Starting phenix.real_space_refine on Thu Jul 24 05:32:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r2h_53530/07_2025/9r2h_53530.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r2h_53530/07_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_53530/07_2025/9r2h_53530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r2h_53530/07_2025/9r2h_53530.map" model { file = "/net/cci-nas-00/data/ceres_data/9r2h_53530/07_2025/9r2h_53530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r2h_53530/07_2025/9r2h_53530.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.96, per 1000 atoms: 0.74 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: 1.21 Conformation dependent library (CDL) restraints added in 378.0 milliseconds 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: 0.52 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: 1.78 Time building geometry restraints manager: 1.51 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: 0.01 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: 3.360 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: 0.100 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.900 Find NCS groups from input model: 0.130 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:14.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.350 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.009 0.004 HIS A 362 PHE 0.031 0.012 PHE C 378 TYR 0.018 0.008 TYR B 394 ARG 0.010 0.002 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.09999 ( 58) hydrogen bonds : angle 7.48639 ( 171) covalent geometry : bond 0.01100 ( 2688) covalent geometry : angle 2.00083 ( 3618) *********************** 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 : 0.431 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: 2.5702 time to fit residues: 288.6381 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 : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- 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 C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.174266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.143097 restraints weight = 7853.058| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 1.87 r_work: 0.3987 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3894 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4195 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= 0.124 Angle : 0.635 4.919 3618 Z= 0.337 Chirality : 0.051 0.148 417 Planarity : 0.004 0.033 471 Dihedral : 7.185 22.548 366 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.98 % Allowed : 14.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.32), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.24), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 330 PHE 0.014 0.002 PHE C 378 TYR 0.006 0.001 TYR A 394 ARG 0.003 0.000 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.02657 ( 58) hydrogen bonds : angle 5.82811 ( 171) covalent geometry : bond 0.00278 ( 2688) covalent geometry : angle 0.63533 ( 3618) *********************** 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 86 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8172 (tt0) cc_final: 0.7922 (mt-10) REVERT: A 340 LYS cc_start: 0.8558 (tmtm) cc_final: 0.8140 (mttt) REVERT: A 342 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7534 (mt-10) REVERT: A 424 GLN cc_start: 0.7200 (mt0) cc_final: 0.6977 (mm-40) REVERT: A 431 GLU cc_start: 0.7761 (tt0) cc_final: 0.7442 (tt0) REVERT: B 418 ASP cc_start: 0.8259 (m-30) cc_final: 0.7961 (m-30) REVERT: C 338 GLU cc_start: 0.8426 (tt0) cc_final: 0.8026 (tm-30) REVERT: C 370 LYS cc_start: 0.8316 (tttp) cc_final: 0.8046 (tmtm) REVERT: C 391 GLU cc_start: 0.8273 (tt0) cc_final: 0.8020 (tt0) REVERT: C 419 MET cc_start: 0.9016 (ttm) cc_final: 0.8809 (ttm) outliers start: 6 outliers final: 1 residues processed: 82 average time/residue: 2.3747 time to fit residues: 199.2176 Evaluate side-chains 68 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 381 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 0.2980 chunk 11 optimal weight: 0.0770 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.173978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.145329 restraints weight = 7858.081| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 1.60 r_work: 0.4021 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2688 Z= 0.099 Angle : 0.546 4.397 3618 Z= 0.289 Chirality : 0.050 0.146 417 Planarity : 0.003 0.021 471 Dihedral : 6.236 22.365 366 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.64 % Allowed : 15.51 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.31), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.24), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 330 PHE 0.010 0.002 PHE A 378 TYR 0.007 0.002 TYR A 394 ARG 0.002 0.000 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.01869 ( 58) hydrogen bonds : angle 5.14362 ( 171) covalent geometry : bond 0.00221 ( 2688) covalent geometry : angle 0.54592 ( 3618) *********************** 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 88 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8088 (tt0) cc_final: 0.7839 (mt-10) REVERT: A 342 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7558 (mt-10) REVERT: A 381 ASN cc_start: 0.6919 (OUTLIER) cc_final: 0.6371 (t0) REVERT: A 402 ASP cc_start: 0.8343 (m-30) cc_final: 0.8094 (m-30) REVERT: B 418 ASP cc_start: 0.8277 (m-30) cc_final: 0.8058 (m-30) REVERT: C 338 GLU cc_start: 0.8340 (tt0) cc_final: 0.7974 (tm-30) REVERT: C 342 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7725 (tt0) REVERT: C 381 ASN cc_start: 0.6935 (OUTLIER) cc_final: 0.6698 (t0) outliers start: 8 outliers final: 4 residues processed: 84 average time/residue: 2.1811 time to fit residues: 187.7611 Evaluate side-chains 76 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 433 SER Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 409 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.166525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.136708 restraints weight = 8036.061| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.72 r_work: 0.3896 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2688 Z= 0.184 Angle : 0.610 4.214 3618 Z= 0.330 Chirality : 0.051 0.137 417 Planarity : 0.004 0.028 471 Dihedral : 6.403 23.056 366 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.95 % Allowed : 18.15 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.32), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.24), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.017 0.003 PHE A 378 TYR 0.012 0.003 TYR A 394 ARG 0.002 0.001 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.01894 ( 58) hydrogen bonds : angle 5.03327 ( 171) covalent geometry : bond 0.00412 ( 2688) covalent geometry : angle 0.60987 ( 3618) *********************** 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 90 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8075 (tt0) cc_final: 0.7737 (mt-10) REVERT: A 340 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8300 (mtpp) REVERT: A 342 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7385 (mt-10) REVERT: A 370 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7908 (tmtm) REVERT: A 381 ASN cc_start: 0.6960 (OUTLIER) cc_final: 0.6493 (t0) REVERT: B 331 LYS cc_start: 0.5170 (OUTLIER) cc_final: 0.4183 (mmtt) REVERT: B 342 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7446 (mt-10) REVERT: B 358 ASP cc_start: 0.8162 (m-30) cc_final: 0.7887 (m-30) REVERT: B 418 ASP cc_start: 0.8369 (m-30) cc_final: 0.8117 (m-30) REVERT: C 338 GLU cc_start: 0.8425 (tt0) cc_final: 0.8012 (tm-30) REVERT: C 340 LYS cc_start: 0.8390 (tptt) cc_final: 0.8166 (tttt) REVERT: C 381 ASN cc_start: 0.7138 (OUTLIER) cc_final: 0.6932 (t0) REVERT: C 428 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7585 (mt) outliers start: 15 outliers final: 8 residues processed: 81 average time/residue: 2.1456 time to fit residues: 178.1428 Evaluate side-chains 87 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain C residue 356 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 Chi-restraints excluded: chain C residue 428 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 0.0270 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- 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 359 ASN C 410 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.171928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.142918 restraints weight = 7877.554| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.74 r_work: 0.3981 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.5766 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= 0.082 Angle : 0.492 4.256 3618 Z= 0.260 Chirality : 0.049 0.136 417 Planarity : 0.003 0.023 471 Dihedral : 5.709 21.621 366 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.63 % Allowed : 18.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.32), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 388 PHE 0.004 0.001 PHE C 378 TYR 0.005 0.001 TYR C 394 ARG 0.003 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.01813 ( 58) hydrogen bonds : angle 4.74188 ( 171) covalent geometry : bond 0.00185 ( 2688) covalent geometry : angle 0.49187 ( 3618) *********************** 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 90 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8073 (tt0) cc_final: 0.7759 (mt-10) REVERT: A 340 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8245 (mtpp) REVERT: A 342 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7453 (mt-10) REVERT: A 402 ASP cc_start: 0.8341 (m-30) cc_final: 0.8083 (m-30) REVERT: B 418 ASP cc_start: 0.8312 (m-30) cc_final: 0.8100 (m-30) REVERT: C 338 GLU cc_start: 0.8324 (tt0) cc_final: 0.7900 (tm-30) REVERT: C 381 ASN cc_start: 0.6872 (OUTLIER) cc_final: 0.6649 (t0) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 2.1429 time to fit residues: 182.3772 Evaluate side-chains 84 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 B residue 433 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: 0.0060 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- 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 = 0.4415 r_free = 0.4415 target = 0.171219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.142499 restraints weight = 7952.904| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 1.76 r_work: 0.3972 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.6015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2688 Z= 0.084 Angle : 0.487 4.097 3618 Z= 0.258 Chirality : 0.049 0.138 417 Planarity : 0.003 0.020 471 Dihedral : 5.464 20.468 366 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.96 % Allowed : 18.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.007 0.001 PHE C 378 TYR 0.007 0.002 TYR B 394 ARG 0.002 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.01743 ( 58) hydrogen bonds : angle 4.57960 ( 171) covalent geometry : bond 0.00190 ( 2688) covalent geometry : angle 0.48739 ( 3618) *********************** 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 84 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8058 (tt0) cc_final: 0.7777 (mt-10) REVERT: A 340 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8259 (mtpp) REVERT: A 342 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7470 (mt-10) REVERT: A 402 ASP cc_start: 0.8386 (m-30) cc_final: 0.8099 (m-30) REVERT: A 418 ASP cc_start: 0.8074 (m-30) cc_final: 0.7806 (m-30) REVERT: B 340 LYS cc_start: 0.8640 (tptp) cc_final: 0.8364 (mttt) REVERT: C 338 GLU cc_start: 0.8300 (tt0) cc_final: 0.7927 (tm-30) REVERT: C 381 ASN cc_start: 0.6888 (OUTLIER) cc_final: 0.6683 (t0) outliers start: 12 outliers final: 5 residues processed: 76 average time/residue: 2.2608 time to fit residues: 176.0375 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 : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain B residue 433 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.4438 r_free = 0.4438 target = 0.173087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.142138 restraints weight = 7859.557| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.82 r_work: 0.4003 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.6140 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= 0.074 Angle : 0.477 3.972 3618 Z= 0.250 Chirality : 0.049 0.136 417 Planarity : 0.003 0.018 471 Dihedral : 5.262 19.662 366 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.30 % Allowed : 18.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 330 PHE 0.006 0.001 PHE C 378 TYR 0.005 0.001 TYR A 394 ARG 0.003 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01673 ( 58) hydrogen bonds : angle 4.44232 ( 171) covalent geometry : bond 0.00172 ( 2688) covalent geometry : angle 0.47685 ( 3618) *********************** 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: 10 poor density : 72 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8042 (tt0) cc_final: 0.7654 (mt-10) REVERT: A 340 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8226 (mtpp) REVERT: A 342 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7488 (mt-10) REVERT: A 402 ASP cc_start: 0.8336 (m-30) cc_final: 0.8037 (m-30) REVERT: B 340 LYS cc_start: 0.8642 (tptp) cc_final: 0.8353 (mttt) REVERT: C 338 GLU cc_start: 0.8285 (tt0) cc_final: 0.7913 (tm-30) REVERT: C 381 ASN cc_start: 0.6818 (OUTLIER) cc_final: 0.6603 (t0) outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 2.1779 time to fit residues: 169.7759 Evaluate side-chains 80 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 433 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** C 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.169378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.138385 restraints weight = 7955.943| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.79 r_work: 0.3934 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.6194 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= 0.100 Angle : 0.504 4.012 3618 Z= 0.267 Chirality : 0.049 0.139 417 Planarity : 0.003 0.019 471 Dihedral : 5.346 19.905 366 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.30 % Allowed : 19.80 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.34), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.010 0.002 PHE C 378 TYR 0.007 0.002 TYR A 394 ARG 0.002 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01671 ( 58) hydrogen bonds : angle 4.50832 ( 171) covalent geometry : bond 0.00220 ( 2688) covalent geometry : angle 0.50431 ( 3618) *********************** 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: 10 poor density : 71 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8039 (tt0) cc_final: 0.7670 (mt-10) REVERT: A 340 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8259 (mtpp) REVERT: A 342 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7460 (mt-10) REVERT: A 402 ASP cc_start: 0.8333 (m-30) cc_final: 0.8057 (m-30) REVERT: B 340 LYS cc_start: 0.8650 (tptp) cc_final: 0.8342 (mttt) REVERT: C 338 GLU cc_start: 0.8309 (tt0) cc_final: 0.7944 (tm-30) REVERT: C 381 ASN cc_start: 0.6875 (OUTLIER) cc_final: 0.6670 (t0) outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 2.3255 time to fit residues: 178.5398 Evaluate side-chains 79 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 370 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 Chi-restraints excluded: chain C residue 421 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4433 r_free = 0.4433 target = 0.171911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.140849 restraints weight = 7806.320| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 1.81 r_work: 0.3972 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.6374 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= 0.078 Angle : 0.477 3.949 3618 Z= 0.250 Chirality : 0.049 0.134 417 Planarity : 0.003 0.019 471 Dihedral : 5.155 19.520 366 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.64 % Allowed : 21.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.34), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 362 PHE 0.006 0.001 PHE C 378 TYR 0.006 0.001 TYR A 394 ARG 0.002 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01692 ( 58) hydrogen bonds : angle 4.46128 ( 171) covalent geometry : bond 0.00177 ( 2688) covalent geometry : angle 0.47724 ( 3618) *********************** 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 77 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8010 (tt0) cc_final: 0.7630 (mt-10) REVERT: A 340 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8220 (mtpp) REVERT: A 342 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7465 (mt-10) REVERT: A 380 GLU cc_start: 0.7258 (mt-10) cc_final: 0.7053 (mt-10) REVERT: A 402 ASP cc_start: 0.8316 (m-30) cc_final: 0.8014 (m-30) REVERT: B 340 LYS cc_start: 0.8633 (tptp) cc_final: 0.8340 (mttt) REVERT: C 338 GLU cc_start: 0.8319 (tt0) cc_final: 0.7904 (tm-30) REVERT: C 381 ASN cc_start: 0.6861 (OUTLIER) cc_final: 0.6600 (t0) outliers start: 8 outliers final: 5 residues processed: 71 average time/residue: 2.3238 time to fit residues: 168.8516 Evaluate side-chains 76 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 370 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 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 6 optimal weight: 0.0570 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.0060 chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.7716 ------------------------------------------------------------------------------- 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 = 0.4435 r_free = 0.4435 target = 0.172065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.141112 restraints weight = 7901.673| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 1.80 r_work: 0.3976 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.6427 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= 0.079 Angle : 0.480 3.979 3618 Z= 0.251 Chirality : 0.049 0.136 417 Planarity : 0.003 0.020 471 Dihedral : 5.069 19.145 366 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.31 % Allowed : 21.78 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.34), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 362 PHE 0.007 0.001 PHE C 378 TYR 0.006 0.001 TYR A 394 ARG 0.002 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01649 ( 58) hydrogen bonds : angle 4.42312 ( 171) covalent geometry : bond 0.00179 ( 2688) covalent geometry : angle 0.48023 ( 3618) ********************** 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 77 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8004 (tt0) cc_final: 0.7638 (mt-10) REVERT: A 340 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8235 (mtpp) REVERT: A 342 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7444 (mt-10) REVERT: A 402 ASP cc_start: 0.8306 (m-30) cc_final: 0.8028 (m-30) REVERT: B 340 LYS cc_start: 0.8641 (tptp) cc_final: 0.8340 (mttt) REVERT: C 338 GLU cc_start: 0.8311 (tt0) cc_final: 0.7916 (tm-30) REVERT: C 381 ASN cc_start: 0.6876 (OUTLIER) cc_final: 0.6617 (t0) outliers start: 7 outliers final: 5 residues processed: 71 average time/residue: 2.3802 time to fit residues: 172.8645 Evaluate side-chains 77 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 370 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 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 25 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.4383 r_free = 0.4383 target = 0.167708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.136155 restraints weight = 7831.670| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 1.83 r_work: 0.3913 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.6386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2688 Z= 0.123 Angle : 0.521 4.202 3618 Z= 0.277 Chirality : 0.049 0.138 417 Planarity : 0.003 0.022 471 Dihedral : 5.326 19.934 366 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.31 % Allowed : 22.11 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.34), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.010 0.002 PHE C 378 TYR 0.009 0.002 TYR A 394 ARG 0.002 0.001 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01545 ( 58) hydrogen bonds : angle 4.45077 ( 171) covalent geometry : bond 0.00265 ( 2688) covalent geometry : angle 0.52130 ( 3618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6017.01 seconds wall clock time: 102 minutes 26.66 seconds (6146.66 seconds total)