Starting phenix.real_space_refine on Wed Mar 12 10:48:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9baa_44402/03_2025/9baa_44402.cif Found real_map, /net/cci-nas-00/data/ceres_data/9baa_44402/03_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_44402/03_2025/9baa_44402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9baa_44402/03_2025/9baa_44402.map" model { file = "/net/cci-nas-00/data/ceres_data/9baa_44402/03_2025/9baa_44402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9baa_44402/03_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-5624/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: 5.84, per 1000 atoms: 0.75 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: 2.02 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.75 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: 2.26 Time building geometry restraints manager: 2.41 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: 3.150 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.790 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.680 ------------------------------------------------------------------------------- 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 : 0.818 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.1906 time to fit residues: 35.6844 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 : 0.828 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.142997 restraints weight = 9187.722| |-----------------------------------------------------------------------------| 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: 0.3481 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.817 Fit side-chains REVERT: A 155 MET cc_start: 0.6309 (mpp) cc_final: 0.5737 (mmt) REVERT: A 304 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.6665 (mp10) REVERT: A 458 ARG cc_start: 0.7433 (ptp-170) cc_final: 0.7142 (ptm160) outliers start: 14 outliers final: 10 residues processed: 128 average time/residue: 0.1895 time to fit residues: 33.3696 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 : 0.913 ------------------------------------------------------------------------------- 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: 0.6980 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 414 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 = 0.4268 r_free = 0.4268 target = 0.195431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.150369 restraints weight = 9365.232| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.90 r_work: 0.3609 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1324 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= 0.179 Angle : 0.548 7.834 10615 Z= 0.280 Chirality : 0.037 0.155 1265 Planarity : 0.003 0.038 1304 Dihedral : 3.896 22.502 1047 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.79 % Favored : 92.11 % Rotamer: Outliers : 1.77 % Allowed : 12.96 % Favored : 85.28 % 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: 1.57 (0.29), residues: 976 helix: 2.31 (0.20), residues: 695 sheet: 0.89 (1.59), residues: 12 loop : -2.59 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.007 0.001 PHE A 257 TYR 0.013 0.001 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 130 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.796 Fit side-chains REVERT: A 155 MET cc_start: 0.6077 (mpp) cc_final: 0.5773 (mmt) REVERT: A 244 MET cc_start: 0.8010 (tpp) cc_final: 0.7794 (tpp) REVERT: A 304 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.6486 (mp10) outliers start: 15 outliers final: 13 residues processed: 122 average time/residue: 0.1813 time to fit residues: 30.5808 Evaluate side-chains 118 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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: 0.7980 chunk 75 optimal weight: 8.9990 chunk 96 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 34 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 42 optimal weight: 30.0000 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 81 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.194432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.145749 restraints weight = 9248.487| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.96 r_work: 0.3646 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7889 Z= 0.151 Angle : 0.533 10.339 10615 Z= 0.271 Chirality : 0.037 0.161 1265 Planarity : 0.003 0.036 1304 Dihedral : 3.797 20.815 1047 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.83 % Allowed : 14.84 % Favored : 82.33 % 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: 1.72 (0.29), residues: 976 helix: 2.43 (0.20), residues: 695 sheet: 1.00 (1.63), residues: 12 loop : -2.55 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.014 0.001 PHE B 128 TYR 0.011 0.001 TYR B 225 ARG 0.003 0.000 ARG A 472 *********************** 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 138 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.969 Fit side-chains REVERT: A 155 MET cc_start: 0.6214 (mpp) cc_final: 0.5892 (mmt) REVERT: A 304 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.6315 (mp10) outliers start: 24 outliers final: 17 residues processed: 128 average time/residue: 0.2000 time to fit residues: 35.9178 Evaluate side-chains 117 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 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 453 VAL Chi-restraints excluded: chain A residue 459 LEU 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 154 MET 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: 2.9990 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.189424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.142727 restraints weight = 9301.690| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.77 r_work: 0.3582 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1647 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= 0.222 Angle : 0.574 10.204 10615 Z= 0.292 Chirality : 0.038 0.179 1265 Planarity : 0.003 0.035 1304 Dihedral : 3.924 23.526 1047 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.94 % Allowed : 15.90 % Favored : 81.15 % 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: 1.54 (0.29), residues: 976 helix: 2.28 (0.20), residues: 696 sheet: 0.59 (1.59), residues: 12 loop : -2.57 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 0.004 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: 25 poor density : 107 time to evaluate : 1.191 Fit side-chains REVERT: A 155 MET cc_start: 0.5935 (mpp) cc_final: 0.5699 (mmt) REVERT: A 244 MET cc_start: 0.8039 (tpp) cc_final: 0.7700 (tpp) REVERT: A 304 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.6446 (mp10) REVERT: A 543 ILE cc_start: -0.2547 (OUTLIER) cc_final: -0.3133 (mp) REVERT: A 630 ARG cc_start: 0.8041 (tpt170) cc_final: 0.7824 (tpt170) REVERT: B 123 TYR cc_start: 0.6390 (m-80) cc_final: 0.6181 (m-10) REVERT: B 604 PHE cc_start: 0.6247 (OUTLIER) cc_final: 0.5456 (p90) outliers start: 25 outliers final: 13 residues processed: 127 average time/residue: 0.1750 time to fit residues: 32.1835 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 : 0.929 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.191517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.142459 restraints weight = 9248.919| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.95 r_work: 0.3604 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1748 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= 0.182 Angle : 0.567 11.176 10615 Z= 0.284 Chirality : 0.037 0.163 1265 Planarity : 0.003 0.034 1304 Dihedral : 3.878 23.709 1047 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.09 % Favored : 91.80 % Rotamer: Outliers : 2.83 % Allowed : 17.08 % Favored : 80.09 % 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: 1.62 (0.29), residues: 976 helix: 2.36 (0.20), residues: 695 sheet: 0.68 (1.60), residues: 12 loop : -2.62 (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 0.008 0.001 PHE B 604 TYR 0.013 0.001 TYR B 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 130 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.928 Fit side-chains REVERT: A 155 MET cc_start: 0.6076 (mpp) cc_final: 0.5867 (mmt) REVERT: A 244 MET cc_start: 0.8023 (tpp) cc_final: 0.7804 (tpp) REVERT: A 304 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.6261 (mp10) REVERT: A 543 ILE cc_start: -0.2544 (OUTLIER) cc_final: -0.3106 (mp) REVERT: A 630 ARG cc_start: 0.8082 (tpt170) cc_final: 0.7858 (tpt170) REVERT: B 604 PHE cc_start: 0.6248 (OUTLIER) cc_final: 0.5465 (p90) outliers start: 24 outliers final: 16 residues processed: 123 average time/residue: 0.1840 time to fit residues: 33.4523 Evaluate side-chains 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 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 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 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: 0.2980 chunk 73 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.192085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.146591 restraints weight = 9290.580| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.01 r_work: 0.3616 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1875 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= 0.171 Angle : 0.555 11.639 10615 Z= 0.278 Chirality : 0.037 0.158 1265 Planarity : 0.003 0.034 1304 Dihedral : 3.826 23.070 1047 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.99 % Favored : 91.91 % Rotamer: Outliers : 2.47 % Allowed : 17.79 % Favored : 79.74 % 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: 1.70 (0.29), residues: 976 helix: 2.44 (0.20), residues: 695 sheet: 0.75 (1.57), residues: 12 loop : -2.65 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.008 0.001 PHE B 604 TYR 0.012 0.001 TYR B 225 ARG 0.003 0.000 ARG B 277 *********************** 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 122 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.819 Fit side-chains REVERT: A 304 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.6300 (mp10) REVERT: A 543 ILE cc_start: -0.2590 (OUTLIER) cc_final: -0.3152 (mp) REVERT: B 123 TYR cc_start: 0.6369 (m-80) cc_final: 0.6146 (m-80) REVERT: B 604 PHE cc_start: 0.6213 (OUTLIER) cc_final: 0.5372 (p90) outliers start: 21 outliers final: 15 residues processed: 117 average time/residue: 0.1592 time to fit residues: 26.8747 Evaluate side-chains 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 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 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 604 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.183532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.133615 restraints weight = 9413.936| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.95 r_work: 0.3503 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 7889 Z= 0.370 Angle : 0.685 10.730 10615 Z= 0.348 Chirality : 0.041 0.179 1265 Planarity : 0.003 0.032 1304 Dihedral : 4.230 26.275 1047 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.30 % Favored : 91.60 % Rotamer: Outliers : 2.94 % Allowed : 18.37 % Favored : 78.68 % 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: 1.10 (0.28), residues: 976 helix: 1.96 (0.20), residues: 699 sheet: 0.06 (1.46), residues: 12 loop : -2.83 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 132 HIS 0.005 0.001 HIS A 249 PHE 0.016 0.002 PHE B 222 TYR 0.021 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: 25 poor density : 106 time to evaluate : 0.929 Fit side-chains REVERT: A 304 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.6444 (mp10) REVERT: B 123 TYR cc_start: 0.6474 (m-80) cc_final: 0.6106 (m-10) REVERT: B 604 PHE cc_start: 0.6379 (OUTLIER) cc_final: 0.5574 (p90) outliers start: 25 outliers final: 16 residues processed: 123 average time/residue: 0.1702 time to fit residues: 29.7448 Evaluate side-chains 120 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 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 604 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 86 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 41 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 414 ASN ** B 31 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 = 0.4174 r_free = 0.4174 target = 0.187433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142352 restraints weight = 9458.146| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.01 r_work: 0.3499 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1975 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= 0.171 Angle : 0.586 11.784 10615 Z= 0.290 Chirality : 0.037 0.189 1265 Planarity : 0.003 0.047 1304 Dihedral : 3.967 24.056 1047 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.09 % Favored : 91.70 % Rotamer: Outliers : 2.36 % Allowed : 18.73 % Favored : 78.92 % 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: 2.36 (0.20), residues: 695 sheet: 0.65 (1.53), residues: 12 loop : -2.62 (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 0.008 0.001 PHE A 257 TYR 0.012 0.001 TYR B 225 ARG 0.003 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: 20 poor density : 107 time to evaluate : 0.892 Fit side-chains REVERT: A 244 MET cc_start: 0.8036 (tpp) cc_final: 0.7677 (tpp) REVERT: A 304 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.6121 (mp10) REVERT: A 543 ILE cc_start: -0.2435 (OUTLIER) cc_final: -0.3058 (mp) REVERT: B 123 TYR cc_start: 0.6434 (m-80) cc_final: 0.6024 (m-10) REVERT: B 293 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7389 (mmt) REVERT: B 604 PHE cc_start: 0.6298 (OUTLIER) cc_final: 0.5478 (p90) outliers start: 20 outliers final: 12 residues processed: 122 average time/residue: 0.1811 time to fit residues: 31.6394 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 : 0.756 ------------------------------------------------------------------------------- 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 356 GLU 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 604 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 82 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 73 optimal weight: 0.0970 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.187220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.136779 restraints weight = 9405.906| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.06 r_work: 0.3514 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1993 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= 0.182 Angle : 0.601 12.092 10615 Z= 0.298 Chirality : 0.038 0.199 1265 Planarity : 0.003 0.042 1304 Dihedral : 3.878 24.002 1047 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.89 % Favored : 91.91 % Rotamer: Outliers : 2.12 % Allowed : 19.20 % Favored : 78.68 % 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: 1.69 (0.29), residues: 976 helix: 2.42 (0.20), residues: 695 sheet: 0.66 (1.49), residues: 12 loop : -2.61 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.011 0.001 PHE B 383 TYR 0.013 0.001 TYR A 225 ARG 0.003 0.000 ARG A 472 ********************** 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 120 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.927 Fit side-chains REVERT: A 244 MET cc_start: 0.7964 (tpp) cc_final: 0.7582 (tpp) REVERT: A 304 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.6182 (mp10) REVERT: B 123 TYR cc_start: 0.6442 (m-80) cc_final: 0.5978 (m-10) REVERT: B 293 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7348 (mmt) REVERT: B 604 PHE cc_start: 0.6266 (OUTLIER) cc_final: 0.5496 (p90) outliers start: 18 outliers final: 13 residues processed: 116 average time/residue: 0.1684 time to fit residues: 28.3555 Evaluate side-chains 112 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 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 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 604 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 33 optimal weight: 0.0000 chunk 3 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN B 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.188924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137852 restraints weight = 9338.756| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.16 r_work: 0.3517 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2123 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= 0.171 Angle : 0.591 12.312 10615 Z= 0.292 Chirality : 0.037 0.196 1265 Planarity : 0.003 0.040 1304 Dihedral : 3.826 23.463 1047 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.89 % Favored : 91.91 % Rotamer: Outliers : 2.36 % Allowed : 19.20 % 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: 1.80 (0.29), residues: 976 helix: 2.50 (0.20), residues: 695 sheet: 0.75 (1.47), residues: 12 loop : -2.55 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.012 0.001 PHE B 383 TYR 0.012 0.001 TYR B 225 ARG 0.004 0.000 ARG A 472 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5064.01 seconds wall clock time: 90 minutes 33.03 seconds (5433.03 seconds total)