Starting phenix.real_space_refine on Fri Aug 22 20:35:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9baa_44402/08_2025/9baa_44402.cif Found real_map, /net/cci-nas-00/data/ceres_data/9baa_44402/08_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_44402/08_2025/9baa_44402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9baa_44402/08_2025/9baa_44402.map" model { file = "/net/cci-nas-00/data/ceres_data/9baa_44402/08_2025/9baa_44402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9baa_44402/08_2025/9baa_44402.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.07, per 1000 atoms: 0.27 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: 0.66 Conformation dependent library (CDL) restraints added in 462.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.23 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: 1.20 Time building geometry restraints manager: 0.88 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: 3.380 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.310 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.290 ------------------------------------------------------------------------------- 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= 0.165 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 472 TYR 0.020 0.002 TYR B 389 PHE 0.010 0.001 PHE B 194 TRP 0.011 0.002 TRP B 132 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 7889) covalent geometry : angle 0.63052 (10615) hydrogen bonds : bond 0.13872 ( 532) hydrogen bonds : angle 5.16092 ( 1572) *********************** 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 : 0.284 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.0848 time to fit residues: 15.8613 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 : 0.306 ------------------------------------------------------------------------------- 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 49 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0870 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.192854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.147371 restraints weight = 9304.590| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.97 r_work: 0.3604 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1116 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= 0.149 Angle : 0.580 8.325 10615 Z= 0.299 Chirality : 0.038 0.169 1265 Planarity : 0.003 0.039 1304 Dihedral : 4.533 50.922 1051 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.40 % Favored : 91.50 % Rotamer: Outliers : 1.65 % Allowed : 10.13 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.29), residues: 976 helix: 2.20 (0.20), residues: 696 sheet: 0.88 (1.62), residues: 12 loop : -2.61 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 559 TYR 0.015 0.001 TYR A 225 PHE 0.009 0.001 PHE B 194 TRP 0.010 0.002 TRP B 132 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7889) covalent geometry : angle 0.58016 (10615) hydrogen bonds : bond 0.04726 ( 532) hydrogen bonds : angle 3.94977 ( 1572) *********************** 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 134 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.303 Fit side-chains REVERT: A 155 MET cc_start: 0.6039 (mpp) cc_final: 0.5604 (mmt) REVERT: A 304 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.6813 (mp10) REVERT: B 128 PHE cc_start: 0.7598 (t80) cc_final: 0.7383 (t80) outliers start: 14 outliers final: 10 residues processed: 129 average time/residue: 0.0822 time to fit residues: 14.7417 Evaluate side-chains 123 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.184865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.139819 restraints weight = 9366.290| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.87 r_work: 0.3506 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7889 Z= 0.205 Angle : 0.624 8.286 10615 Z= 0.323 Chirality : 0.040 0.203 1265 Planarity : 0.003 0.039 1304 Dihedral : 4.209 25.237 1047 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.50 % Favored : 91.39 % Rotamer: Outliers : 2.00 % Allowed : 14.72 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.28), residues: 976 helix: 1.93 (0.20), residues: 696 sheet: 0.40 (1.59), residues: 12 loop : -2.71 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 277 TYR 0.019 0.002 TYR A 225 PHE 0.013 0.002 PHE A 309 TRP 0.024 0.003 TRP B 132 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 7889) covalent geometry : angle 0.62366 (10615) hydrogen bonds : bond 0.05286 ( 532) hydrogen bonds : angle 4.10504 ( 1572) *********************** 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 135 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.230 Fit side-chains REVERT: A 155 MET cc_start: 0.6071 (mpp) cc_final: 0.5734 (mmt) REVERT: A 304 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.6480 (mp10) REVERT: B 123 TYR cc_start: 0.6611 (m-10) cc_final: 0.6350 (m-10) REVERT: B 128 PHE cc_start: 0.7797 (t80) cc_final: 0.7590 (t80) REVERT: B 293 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7460 (mmt) outliers start: 17 outliers final: 12 residues processed: 128 average time/residue: 0.0812 time to fit residues: 14.3010 Evaluate side-chains 124 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 76 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.0010 chunk 97 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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 579 ASN ** 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 = 0.4204 r_free = 0.4204 target = 0.188927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.142312 restraints weight = 9406.372| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.81 r_work: 0.3576 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1630 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= 0.133 Angle : 0.563 8.504 10615 Z= 0.288 Chirality : 0.038 0.178 1265 Planarity : 0.003 0.042 1304 Dihedral : 4.074 24.056 1047 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.71 % Allowed : 16.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.28), residues: 976 helix: 2.21 (0.20), residues: 695 sheet: 0.55 (1.61), residues: 12 loop : -2.69 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 277 TYR 0.013 0.001 TYR B 225 PHE 0.016 0.001 PHE B 128 TRP 0.023 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7889) covalent geometry : angle 0.56271 (10615) hydrogen bonds : bond 0.04426 ( 532) hydrogen bonds : angle 3.82403 ( 1572) *********************** 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: 23 poor density : 110 time to evaluate : 0.348 Fit side-chains REVERT: A 244 MET cc_start: 0.8082 (tpp) cc_final: 0.7850 (tpp) REVERT: A 304 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.6326 (mp10) REVERT: B 123 TYR cc_start: 0.6652 (m-10) cc_final: 0.6292 (m-10) REVERT: B 293 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7442 (mmt) REVERT: B 387 MET cc_start: 0.8575 (tpp) cc_final: 0.8187 (tpp) outliers start: 23 outliers final: 15 residues processed: 126 average time/residue: 0.0725 time to fit residues: 13.2502 Evaluate side-chains 120 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 453 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 643 ILE 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 44 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 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 = 0.4212 r_free = 0.4212 target = 0.189757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.143578 restraints weight = 9350.203| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.72 r_work: 0.3596 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1750 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= 0.132 Angle : 0.563 10.127 10615 Z= 0.287 Chirality : 0.038 0.191 1265 Planarity : 0.003 0.038 1304 Dihedral : 3.999 24.455 1047 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.20 % Favored : 91.70 % Rotamer: Outliers : 3.18 % Allowed : 17.79 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.28), residues: 976 helix: 2.26 (0.20), residues: 695 sheet: 0.58 (1.55), residues: 12 loop : -2.66 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 472 TYR 0.013 0.001 TYR B 225 PHE 0.028 0.001 PHE A 173 TRP 0.026 0.003 TRP B 132 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7889) covalent geometry : angle 0.56346 (10615) hydrogen bonds : bond 0.04324 ( 532) hydrogen bonds : angle 3.78047 ( 1572) *********************** 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 136 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.240 Fit side-chains REVERT: A 155 MET cc_start: 0.6036 (mpp) cc_final: 0.5278 (mmt) REVERT: A 304 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.6354 (mp10) REVERT: A 543 ILE cc_start: -0.2361 (OUTLIER) cc_final: -0.3003 (mp) REVERT: B 123 TYR cc_start: 0.6621 (m-10) cc_final: 0.6273 (m-80) REVERT: B 293 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7386 (mmt) REVERT: B 604 PHE cc_start: 0.6306 (OUTLIER) cc_final: 0.5443 (p90) outliers start: 27 outliers final: 16 residues processed: 127 average time/residue: 0.0704 time to fit residues: 12.8933 Evaluate side-chains 124 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 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 A residue 643 ILE 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 58 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4174 r_free = 0.4174 target = 0.187077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.136469 restraints weight = 9383.566| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.03 r_work: 0.3514 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1863 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= 0.120 Angle : 0.563 11.260 10615 Z= 0.282 Chirality : 0.037 0.154 1265 Planarity : 0.003 0.037 1304 Dihedral : 3.919 23.740 1047 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.20 % Favored : 91.70 % Rotamer: Outliers : 3.30 % Allowed : 18.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.29), residues: 976 helix: 2.37 (0.20), residues: 696 sheet: 0.73 (1.57), residues: 12 loop : -2.60 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.012 0.001 TYR B 225 PHE 0.032 0.001 PHE A 173 TRP 0.027 0.003 TRP B 132 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7889) covalent geometry : angle 0.56319 (10615) hydrogen bonds : bond 0.04100 ( 532) hydrogen bonds : angle 3.70387 ( 1572) *********************** 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 135 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.306 Fit side-chains REVERT: A 155 MET cc_start: 0.6237 (mpp) cc_final: 0.5564 (mmt) REVERT: A 244 MET cc_start: 0.7952 (tpp) cc_final: 0.7590 (tpp) REVERT: A 304 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.6310 (mp10) REVERT: A 543 ILE cc_start: -0.2447 (OUTLIER) cc_final: -0.3037 (mp) REVERT: B 123 TYR cc_start: 0.6637 (m-10) cc_final: 0.6163 (m-80) REVERT: B 293 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7335 (mmt) REVERT: B 604 PHE cc_start: 0.6236 (OUTLIER) cc_final: 0.5387 (p90) outliers start: 28 outliers final: 20 residues processed: 126 average time/residue: 0.0697 time to fit residues: 12.6630 Evaluate side-chains 125 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain B residue 389 TYR 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 1 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 75 optimal weight: 0.0970 chunk 68 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** B 602 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.194763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.145030 restraints weight = 9404.007| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.93 r_work: 0.3609 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1926 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= 0.120 Angle : 0.582 11.856 10615 Z= 0.287 Chirality : 0.037 0.192 1265 Planarity : 0.003 0.036 1304 Dihedral : 3.869 23.314 1047 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.09 % Favored : 91.80 % Rotamer: Outliers : 3.30 % Allowed : 18.61 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.29), residues: 976 helix: 2.43 (0.20), residues: 698 sheet: 0.77 (1.57), residues: 12 loop : -2.53 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.012 0.001 TYR B 225 PHE 0.031 0.001 PHE A 173 TRP 0.020 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7889) covalent geometry : angle 0.58153 (10615) hydrogen bonds : bond 0.04045 ( 532) hydrogen bonds : angle 3.68048 ( 1572) *********************** 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 137 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.305 Fit side-chains REVERT: A 155 MET cc_start: 0.6094 (mpp) cc_final: 0.5505 (mmt) REVERT: A 244 MET cc_start: 0.7991 (tpp) cc_final: 0.7705 (tpp) REVERT: A 304 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.6422 (mp10) REVERT: A 543 ILE cc_start: -0.2422 (OUTLIER) cc_final: -0.3030 (mp) REVERT: B 123 TYR cc_start: 0.6637 (m-10) cc_final: 0.6161 (m-80) REVERT: B 604 PHE cc_start: 0.6248 (OUTLIER) cc_final: 0.5402 (p90) outliers start: 28 outliers final: 19 residues processed: 128 average time/residue: 0.0717 time to fit residues: 13.1267 Evaluate side-chains 124 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 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 361 PHE Chi-restraints excluded: chain B residue 389 TYR 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 37 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 54 optimal weight: 0.0370 chunk 73 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.192933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.144652 restraints weight = 9373.008| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.96 r_work: 0.3627 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2068 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= 0.113 Angle : 0.575 12.026 10615 Z= 0.284 Chirality : 0.037 0.195 1265 Planarity : 0.003 0.036 1304 Dihedral : 3.796 22.438 1047 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.89 % Favored : 92.01 % Rotamer: Outliers : 2.94 % Allowed : 18.73 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.29), residues: 976 helix: 2.53 (0.20), residues: 698 sheet: 0.85 (1.52), residues: 12 loop : -2.44 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 472 TYR 0.011 0.001 TYR B 225 PHE 0.030 0.001 PHE A 173 TRP 0.018 0.002 TRP B 132 HIS 0.005 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 7889) covalent geometry : angle 0.57460 (10615) hydrogen bonds : bond 0.03809 ( 532) hydrogen bonds : angle 3.59227 ( 1572) *********************** 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 133 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.307 Fit side-chains REVERT: A 244 MET cc_start: 0.8070 (tpp) cc_final: 0.7790 (tpp) REVERT: A 304 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.6446 (mp10) REVERT: A 543 ILE cc_start: -0.2468 (OUTLIER) cc_final: -0.3073 (mp) REVERT: B 123 TYR cc_start: 0.6530 (m-10) cc_final: 0.6074 (m-80) REVERT: B 604 PHE cc_start: 0.6278 (OUTLIER) cc_final: 0.5460 (p90) outliers start: 25 outliers final: 18 residues processed: 127 average time/residue: 0.0725 time to fit residues: 13.3148 Evaluate side-chains 124 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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 137 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 389 TYR 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 21 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.191529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.143118 restraints weight = 9281.527| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.96 r_work: 0.3612 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2069 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= 0.122 Angle : 0.583 11.804 10615 Z= 0.290 Chirality : 0.038 0.203 1265 Planarity : 0.003 0.035 1304 Dihedral : 3.819 22.594 1047 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.79 % Favored : 92.11 % Rotamer: Outliers : 2.71 % Allowed : 19.20 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.29), residues: 976 helix: 2.46 (0.20), residues: 705 sheet: 0.67 (1.46), residues: 12 loop : -2.55 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 472 TYR 0.013 0.001 TYR A 225 PHE 0.029 0.001 PHE A 173 TRP 0.026 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7889) covalent geometry : angle 0.58269 (10615) hydrogen bonds : bond 0.03967 ( 532) hydrogen bonds : angle 3.62323 ( 1572) *********************** 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 126 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.324 Fit side-chains REVERT: A 155 MET cc_start: 0.6271 (mpp) cc_final: 0.5263 (mmt) REVERT: A 244 MET cc_start: 0.8071 (tpp) cc_final: 0.7840 (tpp) REVERT: A 304 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.6478 (mp10) REVERT: A 434 TYR cc_start: 0.8832 (m-80) cc_final: 0.8496 (m-80) REVERT: A 543 ILE cc_start: -0.2521 (OUTLIER) cc_final: -0.3119 (mp) REVERT: B 604 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5269 (p90) outliers start: 23 outliers final: 18 residues processed: 119 average time/residue: 0.0730 time to fit residues: 12.3000 Evaluate side-chains 119 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 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 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 137 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 250 VAL 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 26 optimal weight: 0.0870 chunk 51 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 84 optimal weight: 0.1980 chunk 56 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- 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 = 0.4261 r_free = 0.4261 target = 0.194431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.146469 restraints weight = 9294.104| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.96 r_work: 0.3649 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2233 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= 0.111 Angle : 0.574 12.280 10615 Z= 0.284 Chirality : 0.037 0.202 1265 Planarity : 0.003 0.036 1304 Dihedral : 3.761 21.844 1047 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.89 % Favored : 91.91 % Rotamer: Outliers : 2.47 % Allowed : 19.43 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.29), residues: 976 helix: 2.58 (0.20), residues: 703 sheet: 0.76 (1.45), residues: 12 loop : -2.44 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 472 TYR 0.011 0.001 TYR B 225 PHE 0.029 0.001 PHE A 173 TRP 0.025 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 7889) covalent geometry : angle 0.57361 (10615) hydrogen bonds : bond 0.03696 ( 532) hydrogen bonds : angle 3.54683 ( 1572) ********************** 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 130 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.256 Fit side-chains REVERT: A 155 MET cc_start: 0.6258 (mpp) cc_final: 0.5235 (mmt) REVERT: A 244 MET cc_start: 0.8103 (tpp) cc_final: 0.7837 (tpp) REVERT: A 304 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.6308 (mp10) REVERT: A 434 TYR cc_start: 0.8771 (m-80) cc_final: 0.8493 (m-80) REVERT: A 543 ILE cc_start: -0.2565 (OUTLIER) cc_final: -0.3145 (mp) REVERT: B 604 PHE cc_start: 0.6172 (OUTLIER) cc_final: 0.5324 (p90) outliers start: 21 outliers final: 17 residues processed: 125 average time/residue: 0.0790 time to fit residues: 14.1223 Evaluate side-chains 120 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 137 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 389 TYR 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 5 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 29 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4267 r_free = 0.4267 target = 0.195149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.145789 restraints weight = 9421.678| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.92 r_work: 0.3619 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7889 Z= 0.126 Angle : 0.597 11.707 10615 Z= 0.299 Chirality : 0.038 0.197 1265 Planarity : 0.003 0.035 1304 Dihedral : 3.803 22.188 1047 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.68 % Favored : 92.11 % Rotamer: Outliers : 2.47 % Allowed : 20.26 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.29), residues: 976 helix: 2.50 (0.20), residues: 705 sheet: 0.62 (1.44), residues: 12 loop : -2.50 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.013 0.001 TYR A 225 PHE 0.027 0.001 PHE B 128 TRP 0.025 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7889) covalent geometry : angle 0.59715 (10615) hydrogen bonds : bond 0.03968 ( 532) hydrogen bonds : angle 3.61970 ( 1572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.23 seconds wall clock time: 38 minutes 48.28 seconds (2328.28 seconds total)