Starting phenix.real_space_refine on Fri Aug 22 15:49:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r2h_53530/08_2025/9r2h_53530.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r2h_53530/08_2025/9r2h_53530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r2h_53530/08_2025/9r2h_53530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r2h_53530/08_2025/9r2h_53530.map" model { file = "/net/cci-nas-00/data/ceres_data/9r2h_53530/08_2025/9r2h_53530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r2h_53530/08_2025/9r2h_53530.cif" } resolution = 2.6 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 3 5.16 5 C 1623 2.51 5 N 483 2.21 5 O 540 1.98 5 H 2667 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s 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: 5316 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1772 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1772 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "C" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1772 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Time building chain proxies: 0.91, per 1000 atoms: 0.17 Number of scatterers: 5316 At special positions: 0 Unit cell: (107.38, 82.6, 33.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 O 540 8.00 N 483 7.00 C 1623 6.00 H 2667 1.00 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: 0.32 Conformation dependent library (CDL) restraints added in 109.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 642 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 46.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.669A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 323 through 324 removed outlier: 6.525A pdb=" N GLY A 323 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 323 through 324 removed outlier: 6.525A pdb=" N GLY A 323 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER C 324 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 325 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.656A pdb=" N VAL A 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LYS B 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL A 339 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 343 through 347 removed outlier: 6.480A pdb=" N LEU A 344 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LYS B 347 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE A 346 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 351 through 354 removed outlier: 6.581A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 357 through 362 removed outlier: 6.702A pdb=" N LEU A 357 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE B 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN A 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N HIS B 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 369 through 381 removed outlier: 6.420A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLU B 380 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG A 379 " --> pdb=" O GLU B 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 384 through 385 removed outlier: 7.348A pdb=" N ALA A 384 " --> pdb=" O LYS B 385 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 390 through 394 removed outlier: 6.582A pdb=" N GLU A 391 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N TYR C 394 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 393 " --> pdb=" O TYR C 394 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 406 through 409 removed outlier: 6.416A pdb=" N ARG A 406 " --> pdb=" O HIS B 407 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER B 409 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU A 408 " --> pdb=" O SER B 409 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 412 through 413 removed outlier: 6.489A pdb=" N SER A 412 " --> pdb=" O SER C 413 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 416 through 421 Processing sheet with id=AB5, first strand: chain 'B' and resid 424 through 425 removed outlier: 6.382A pdb=" N GLN A 424 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 430 through 432 removed outlier: 6.443A pdb=" N ASP A 430 " --> pdb=" O GLU B 431 " (cutoff:3.500A) 58 hydrogen bonds defined for protein. 171 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: 0.89 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 2667 1.12 - 1.30: 469 1.30 - 1.47: 887 1.47 - 1.64: 1326 1.64 - 1.81: 6 Bond restraints: 5355 Sorted by residual: bond pdb=" N SER C 316 " pdb=" H SER C 316 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD2 HIS A 374 " pdb=" HD2 HIS A 374 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASN B 359 " pdb=" H ASN B 359 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N LEU C 357 " pdb=" H LEU C 357 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N SER A 412 " pdb=" H SER A 412 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 5350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 6919 1.82 - 3.65: 1852 3.65 - 5.47: 673 5.47 - 7.29: 259 7.29 - 9.11: 23 Bond angle restraints: 9726 Sorted by residual: angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 120.10 -7.50 1.00e+00 1.00e+00 5.63e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 119.15 -6.55 1.00e+00 1.00e+00 4.29e+01 angle pdb=" CA ASP C 418 " pdb=" CB ASP C 418 " pdb=" CG ASP C 418 " ideal model delta sigma weight residual 112.60 118.86 -6.26 1.00e+00 1.00e+00 3.92e+01 angle pdb=" N VAL C 399 " pdb=" CA VAL C 399 " pdb=" C VAL C 399 " ideal model delta sigma weight residual 111.48 116.19 -4.71 9.40e-01 1.13e+00 2.51e+01 angle pdb=" CA PHE A 346 " pdb=" CB PHE A 346 " pdb=" CG PHE A 346 " ideal model delta sigma weight residual 113.80 118.81 -5.01 1.00e+00 1.00e+00 2.51e+01 ... (remaining 9721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 2250 15.36 - 30.71: 153 30.71 - 46.07: 40 46.07 - 61.42: 59 61.42 - 76.78: 9 Dihedral angle restraints: 2511 sinusoidal: 1410 harmonic: 1101 Sorted by residual: dihedral pdb=" C ASP A 358 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " ideal model delta harmonic sigma weight residual -122.60 -140.14 17.54 0 2.50e+00 1.60e-01 4.92e+01 dihedral pdb=" C THR A 386 " pdb=" N THR A 386 " pdb=" CA THR A 386 " pdb=" CB THR A 386 " ideal model delta harmonic sigma weight residual -122.00 -137.26 15.26 0 2.50e+00 1.60e-01 3.73e+01 dihedral pdb=" N ASP A 358 " pdb=" C ASP A 358 " pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " ideal model delta harmonic sigma weight residual 122.80 137.89 -15.09 0 2.50e+00 1.60e-01 3.64e+01 ... (remaining 2508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 327 0.134 - 0.268: 73 0.268 - 0.401: 12 0.401 - 0.535: 4 0.535 - 0.669: 1 Chirality restraints: 417 Sorted by residual: chirality pdb=" CA ASP A 358 " pdb=" N ASP A 358 " pdb=" C ASP A 358 " pdb=" CB ASP A 358 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CA THR A 386 " pdb=" N THR A 386 " pdb=" C THR A 386 " pdb=" CB THR A 386 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.53 2.00e-01 2.50e+01 7.14e+00 chirality pdb=" CA ASP C 358 " pdb=" N ASP C 358 " pdb=" C ASP C 358 " pdb=" CB ASP C 358 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.09e+00 ... (remaining 414 not shown) Planarity restraints: 810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 349 " 0.387 9.50e-02 1.11e+02 1.55e-01 1.86e+02 pdb=" NE ARG B 349 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG B 349 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 349 " 0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG B 349 " -0.067 2.00e-02 2.50e+03 pdb="HH11 ARG B 349 " -0.013 2.00e-02 2.50e+03 pdb="HH12 ARG B 349 " -0.103 2.00e-02 2.50e+03 pdb="HH21 ARG B 349 " -0.112 2.00e-02 2.50e+03 pdb="HH22 ARG B 349 " 0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 407 " 0.048 2.00e-02 2.50e+03 4.76e-02 5.66e+01 pdb=" CG HIS C 407 " -0.049 2.00e-02 2.50e+03 pdb=" ND1 HIS C 407 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 HIS C 407 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 HIS C 407 " -0.045 2.00e-02 2.50e+03 pdb=" NE2 HIS C 407 " -0.041 2.00e-02 2.50e+03 pdb=" HD1 HIS C 407 " 0.056 2.00e-02 2.50e+03 pdb=" HD2 HIS C 407 " 0.030 2.00e-02 2.50e+03 pdb=" HE1 HIS C 407 " 0.037 2.00e-02 2.50e+03 pdb=" HE2 HIS C 407 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 349 " 0.132 9.50e-02 1.11e+02 6.56e-02 5.51e+01 pdb=" NE ARG C 349 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG C 349 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG C 349 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 349 " -0.049 2.00e-02 2.50e+03 pdb="HH11 ARG C 349 " 0.041 2.00e-02 2.50e+03 pdb="HH12 ARG C 349 " 0.014 2.00e-02 2.50e+03 pdb="HH21 ARG C 349 " 0.107 2.00e-02 2.50e+03 pdb="HH22 ARG C 349 " -0.045 2.00e-02 2.50e+03 ... (remaining 807 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 536 2.21 - 2.81: 9634 2.81 - 3.41: 13371 3.41 - 4.00: 18471 4.00 - 4.60: 25456 Nonbonded interactions: 67468 Sorted by model distance: nonbonded pdb=" OD2 ASP A 430 " pdb=" HH TYR B 394 " model vdw 1.614 2.450 nonbonded pdb=" OD1 ASP C 387 " pdb=" HD1 HIS C 388 " model vdw 1.640 2.450 nonbonded pdb=" HZ1 LYS A 395 " pdb=" OD2 ASP C 430 " model vdw 1.648 2.450 nonbonded pdb=" OD1 ASP A 387 " pdb=" HD1 HIS A 388 " model vdw 1.653 2.450 nonbonded pdb=" OD1 ASP B 387 " pdb=" HD1 HIS B 388 " model vdw 1.653 2.450 ... (remaining 67463 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.790 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: 0.050 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.880 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.011 0.037 2688 Z= 0.726 Angle : 2.001 9.010 3618 Z= 1.343 Chirality : 0.124 0.669 417 Planarity : 0.012 0.127 471 Dihedral : 11.469 76.776 1008 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 1.87 % 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: -3.09 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 406 TYR 0.018 0.008 TYR B 394 PHE 0.031 0.012 PHE C 378 HIS 0.009 0.004 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.01100 ( 2688) covalent geometry : angle 2.00083 ( 3618) hydrogen bonds : bond 0.09999 ( 58) hydrogen bonds : angle 7.48639 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8177 (tt0) cc_final: 0.7575 (tm-30) REVERT: A 342 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7092 (mt-10) REVERT: A 379 ARG cc_start: 0.7555 (ptp-170) cc_final: 0.7325 (ptp-170) REVERT: A 402 ASP cc_start: 0.8431 (m-30) cc_final: 0.8159 (m-30) REVERT: B 343 LYS cc_start: 0.7414 (tttt) cc_final: 0.6289 (tppt) REVERT: C 342 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7078 (mt-10) REVERT: C 419 MET cc_start: 0.8819 (ttm) cc_final: 0.8577 (ttm) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 1.2162 time to fit residues: 136.2764 Evaluate side-chains 75 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 362 HIS A 410 ASN B 410 ASN C 351 GLN C 410 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.171322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.140117 restraints weight = 7938.513| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.83 r_work: 0.3955 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3861 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2688 Z= 0.156 Angle : 0.651 4.985 3618 Z= 0.347 Chirality : 0.052 0.148 417 Planarity : 0.004 0.037 471 Dihedral : 7.244 22.662 366 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.31 % Allowed : 14.19 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.15 (0.32), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.24), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 379 TYR 0.007 0.002 TYR A 394 PHE 0.017 0.003 PHE C 378 HIS 0.006 0.002 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 2688) covalent geometry : angle 0.65146 ( 3618) hydrogen bonds : bond 0.02503 ( 58) hydrogen bonds : angle 5.77400 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8136 (tt0) cc_final: 0.7875 (mt-10) REVERT: A 340 LYS cc_start: 0.8547 (tmtm) cc_final: 0.8316 (mtpp) REVERT: A 342 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7319 (mt-10) REVERT: A 370 LYS cc_start: 0.8346 (tttp) cc_final: 0.8136 (tmtm) REVERT: A 424 GLN cc_start: 0.7160 (mt0) cc_final: 0.6938 (mm-40) REVERT: A 431 GLU cc_start: 0.7765 (tt0) cc_final: 0.7457 (tt0) REVERT: B 342 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7436 (mt-10) REVERT: B 418 ASP cc_start: 0.8257 (m-30) cc_final: 0.7982 (m-30) REVERT: C 338 GLU cc_start: 0.8413 (tt0) cc_final: 0.7992 (tm-30) REVERT: C 342 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7611 (mt-10) REVERT: C 391 GLU cc_start: 0.8294 (tt0) cc_final: 0.8014 (tt0) outliers start: 7 outliers final: 3 residues processed: 85 average time/residue: 1.1547 time to fit residues: 100.2260 Evaluate side-chains 80 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 421 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 32 optimal weight: 0.0010 chunk 19 optimal weight: 0.0870 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.1568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN B 410 ASN C 410 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.172042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.143061 restraints weight = 7814.868| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.87 r_work: 0.3971 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2688 Z= 0.102 Angle : 0.550 4.453 3618 Z= 0.293 Chirality : 0.050 0.144 417 Planarity : 0.003 0.024 471 Dihedral : 6.268 22.763 366 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.97 % Allowed : 14.85 % Favored : 82.18 % 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: -3.22 (0.31), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.24), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 379 TYR 0.007 0.002 TYR A 394 PHE 0.009 0.001 PHE A 378 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 2688) covalent geometry : angle 0.55029 ( 3618) hydrogen bonds : bond 0.01929 ( 58) hydrogen bonds : angle 5.15012 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8275 (mtpp) REVERT: A 342 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7509 (mt-10) REVERT: A 381 ASN cc_start: 0.6953 (OUTLIER) cc_final: 0.6413 (t0) REVERT: A 402 ASP cc_start: 0.8308 (m-30) cc_final: 0.8066 (m-30) REVERT: B 418 ASP cc_start: 0.8306 (m-30) cc_final: 0.8051 (m-30) REVERT: B 431 GLU cc_start: 0.8061 (tt0) cc_final: 0.7848 (tt0) REVERT: C 338 GLU cc_start: 0.8424 (tt0) cc_final: 0.8022 (tm-30) REVERT: C 381 ASN cc_start: 0.7032 (OUTLIER) cc_final: 0.6808 (t0) outliers start: 9 outliers final: 4 residues processed: 88 average time/residue: 1.0065 time to fit residues: 90.6775 Evaluate side-chains 82 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 421 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 31 optimal weight: 0.2980 chunk 30 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN B 410 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.172714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.143671 restraints weight = 7854.914| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 1.73 r_work: 0.3993 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2688 Z= 0.098 Angle : 0.521 4.316 3618 Z= 0.277 Chirality : 0.050 0.140 417 Planarity : 0.003 0.023 471 Dihedral : 5.904 21.944 366 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.64 % Allowed : 19.47 % Favored : 77.89 % 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: -3.24 (0.32), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.24), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 379 TYR 0.007 0.002 TYR B 394 PHE 0.009 0.001 PHE C 378 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 2688) covalent geometry : angle 0.52091 ( 3618) hydrogen bonds : bond 0.01683 ( 58) hydrogen bonds : angle 4.85606 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8519 (tmtm) cc_final: 0.8297 (mtpp) REVERT: A 342 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7433 (mt-10) REVERT: A 381 ASN cc_start: 0.6950 (OUTLIER) cc_final: 0.6722 (t0) REVERT: A 402 ASP cc_start: 0.8318 (m-30) cc_final: 0.8061 (m-30) REVERT: C 338 GLU cc_start: 0.8375 (tt0) cc_final: 0.7970 (tm-30) REVERT: C 381 ASN cc_start: 0.6954 (OUTLIER) cc_final: 0.6710 (t0) outliers start: 8 outliers final: 4 residues processed: 85 average time/residue: 1.0194 time to fit residues: 88.6464 Evaluate side-chains 85 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 409 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.170299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.138468 restraints weight = 7944.943| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 1.85 r_work: 0.3948 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2688 Z= 0.104 Angle : 0.510 4.006 3618 Z= 0.272 Chirality : 0.050 0.140 417 Planarity : 0.003 0.023 471 Dihedral : 5.731 22.000 366 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.63 % Allowed : 18.81 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.20 (0.32), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 349 TYR 0.008 0.002 TYR A 394 PHE 0.010 0.002 PHE A 378 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 2688) covalent geometry : angle 0.51034 ( 3618) hydrogen bonds : bond 0.01676 ( 58) hydrogen bonds : angle 4.72619 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8295 (mtpp) REVERT: A 342 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7450 (mt-10) REVERT: A 402 ASP cc_start: 0.8400 (m-30) cc_final: 0.8112 (m-30) REVERT: C 338 GLU cc_start: 0.8383 (tt0) cc_final: 0.7966 (tm-30) REVERT: C 370 LYS cc_start: 0.8411 (tttp) cc_final: 0.8151 (tmtm) REVERT: C 381 ASN cc_start: 0.6940 (OUTLIER) cc_final: 0.6713 (t0) outliers start: 11 outliers final: 5 residues processed: 83 average time/residue: 1.0740 time to fit residues: 91.0088 Evaluate side-chains 87 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 421 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 11 optimal weight: 0.0040 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 0.0270 overall best weight: 0.4254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN C 410 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.175988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.144898 restraints weight = 7923.944| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 1.87 r_work: 0.4034 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3937 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2688 Z= 0.071 Angle : 0.466 4.064 3618 Z= 0.244 Chirality : 0.049 0.139 417 Planarity : 0.003 0.018 471 Dihedral : 5.254 19.562 366 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.96 % Allowed : 18.81 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.09 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.004 0.001 TYR A 394 PHE 0.005 0.001 PHE C 378 HIS 0.001 0.000 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00167 ( 2688) covalent geometry : angle 0.46601 ( 3618) hydrogen bonds : bond 0.01719 ( 58) hydrogen bonds : angle 4.58322 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8275 (mtpp) REVERT: A 342 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7488 (mt-10) REVERT: A 402 ASP cc_start: 0.8284 (m-30) cc_final: 0.7981 (m-30) REVERT: A 418 ASP cc_start: 0.7979 (m-30) cc_final: 0.7747 (m-30) REVERT: C 338 GLU cc_start: 0.8322 (tt0) cc_final: 0.7924 (tm-30) REVERT: C 381 ASN cc_start: 0.6844 (OUTLIER) cc_final: 0.6611 (t0) outliers start: 12 outliers final: 4 residues processed: 80 average time/residue: 1.1157 time to fit residues: 91.1688 Evaluate side-chains 82 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 409 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.0570 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.168436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.137032 restraints weight = 7890.023| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 1.84 r_work: 0.3925 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3825 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.6117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2688 Z= 0.116 Angle : 0.521 4.136 3618 Z= 0.278 Chirality : 0.049 0.140 417 Planarity : 0.003 0.020 471 Dihedral : 5.486 20.164 366 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.64 % Allowed : 20.79 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.02 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.009 0.002 TYR A 394 PHE 0.012 0.002 PHE C 378 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 2688) covalent geometry : angle 0.52146 ( 3618) hydrogen bonds : bond 0.01714 ( 58) hydrogen bonds : angle 4.62027 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8296 (mtpp) REVERT: A 342 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7483 (mt-10) REVERT: A 402 ASP cc_start: 0.8400 (m-30) cc_final: 0.8087 (m-30) REVERT: B 340 LYS cc_start: 0.8630 (tptp) cc_final: 0.8337 (mttt) REVERT: C 338 GLU cc_start: 0.8347 (tt0) cc_final: 0.7953 (tm-30) REVERT: C 381 ASN cc_start: 0.6947 (OUTLIER) cc_final: 0.6697 (t0) outliers start: 8 outliers final: 5 residues processed: 76 average time/residue: 1.0361 time to fit residues: 80.3778 Evaluate side-chains 79 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 421 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.169242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.138198 restraints weight = 7864.266| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.81 r_work: 0.3946 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.6255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2688 Z= 0.099 Angle : 0.493 4.100 3618 Z= 0.261 Chirality : 0.048 0.134 417 Planarity : 0.003 0.020 471 Dihedral : 5.365 20.360 366 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.97 % Allowed : 20.46 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.00 (0.34), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.007 0.001 TYR A 394 PHE 0.008 0.001 PHE C 378 HIS 0.002 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 2688) covalent geometry : angle 0.49289 ( 3618) hydrogen bonds : bond 0.01663 ( 58) hydrogen bonds : angle 4.59600 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8283 (mtpp) REVERT: A 342 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7478 (mt-10) REVERT: A 402 ASP cc_start: 0.8344 (m-30) cc_final: 0.8023 (m-30) REVERT: B 340 LYS cc_start: 0.8629 (tptp) cc_final: 0.8347 (mttt) REVERT: C 338 GLU cc_start: 0.8322 (tt0) cc_final: 0.7925 (tm-30) REVERT: C 381 ASN cc_start: 0.6960 (OUTLIER) cc_final: 0.6728 (t0) outliers start: 9 outliers final: 6 residues processed: 75 average time/residue: 1.0755 time to fit residues: 82.4090 Evaluate side-chains 80 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 409 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.0270 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 0.0170 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.172941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.141922 restraints weight = 7913.895| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 1.83 r_work: 0.4002 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.6376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2688 Z= 0.072 Angle : 0.466 4.028 3618 Z= 0.244 Chirality : 0.048 0.134 417 Planarity : 0.003 0.020 471 Dihedral : 5.050 19.185 366 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.30 % Allowed : 19.47 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.00 (0.34), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 349 TYR 0.005 0.001 TYR A 394 PHE 0.005 0.001 PHE C 378 HIS 0.001 0.000 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00167 ( 2688) covalent geometry : angle 0.46613 ( 3618) hydrogen bonds : bond 0.01615 ( 58) hydrogen bonds : angle 4.36024 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8234 (mtpp) REVERT: A 342 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7475 (mt-10) REVERT: A 402 ASP cc_start: 0.8274 (m-30) cc_final: 0.7958 (m-30) REVERT: B 340 LYS cc_start: 0.8617 (tptp) cc_final: 0.8341 (mttt) REVERT: C 338 GLU cc_start: 0.8286 (tt0) cc_final: 0.7890 (tm-30) REVERT: C 381 ASN cc_start: 0.6823 (OUTLIER) cc_final: 0.6557 (t0) outliers start: 10 outliers final: 6 residues processed: 78 average time/residue: 1.0744 time to fit residues: 85.5132 Evaluate side-chains 82 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 409 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 0.0570 chunk 20 optimal weight: 0.0470 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.173416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.142497 restraints weight = 7936.879| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 1.83 r_work: 0.4010 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3912 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2688 Z= 0.075 Angle : 0.508 6.374 3618 Z= 0.257 Chirality : 0.048 0.134 417 Planarity : 0.003 0.020 471 Dihedral : 4.987 18.483 366 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.31 % Allowed : 21.45 % Favored : 76.24 % 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: -2.98 (0.34), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.005 0.001 TYR A 394 PHE 0.006 0.001 PHE C 378 HIS 0.001 0.000 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00178 ( 2688) covalent geometry : angle 0.50752 ( 3618) hydrogen bonds : bond 0.01610 ( 58) hydrogen bonds : angle 4.36492 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8226 (mtpp) REVERT: A 342 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7465 (mt-10) REVERT: A 402 ASP cc_start: 0.8292 (m-30) cc_final: 0.7964 (m-30) REVERT: B 340 LYS cc_start: 0.8620 (tptp) cc_final: 0.8340 (mttt) REVERT: C 338 GLU cc_start: 0.8283 (tt0) cc_final: 0.7871 (tm-30) REVERT: C 381 ASN cc_start: 0.6791 (OUTLIER) cc_final: 0.6521 (t0) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.9995 time to fit residues: 73.5733 Evaluate side-chains 78 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 409 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.172310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.141037 restraints weight = 7783.817| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 1.82 r_work: 0.3986 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2688 Z= 0.082 Angle : 0.496 5.601 3618 Z= 0.255 Chirality : 0.048 0.136 417 Planarity : 0.003 0.019 471 Dihedral : 4.991 18.697 366 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.64 % Allowed : 20.79 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.95 (0.34), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.006 0.001 TYR A 394 PHE 0.007 0.001 PHE C 378 HIS 0.002 0.000 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 2688) covalent geometry : angle 0.49584 ( 3618) hydrogen bonds : bond 0.01592 ( 58) hydrogen bonds : angle 4.39092 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2764.32 seconds wall clock time: 47 minutes 26.36 seconds (2846.36 seconds total)