: 0.74 (0.29), residues: 792 helix: 1.03 (0.26), residues: 390 sheet: 0.11 (0.72), residues: 49 loop : 0.07 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 165 HIS 0.003 0.001 HIS D 241 PHE 0.020 0.002 PHE D 400 TYR 0.017 0.001 TYR D 385 ARG 0.006 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8390 (tp) cc_final: 0.8181 (tt) REVERT: A 444 LYS cc_start: 0.8873 (mttt) cc_final: 0.8468 (mttp) REVERT: A 500 THR cc_start: 0.9384 (p) cc_final: 0.9181 (p) REVERT: D 115 ARG cc_start: 0.8211 (tpm-80) cc_final: 0.7929 (tpm-80) REVERT: D 123 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7350 (mtt) REVERT: D 471 ASP cc_start: 0.8753 (p0) cc_final: 0.8525 (p0) REVERT: D 472 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7898 (mm-40) REVERT: D 579 MET cc_start: 0.9224 (mtm) cc_final: 0.8916 (ttm) outliers start: 19 outliers final: 7 residues processed: 121 average time/residue: 1.3341 time to fit residues: 169.8964 Evaluate side-chains 102 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 0.0060 chunk 45 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN D 522 GLN ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.104523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.078281 restraints weight = 12163.092| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.85 r_work: 0.2970 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6752 Z= 0.198 Angle : 0.597 10.296 9176 Z= 0.302 Chirality : 0.043 0.229 980 Planarity : 0.004 0.033 1179 Dihedral : 4.683 53.673 1013 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.13 % Allowed : 18.52 % Favored : 78.35 % 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: 1.03 (0.30), residues: 792 helix: 1.24 (0.26), residues: 391 sheet: 0.18 (0.72), residues: 49 loop : 0.27 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 165 HIS 0.003 0.001 HIS D 241 PHE 0.015 0.001 PHE D 369 TYR 0.015 0.001 TYR D 385 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8850 (mttt) cc_final: 0.8439 (mttp) REVERT: A 500 THR cc_start: 0.9382 (p) cc_final: 0.9169 (p) REVERT: D 114 LYS cc_start: 0.9001 (mmpt) cc_final: 0.8537 (tppt) REVERT: D 115 ARG cc_start: 0.8245 (tpm-80) cc_final: 0.7874 (tpm-80) REVERT: D 123 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7412 (mtt) REVERT: D 287 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8947 (tm-30) REVERT: D 297 MET cc_start: 0.9037 (mtm) cc_final: 0.8729 (mtp) REVERT: D 383 MET cc_start: 0.9032 (mtp) cc_final: 0.8813 (mtm) REVERT: D 440 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8569 (tp) REVERT: D 471 ASP cc_start: 0.8778 (p0) cc_final: 0.8555 (p0) REVERT: D 472 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7871 (mm-40) REVERT: D 497 TYR cc_start: 0.7985 (m-80) cc_final: 0.7625 (m-80) REVERT: D 579 MET cc_start: 0.9224 (mtm) cc_final: 0.8909 (ttm) REVERT: D 596 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8737 (mttm) outliers start: 22 outliers final: 6 residues processed: 118 average time/residue: 1.1783 time to fit residues: 146.8810 Evaluate side-chains 104 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 7 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN D 175 GLN D 522 GLN ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.102239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.075729 restraints weight = 12157.750| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.85 r_work: 0.2887 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6752 Z= 0.313 Angle : 0.654 11.412 9176 Z= 0.328 Chirality : 0.046 0.281 980 Planarity : 0.004 0.032 1179 Dihedral : 4.853 54.941 1013 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.85 % Allowed : 17.66 % Favored : 78.49 % 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: 1.12 (0.30), residues: 792 helix: 1.33 (0.26), residues: 391 sheet: 0.24 (0.72), residues: 49 loop : 0.29 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 165 HIS 0.004 0.001 HIS D 241 PHE 0.019 0.002 PHE D 400 TYR 0.017 0.001 TYR D 385 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 THR cc_start: 0.9364 (p) cc_final: 0.9140 (p) REVERT: D 115 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7862 (tpm-80) REVERT: D 123 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7438 (mtt) REVERT: D 189 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8529 (tp30) REVERT: D 287 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8844 (tm-30) REVERT: D 291 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7756 (pt) REVERT: D 297 MET cc_start: 0.9138 (mtm) cc_final: 0.8617 (mtp) REVERT: D 383 MET cc_start: 0.9093 (mtp) cc_final: 0.8882 (mtm) REVERT: D 472 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7970 (mm-40) REVERT: D 579 MET cc_start: 0.9252 (mtm) cc_final: 0.8921 (ttm) REVERT: D 596 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8715 (mttm) REVERT: D 598 GLN cc_start: 0.8308 (mt0) cc_final: 0.8076 (mt0) outliers start: 27 outliers final: 10 residues processed: 118 average time/residue: 1.1090 time to fit residues: 138.3743 Evaluate side-chains 114 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN D 522 GLN D 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.103661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.077365 restraints weight = 11948.824| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.84 r_work: 0.2953 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6752 Z= 0.213 Angle : 0.625 11.166 9176 Z= 0.312 Chirality : 0.044 0.277 980 Planarity : 0.004 0.033 1179 Dihedral : 4.637 53.789 1013 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.42 % Allowed : 19.37 % Favored : 77.21 % 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: 1.18 (0.30), residues: 792 helix: 1.35 (0.26), residues: 399 sheet: -0.15 (0.64), residues: 59 loop : 0.44 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 165 HIS 0.003 0.001 HIS D 241 PHE 0.015 0.001 PHE D 369 TYR 0.014 0.001 TYR D 385 ARG 0.003 0.000 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ARG cc_start: 0.8332 (tpm-80) cc_final: 0.7871 (tpm-80) REVERT: D 123 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7480 (mtt) REVERT: D 189 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8505 (tp30) REVERT: D 291 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7696 (pt) REVERT: D 297 MET cc_start: 0.9153 (mtm) cc_final: 0.8856 (mtp) REVERT: D 332 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8604 (ptp) REVERT: D 383 MET cc_start: 0.9098 (mtp) cc_final: 0.8857 (mtm) REVERT: D 440 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8570 (tp) REVERT: D 470 LYS cc_start: 0.8827 (tppp) cc_final: 0.8625 (tppp) REVERT: D 471 ASP cc_start: 0.8968 (p0) cc_final: 0.8688 (p0) REVERT: D 472 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7938 (mm-40) REVERT: D 497 TYR cc_start: 0.8055 (m-80) cc_final: 0.7626 (m-10) REVERT: D 579 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8954 (ttm) REVERT: D 596 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8721 (mttm) outliers start: 24 outliers final: 9 residues processed: 117 average time/residue: 1.1192 time to fit residues: 138.5278 Evaluate side-chains 113 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.102429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.076016 restraints weight = 11927.604| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.83 r_work: 0.2925 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6752 Z= 0.283 Angle : 0.658 11.974 9176 Z= 0.330 Chirality : 0.045 0.309 980 Planarity : 0.004 0.032 1179 Dihedral : 4.723 54.603 1013 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.85 % Allowed : 19.66 % Favored : 76.50 % 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: 1.28 (0.30), residues: 792 helix: 1.45 (0.26), residues: 392 sheet: -0.20 (0.64), residues: 59 loop : 0.49 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 165 HIS 0.004 0.001 HIS D 241 PHE 0.015 0.001 PHE D 369 TYR 0.016 0.001 TYR D 385 ARG 0.003 0.000 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7861 (tpm-80) REVERT: D 123 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7531 (mtt) REVERT: D 189 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8551 (tp30) REVERT: D 287 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8908 (tm-30) REVERT: D 291 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7714 (tp) REVERT: D 297 MET cc_start: 0.9123 (mtm) cc_final: 0.8562 (mtp) REVERT: D 341 LYS cc_start: 0.8185 (tppt) cc_final: 0.7933 (tppt) REVERT: D 383 MET cc_start: 0.9102 (mtp) cc_final: 0.8888 (mtm) REVERT: D 440 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8519 (tp) REVERT: D 470 LYS cc_start: 0.8848 (tppp) cc_final: 0.8579 (tppp) REVERT: D 471 ASP cc_start: 0.8922 (p0) cc_final: 0.8712 (p0) REVERT: D 472 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7978 (mm-40) REVERT: D 579 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8982 (ttm) REVERT: D 596 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8713 (mttm) outliers start: 27 outliers final: 9 residues processed: 117 average time/residue: 1.1030 time to fit residues: 136.5684 Evaluate side-chains 114 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 0.6980 chunk 75 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 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 = 0.3503 r_free = 0.3503 target = 0.103868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.077405 restraints weight = 12018.725| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.84 r_work: 0.2950 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6752 Z= 0.221 Angle : 0.643 12.566 9176 Z= 0.320 Chirality : 0.044 0.313 980 Planarity : 0.004 0.031 1179 Dihedral : 4.595 53.611 1013 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.56 % Allowed : 20.23 % Favored : 76.21 % 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: 1.31 (0.30), residues: 792 helix: 1.60 (0.26), residues: 384 sheet: -0.30 (0.64), residues: 59 loop : 0.39 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 165 HIS 0.003 0.001 HIS D 241 PHE 0.015 0.001 PHE D 369 TYR 0.014 0.001 TYR D 385 ARG 0.004 0.000 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 ASN cc_start: 0.7668 (t0) cc_final: 0.7354 (t0) REVERT: D 55 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7328 (p) REVERT: D 114 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8638 (tppt) REVERT: D 115 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7929 (tpm-80) REVERT: D 123 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7578 (mtt) REVERT: D 160 GLU cc_start: 0.8257 (tt0) cc_final: 0.7923 (tp30) REVERT: D 189 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8558 (tp30) REVERT: D 287 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8915 (tm-30) REVERT: D 291 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7721 (tp) REVERT: D 297 MET cc_start: 0.9101 (mtm) cc_final: 0.8583 (mtp) REVERT: D 341 LYS cc_start: 0.8161 (tppt) cc_final: 0.7898 (tppt) REVERT: D 383 MET cc_start: 0.9087 (mtp) cc_final: 0.8866 (mtm) REVERT: D 440 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8567 (tp) REVERT: D 470 LYS cc_start: 0.8839 (tppp) cc_final: 0.8578 (tppp) REVERT: D 472 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7958 (mm-40) REVERT: D 479 GLU cc_start: 0.8135 (tt0) cc_final: 0.7859 (mt-10) REVERT: D 497 TYR cc_start: 0.8080 (m-80) cc_final: 0.7770 (m-80) REVERT: D 579 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8967 (ttm) REVERT: D 596 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8755 (mttm) outliers start: 25 outliers final: 9 residues processed: 115 average time/residue: 1.1536 time to fit residues: 140.6907 Evaluate side-chains 114 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.102565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.076047 restraints weight = 12195.197| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.85 r_work: 0.2923 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6752 Z= 0.279 Angle : 0.678 15.358 9176 Z= 0.339 Chirality : 0.045 0.340 980 Planarity : 0.004 0.031 1179 Dihedral : 4.708 54.427 1013 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.85 % Allowed : 21.37 % Favored : 75.78 % 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: 1.36 (0.30), residues: 792 helix: 1.50 (0.26), residues: 391 sheet: 0.11 (0.66), residues: 53 loop : 0.48 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 165 HIS 0.004 0.001 HIS D 241 PHE 0.016 0.001 PHE D 369 TYR 0.015 0.001 TYR D 385 ARG 0.004 0.000 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 55 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7319 (p) REVERT: D 115 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7901 (tpm-80) REVERT: D 123 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7561 (mtt) REVERT: D 189 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8575 (tp30) REVERT: D 287 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8892 (tm-30) REVERT: D 291 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7737 (tp) REVERT: D 341 LYS cc_start: 0.8155 (tppt) cc_final: 0.7901 (tppt) REVERT: D 383 MET cc_start: 0.9092 (mtp) cc_final: 0.8877 (mtm) REVERT: D 440 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8511 (tp) REVERT: D 470 LYS cc_start: 0.8831 (tppp) cc_final: 0.8571 (tppp) REVERT: D 471 ASP cc_start: 0.8983 (p0) cc_final: 0.8726 (p0) REVERT: D 472 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8023 (mm-40) REVERT: D 479 GLU cc_start: 0.8233 (tt0) cc_final: 0.7949 (mt-10) REVERT: D 579 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8970 (ttm) REVERT: D 596 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8709 (mttm) outliers start: 20 outliers final: 9 residues processed: 109 average time/residue: 1.1156 time to fit residues: 128.8408 Evaluate side-chains 109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 42 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 chunk 76 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 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 = 0.3504 r_free = 0.3504 target = 0.103863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.077756 restraints weight = 12076.535| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.81 r_work: 0.2929 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6752 Z= 0.219 Angle : 0.658 14.579 9176 Z= 0.326 Chirality : 0.044 0.301 980 Planarity : 0.004 0.031 1179 Dihedral : 4.622 53.698 1013 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.13 % Allowed : 20.94 % Favored : 75.93 % 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: 1.37 (0.30), residues: 792 helix: 1.59 (0.26), residues: 385 sheet: 0.12 (0.66), residues: 53 loop : 0.41 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 165 HIS 0.004 0.001 HIS D 493 PHE 0.017 0.001 PHE A 374 TYR 0.014 0.001 TYR D 497 ARG 0.005 0.000 ARG D 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 ASN cc_start: 0.7598 (t0) cc_final: 0.7286 (t0) REVERT: D 55 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7225 (p) REVERT: D 115 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7867 (tpm-80) REVERT: D 123 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7581 (mtt) REVERT: D 189 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8565 (tp30) REVERT: D 287 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8890 (tm-30) REVERT: D 291 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7743 (tp) REVERT: D 297 MET cc_start: 0.9044 (mtm) cc_final: 0.8656 (mtp) REVERT: D 341 LYS cc_start: 0.8134 (tppt) cc_final: 0.7843 (tppt) REVERT: D 383 MET cc_start: 0.9101 (mtp) cc_final: 0.8891 (mtm) REVERT: D 440 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8499 (tp) REVERT: D 470 LYS cc_start: 0.8808 (tppp) cc_final: 0.8548 (tppp) REVERT: D 472 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8150 (mm-40) REVERT: D 479 GLU cc_start: 0.8220 (tt0) cc_final: 0.7818 (mt-10) REVERT: D 483 GLU cc_start: 0.8035 (pt0) cc_final: 0.7835 (pt0) REVERT: D 579 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8956 (ttm) REVERT: D 596 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8750 (mttm) outliers start: 22 outliers final: 10 residues processed: 116 average time/residue: 1.0553 time to fit residues: 130.0193 Evaluate side-chains 111 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 0.0270 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.3638 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.105052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.079092 restraints weight = 12102.021| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.82 r_work: 0.2978 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6752 Z= 0.188 Angle : 0.656 15.790 9176 Z= 0.328 Chirality : 0.044 0.314 980 Planarity : 0.004 0.031 1179 Dihedral : 4.568 53.260 1013 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.71 % Allowed : 22.36 % Favored : 74.93 % 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: 1.37 (0.30), residues: 792 helix: 1.58 (0.26), residues: 385 sheet: 0.09 (0.66), residues: 53 loop : 0.43 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 165 HIS 0.005 0.001 HIS D 493 PHE 0.015 0.001 PHE D 369 TYR 0.020 0.001 TYR D 497 ARG 0.004 0.000 ARG D 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5173.80 seconds wall clock time: 92 minutes 28.20 seconds (5548.20 seconds total)