Starting phenix.real_space_refine on Wed Jan 15 01:24:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9baa_44402/01_2025/9baa_44402.cif Found real_map, /net/cci-nas-00/data/ceres_data/9baa_44402/01_2025/9baa_44402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9baa_44402/01_2025/9baa_44402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9baa_44402/01_2025/9baa_44402.map" model { file = "/net/cci-nas-00/data/ceres_data/9baa_44402/01_2025/9baa_44402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9baa_44402/01_2025/9baa_44402.cif" } resolution = 3.39 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= 0.002 sd= 0.042 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 43 5.16 5 C 5072 2.51 5 N 1264 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7771 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3372 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 8, 'TRANS': 422} Chain breaks: 2 Chain: "B" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4399 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain breaks: 5 Time building chain proxies: 4.99, per 1000 atoms: 0.64 Number of scatterers: 7771 At special positions: 0 Unit cell: (91.227, 97.05, 116.46, 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 43 16.00 O 1392 8.00 N 1264 7.00 C 5072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 992.4 milliseconds 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1852 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 2 sheets defined 75.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 152 through 163 removed outlier: 3.547A pdb=" N VAL A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 188 Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.643A pdb=" N PHE A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 251 Processing helix chain 'A' and resid 254 through 260 removed outlier: 3.674A pdb=" N PHE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 260 " --> pdb=" O ASN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 289 removed outlier: 3.630A pdb=" N ILE A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 305 removed outlier: 3.662A pdb=" N GLY A 297 " --> pdb=" O MET A 293 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 354 removed outlier: 4.621A pdb=" N LYS A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 363 through 418 removed outlier: 3.520A pdb=" N THR A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 432 removed outlier: 4.014A pdb=" N LEU A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 444 Proline residue: A 438 - end of helix Processing helix chain 'A' and resid 445 through 464 removed outlier: 3.578A pdb=" N ILE A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.561A pdb=" N LEU A 471 " --> pdb=" O GLU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'A' and resid 554 through 562 removed outlier: 4.076A pdb=" N ILE A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 585 through 595 Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.536A pdb=" N ALA A 634 " --> pdb=" O ARG A 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 33 Processing helix chain 'B' and resid 38 through 46 Processing helix chain 'B' and resid 54 through 66 Processing helix chain 'B' and resid 131 through 135 removed outlier: 4.248A pdb=" N GLY B 134 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 166 through 187 Processing helix chain 'B' and resid 188 through 196 removed outlier: 3.684A pdb=" N ASP B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 253 Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.952A pdb=" N PHE B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 261 " --> pdb=" O PHE B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 305 removed outlier: 4.092A pdb=" N ILE B 266 " --> pdb=" O LYS B 262 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS B 275 " --> pdb=" O MET B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 353 removed outlier: 3.739A pdb=" N PHE B 326 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 327 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 364 through 417 Processing helix chain 'B' and resid 421 through 444 removed outlier: 3.736A pdb=" N LEU B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Proline residue: B 438 - end of helix Processing helix chain 'B' and resid 444 through 464 removed outlier: 4.781A pdb=" N LEU B 448 " --> pdb=" O ASP B 444 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU B 461 " --> pdb=" O ASN B 457 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ILE B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 533 removed outlier: 3.888A pdb=" N MET B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 553 removed outlier: 3.541A pdb=" N ASN B 552 " --> pdb=" O SER B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 removed outlier: 3.582A pdb=" N ILE B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 580 Processing helix chain 'B' and resid 590 through 596 Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 629 through 639 Processing sheet with id=AA1, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.866A pdb=" N ALA B 87 " --> pdb=" O ILE B 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 562 through 564 removed outlier: 6.268A pdb=" N ALA B 563 " --> pdb=" O ILE B 645 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 532 hydrogen bonds defined for protein. 1572 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: 1.89 Time building geometry restraints manager: 2.37 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: 2415 1.34 - 1.46: 1571 1.46 - 1.58: 3825 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 7889 Sorted by residual: bond pdb=" N PHE A 188 " pdb=" CA PHE A 188 " ideal model delta sigma weight residual 1.458 1.478 -0.020 1.42e-02 4.96e+03 1.97e+00 bond pdb=" CA PHE A 188 " pdb=" C PHE A 188 " ideal model delta sigma weight residual 1.522 1.542 -0.021 1.72e-02 3.38e+03 1.44e+00 bond pdb=" N ASP A 590 " pdb=" CA ASP A 590 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.14e+00 bond pdb=" CB MET B 387 " pdb=" CG MET B 387 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CG1 ILE A 337 " pdb=" CD1 ILE A 337 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.11e-01 ... (remaining 7884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 10388 1.83 - 3.65: 182 3.65 - 5.48: 35 5.48 - 7.31: 8 7.31 - 9.14: 2 Bond angle restraints: 10615 Sorted by residual: angle pdb=" CA ARG A 630 " pdb=" CB ARG A 630 " pdb=" CG ARG A 630 " ideal model delta sigma weight residual 114.10 120.94 -6.84 2.00e+00 2.50e-01 1.17e+01 angle pdb=" CB MET B 387 " pdb=" CG MET B 387 " pdb=" SD MET B 387 " ideal model delta sigma weight residual 112.70 103.65 9.05 3.00e+00 1.11e-01 9.11e+00 angle pdb=" C ASN B 153 " pdb=" N MET B 154 " pdb=" CA MET B 154 " ideal model delta sigma weight residual 120.63 124.99 -4.36 1.61e+00 3.86e-01 7.34e+00 angle pdb=" N VAL A 415 " pdb=" CA VAL A 415 " pdb=" C VAL A 415 " ideal model delta sigma weight residual 110.42 107.91 2.51 9.60e-01 1.09e+00 6.84e+00 angle pdb=" CA LEU B 165 " pdb=" CB LEU B 165 " pdb=" CG LEU B 165 " ideal model delta sigma weight residual 116.30 125.44 -9.14 3.50e+00 8.16e-02 6.81e+00 ... (remaining 10610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 4201 16.54 - 33.08: 435 33.08 - 49.62: 111 49.62 - 66.15: 19 66.15 - 82.69: 11 Dihedral angle restraints: 4777 sinusoidal: 1907 harmonic: 2870 Sorted by residual: dihedral pdb=" CA VAL B 93 " pdb=" C VAL B 93 " pdb=" N ASP B 94 " pdb=" CA ASP B 94 " ideal model delta harmonic sigma weight residual 180.00 157.18 22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ASN B 153 " pdb=" C ASN B 153 " pdb=" N MET B 154 " pdb=" CA MET B 154 " ideal model delta harmonic sigma weight residual -180.00 -158.05 -21.95 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PHE B 200 " pdb=" C PHE B 200 " pdb=" N GLU B 201 " pdb=" CA GLU B 201 " ideal model delta harmonic sigma weight residual 180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 4774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 794 0.032 - 0.064: 349 0.064 - 0.097: 94 0.097 - 0.129: 25 0.129 - 0.161: 3 Chirality restraints: 1265 Sorted by residual: chirality pdb=" CA ASP A 590 " pdb=" N ASP A 590 " pdb=" C ASP A 590 " pdb=" CB ASP A 590 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CB VAL A 587 " pdb=" CA VAL A 587 " pdb=" CG1 VAL A 587 " pdb=" CG2 VAL A 587 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA LYS B 328 " pdb=" N LYS B 328 " pdb=" C LYS B 328 " pdb=" CB LYS B 328 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 1262 not shown) Planarity restraints: 1304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 589 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C MET A 589 " 0.037 2.00e-02 2.50e+03 pdb=" O MET A 589 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP A 590 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 253 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 254 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 498 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C ARG B 498 " -0.028 2.00e-02 2.50e+03 pdb=" O ARG B 498 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS B 499 " 0.009 2.00e-02 2.50e+03 ... (remaining 1301 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1389 2.76 - 3.30: 8121 3.30 - 3.83: 12522 3.83 - 4.37: 13340 4.37 - 4.90: 23918 Nonbonded interactions: 59290 Sorted by model distance: nonbonded pdb=" O SER A 281 " pdb=" OG1 THR A 284 " model vdw 2.231 3.040 nonbonded pdb=" O LYS B 252 " pdb=" OG1 THR B 467 " model vdw 2.232 3.040 nonbonded pdb=" OG SER A 421 " pdb=" OE1 GLN A 424 " model vdw 2.243 3.040 nonbonded pdb=" O LYS A 561 " pdb=" N ASP A 642 " model vdw 2.317 3.120 nonbonded pdb=" OD1 ASN B 259 " pdb=" OH TYR B 536 " model vdw 2.323 3.040 ... (remaining 59285 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: 2.910 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.990 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.004 0.034 7889 Z= 0.244 Angle : 0.631 9.137 10615 Z= 0.330 Chirality : 0.039 0.161 1265 Planarity : 0.004 0.041 1304 Dihedral : 14.975 82.693 2925 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.09 % Favored : 91.70 % Rotamer: Outliers : 0.12 % Allowed : 0.35 % Favored : 99.53 % 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: 1.06 (0.28), residues: 976 helix: 1.85 (0.20), residues: 704 sheet: 0.27 (1.61), residues: 12 loop : -2.65 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 132 HIS 0.005 0.001 HIS A 249 PHE 0.010 0.001 PHE B 194 TYR 0.020 0.002 TYR B 389 ARG 0.004 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 1.035 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.1957 time to fit residues: 36.1721 Evaluate side-chains 110 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 499 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.0070 chunk 40 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.192102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.142997 restraints weight = 9187.721| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.93 r_work: 0.3613 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7889 Z= 0.190 Angle : 0.570 8.296 10615 Z= 0.293 Chirality : 0.038 0.158 1265 Planarity : 0.003 0.039 1304 Dihedral : 4.501 52.303 1051 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.40 % Favored : 91.50 % Rotamer: Outliers : 1.65 % Allowed : 9.89 % Favored : 88.46 % 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: 1.52 (0.29), residues: 976 helix: 2.26 (0.20), residues: 695 sheet: 0.89 (1.62), residues: 12 loop : -2.59 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 132 HIS 0.003 0.001 HIS A 249 PHE 0.009 0.001 PHE B 128 TYR 0.013 0.001 TYR A 225 ARG 0.003 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.868 Fit side-chains REVERT: A 155 MET cc_start: 0.6370 (mpp) cc_final: 0.5808 (mmt) REVERT: A 304 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.6664 (mp10) REVERT: A 458 ARG cc_start: 0.7416 (ptp-170) cc_final: 0.7123 (ptm160) outliers start: 14 outliers final: 10 residues processed: 128 average time/residue: 0.1958 time to fit residues: 34.4700 Evaluate side-chains 120 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 250 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 ASN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.188946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.141976 restraints weight = 9414.814| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.77 r_work: 0.3563 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7889 Z= 0.232 Angle : 0.577 7.977 10615 Z= 0.297 Chirality : 0.038 0.157 1265 Planarity : 0.003 0.038 1304 Dihedral : 4.003 23.690 1047 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.09 % Favored : 91.80 % Rotamer: Outliers : 1.77 % Allowed : 14.02 % Favored : 84.22 % 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: 1.39 (0.28), residues: 976 helix: 2.18 (0.20), residues: 694 sheet: 0.72 (1.58), residues: 12 loop : -2.63 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 132 HIS 0.004 0.001 HIS A 249 PHE 0.010 0.001 PHE A 309 TYR 0.016 0.002 TYR A 225 ARG 0.003 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.832 Fit side-chains REVERT: A 155 MET cc_start: 0.6110 (mpp) cc_final: 0.5833 (mmt) REVERT: A 244 MET cc_start: 0.8012 (tpp) cc_final: 0.7777 (tpp) REVERT: A 304 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.6463 (mp10) REVERT: A 458 ARG cc_start: 0.7363 (ptp-170) cc_final: 0.7160 (ptm160) REVERT: B 123 TYR cc_start: 0.6600 (m-10) cc_final: 0.6371 (m-10) outliers start: 15 outliers final: 13 residues processed: 121 average time/residue: 0.1936 time to fit residues: 32.1752 Evaluate side-chains 117 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 361 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 96 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.192362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.147808 restraints weight = 9254.934| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.14 r_work: 0.3600 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7889 Z= 0.165 Angle : 0.543 10.035 10615 Z= 0.277 Chirality : 0.037 0.152 1265 Planarity : 0.003 0.037 1304 Dihedral : 3.895 21.729 1047 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.47 % Allowed : 16.25 % Favored : 81.27 % 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: 1.61 (0.29), residues: 976 helix: 2.35 (0.20), residues: 695 sheet: 0.76 (1.60), residues: 12 loop : -2.60 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.012 0.001 PHE B 128 TYR 0.012 0.001 TYR B 225 ARG 0.003 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.817 Fit side-chains REVERT: A 155 MET cc_start: 0.6091 (mpp) cc_final: 0.5785 (mmt) REVERT: A 304 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.6301 (mp10) REVERT: B 123 TYR cc_start: 0.6603 (m-10) cc_final: 0.6298 (m-80) outliers start: 21 outliers final: 15 residues processed: 126 average time/residue: 0.1974 time to fit residues: 34.0265 Evaluate side-chains 116 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 361 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 0.0050 chunk 75 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.185558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.138125 restraints weight = 9262.844| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.96 r_work: 0.3472 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7889 Z= 0.208 Angle : 0.572 10.223 10615 Z= 0.291 Chirality : 0.038 0.199 1265 Planarity : 0.003 0.036 1304 Dihedral : 3.921 23.037 1047 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.20 % Favored : 91.70 % Rotamer: Outliers : 3.06 % Allowed : 16.37 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.50 (0.28), residues: 976 helix: 2.27 (0.20), residues: 695 sheet: 0.57 (1.60), residues: 12 loop : -2.65 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.009 0.001 PHE A 217 TYR 0.015 0.001 TYR A 225 ARG 0.004 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.824 Fit side-chains REVERT: A 155 MET cc_start: 0.6121 (mpp) cc_final: 0.5887 (mmt) REVERT: A 244 MET cc_start: 0.7998 (tpp) cc_final: 0.7671 (tpp) REVERT: A 304 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.6333 (mp10) REVERT: A 543 ILE cc_start: -0.2530 (OUTLIER) cc_final: -0.3112 (mp) REVERT: B 123 TYR cc_start: 0.6581 (m-10) cc_final: 0.6231 (m-80) REVERT: B 604 PHE cc_start: 0.6240 (OUTLIER) cc_final: 0.5469 (p90) outliers start: 26 outliers final: 15 residues processed: 126 average time/residue: 0.1773 time to fit residues: 32.0773 Evaluate side-chains 118 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 96 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 579 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.189633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140383 restraints weight = 9245.602| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.95 r_work: 0.3575 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7889 Z= 0.208 Angle : 0.583 10.916 10615 Z= 0.291 Chirality : 0.038 0.190 1265 Planarity : 0.003 0.035 1304 Dihedral : 3.940 24.099 1047 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.30 % Favored : 91.60 % Rotamer: Outliers : 3.18 % Allowed : 16.96 % Favored : 79.86 % 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: 1.51 (0.28), residues: 976 helix: 2.28 (0.20), residues: 695 sheet: 0.46 (1.55), residues: 12 loop : -2.65 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.009 0.001 PHE A 217 TYR 0.014 0.001 TYR A 225 ARG 0.003 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.820 Fit side-chains REVERT: A 304 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.6326 (mp10) REVERT: A 543 ILE cc_start: -0.2493 (OUTLIER) cc_final: -0.3081 (mp) REVERT: B 123 TYR cc_start: 0.6595 (m-10) cc_final: 0.6205 (m-80) REVERT: B 604 PHE cc_start: 0.6271 (OUTLIER) cc_final: 0.5466 (p90) outliers start: 27 outliers final: 21 residues processed: 129 average time/residue: 0.1793 time to fit residues: 32.8006 Evaluate side-chains 126 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.188872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.139491 restraints weight = 9337.111| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.96 r_work: 0.3574 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7889 Z= 0.218 Angle : 0.592 11.385 10615 Z= 0.298 Chirality : 0.038 0.189 1265 Planarity : 0.003 0.035 1304 Dihedral : 3.944 23.802 1047 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.61 % Favored : 91.29 % Rotamer: Outliers : 3.18 % Allowed : 18.26 % Favored : 78.56 % 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: 1.53 (0.28), residues: 976 helix: 2.29 (0.20), residues: 695 sheet: 0.48 (1.52), residues: 12 loop : -2.62 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.012 0.001 PHE B 572 TYR 0.015 0.001 TYR A 225 ARG 0.003 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.943 Fit side-chains REVERT: A 244 MET cc_start: 0.8014 (tpp) cc_final: 0.7797 (tpp) REVERT: A 304 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.6338 (mp10) REVERT: A 543 ILE cc_start: -0.2527 (OUTLIER) cc_final: -0.3131 (mp) REVERT: B 123 TYR cc_start: 0.6674 (m-10) cc_final: 0.6239 (m-80) REVERT: B 571 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7110 (pt) REVERT: B 604 PHE cc_start: 0.6274 (OUTLIER) cc_final: 0.5404 (p90) outliers start: 27 outliers final: 20 residues processed: 123 average time/residue: 0.1761 time to fit residues: 31.1631 Evaluate side-chains 126 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.185761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.136011 restraints weight = 9358.515| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.96 r_work: 0.3529 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7889 Z= 0.285 Angle : 0.638 11.380 10615 Z= 0.322 Chirality : 0.040 0.196 1265 Planarity : 0.003 0.034 1304 Dihedral : 4.120 25.082 1047 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.40 % Favored : 91.50 % Rotamer: Outliers : 3.06 % Allowed : 18.49 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.30 (0.28), residues: 976 helix: 2.10 (0.20), residues: 700 sheet: 0.27 (1.47), residues: 12 loop : -2.74 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 132 HIS 0.004 0.001 HIS A 249 PHE 0.012 0.002 PHE B 222 TYR 0.018 0.002 TYR A 225 ARG 0.004 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.826 Fit side-chains REVERT: A 304 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.6395 (mp10) REVERT: B 123 TYR cc_start: 0.6650 (m-10) cc_final: 0.6173 (m-80) REVERT: B 293 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7493 (mmt) REVERT: B 604 PHE cc_start: 0.6357 (OUTLIER) cc_final: 0.5506 (p90) outliers start: 26 outliers final: 17 residues processed: 121 average time/residue: 0.1749 time to fit residues: 30.1859 Evaluate side-chains 122 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 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 586 ASN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.195169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.151766 restraints weight = 9455.321| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.06 r_work: 0.3684 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7889 Z= 0.205 Angle : 0.611 12.000 10615 Z= 0.305 Chirality : 0.038 0.190 1265 Planarity : 0.003 0.046 1304 Dihedral : 3.998 24.294 1047 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.30 % Favored : 91.50 % Rotamer: Outliers : 2.71 % Allowed : 19.67 % Favored : 77.62 % 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: 1.55 (0.29), residues: 976 helix: 2.30 (0.20), residues: 695 sheet: 0.59 (1.51), residues: 12 loop : -2.58 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.009 0.001 PHE B 200 TYR 0.014 0.001 TYR B 33 ARG 0.004 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.841 Fit side-chains REVERT: A 304 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.6317 (mp10) REVERT: B 123 TYR cc_start: 0.6691 (m-10) cc_final: 0.6197 (m-80) REVERT: B 293 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7418 (mmt) REVERT: B 604 PHE cc_start: 0.6342 (OUTLIER) cc_final: 0.5526 (p90) outliers start: 23 outliers final: 16 residues processed: 119 average time/residue: 0.1863 time to fit residues: 31.6222 Evaluate side-chains 123 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 82 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 73 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 ASN B 579 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.192039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.147664 restraints weight = 9204.459| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.00 r_work: 0.3621 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7889 Z= 0.164 Angle : 0.596 12.304 10615 Z= 0.295 Chirality : 0.037 0.204 1265 Planarity : 0.003 0.042 1304 Dihedral : 3.836 23.022 1047 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.20 % Favored : 91.60 % Rotamer: Outliers : 2.36 % Allowed : 20.02 % Favored : 77.62 % 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 (0.29), residues: 976 helix: 2.47 (0.20), residues: 695 sheet: 0.87 (1.51), residues: 12 loop : -2.51 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.009 0.001 PHE B 383 TYR 0.011 0.001 TYR B 225 ARG 0.004 0.000 ARG A 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.846 Fit side-chains REVERT: A 244 MET cc_start: 0.8018 (tpp) cc_final: 0.7742 (tpp) REVERT: A 304 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.6214 (mp10) REVERT: A 434 TYR cc_start: 0.8812 (m-80) cc_final: 0.8493 (m-80) REVERT: A 543 ILE cc_start: -0.2417 (OUTLIER) cc_final: -0.3059 (mp) REVERT: B 125 MET cc_start: 0.7527 (tpt) cc_final: 0.6759 (mpp) REVERT: B 293 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7432 (mmt) REVERT: B 604 PHE cc_start: 0.6294 (OUTLIER) cc_final: 0.5521 (p90) outliers start: 20 outliers final: 13 residues processed: 127 average time/residue: 0.1866 time to fit residues: 33.6754 Evaluate side-chains 118 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 86 optimal weight: 0.0060 chunk 59 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 33 optimal weight: 0.0970 chunk 3 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.188651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.138675 restraints weight = 9339.440| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.05 r_work: 0.3531 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.141 7889 Z= 0.234 Angle : 0.949 59.200 10615 Z= 0.551 Chirality : 0.043 0.655 1265 Planarity : 0.004 0.057 1304 Dihedral : 4.062 42.909 1047 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.30 % Favored : 91.39 % Rotamer: Outliers : 2.47 % Allowed : 20.73 % Favored : 76.80 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.76 (0.29), residues: 976 helix: 2.45 (0.20), residues: 695 sheet: 0.88 (1.51), residues: 12 loop : -2.50 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.015 0.001 PHE A 535 TYR 0.011 0.001 TYR B 226 ARG 0.003 0.000 ARG A 472 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4417.35 seconds wall clock time: 80 minutes 25.59 seconds (4825.59 seconds total)