Starting phenix.real_space_refine on Wed Sep 17 03:19:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9erm_19926/09_2025/9erm_19926.cif Found real_map, /net/cci-nas-00/data/ceres_data/9erm_19926/09_2025/9erm_19926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9erm_19926/09_2025/9erm_19926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9erm_19926/09_2025/9erm_19926.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9erm_19926/09_2025/9erm_19926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9erm_19926/09_2025/9erm_19926.map" } resolution = 2.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1800 2.51 5 N 530 2.21 5 O 535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.54, per 1000 atoms: 0.19 Number of scatterers: 2870 At special positions: 0 Unit cell: (105.472, 123.6, 32.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 535 8.00 N 530 7.00 C 1800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.12 Conformation dependent library (CDL) restraints added in 104.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 56.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.557A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.822A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.437A pdb=" N VAL A 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N LYS D 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER A 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.843A pdb=" N GLY C 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN A 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY A 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N HIS D 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 346 removed outlier: 8.960A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 9.403A pdb=" N LEU C 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU A 338 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL D 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS A 340 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER D 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU A 342 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS D 343 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.431A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N SER C 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY A 355 " --> pdb=" O SER C 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.472A pdb=" N THR A 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.365A pdb=" N LYS A 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N THR D 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU A 372 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LYS D 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N HIS A 374 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N THR D 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 310 Processing sheet with id=AB1, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AB2, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.437A pdb=" N VAL B 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N LYS E 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER B 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 325 through 330 removed outlier: 6.128A pdb=" N GLY B 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N HIS E 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE B 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 337 through 346 removed outlier: 6.991A pdb=" N GLU B 338 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL E 339 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS B 340 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER E 341 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU B 342 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS E 343 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 357 Processing sheet with id=AB6, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.472A pdb=" N THR B 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 369 through 378 removed outlier: 6.365A pdb=" N LYS B 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N THR E 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU B 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LYS E 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N HIS B 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N THR E 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 49 hydrogen bonds defined for protein. 147 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: 0.45 Time building geometry restraints manager: 0.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 641 1.33 - 1.45: 563 1.45 - 1.57: 1706 1.57 - 1.69: 0 1.69 - 1.80: 5 Bond restraints: 2915 Sorted by residual: bond pdb=" C GLY E 355 " pdb=" O GLY E 355 " ideal model delta sigma weight residual 1.236 1.223 0.013 5.30e-03 3.56e+04 5.60e+00 bond pdb=" C GLY A 355 " pdb=" O GLY A 355 " ideal model delta sigma weight residual 1.236 1.223 0.012 5.30e-03 3.56e+04 5.56e+00 bond pdb=" C GLY B 355 " pdb=" O GLY B 355 " ideal model delta sigma weight residual 1.236 1.223 0.012 5.30e-03 3.56e+04 5.51e+00 bond pdb=" C GLY C 355 " pdb=" O GLY C 355 " ideal model delta sigma weight residual 1.236 1.224 0.012 5.30e-03 3.56e+04 5.44e+00 bond pdb=" C GLY D 355 " pdb=" O GLY D 355 " ideal model delta sigma weight residual 1.236 1.224 0.012 5.30e-03 3.56e+04 5.42e+00 ... (remaining 2910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 2986 1.48 - 2.95: 719 2.95 - 4.43: 160 4.43 - 5.90: 15 5.90 - 7.38: 20 Bond angle restraints: 3900 Sorted by residual: angle pdb=" C LEU E 376 " pdb=" CA LEU E 376 " pdb=" CB LEU E 376 " ideal model delta sigma weight residual 110.14 117.52 -7.38 1.60e+00 3.91e-01 2.13e+01 angle pdb=" C LEU D 376 " pdb=" CA LEU D 376 " pdb=" CB LEU D 376 " ideal model delta sigma weight residual 110.14 117.51 -7.37 1.60e+00 3.91e-01 2.12e+01 angle pdb=" C LEU A 376 " pdb=" CA LEU A 376 " pdb=" CB LEU A 376 " ideal model delta sigma weight residual 110.14 117.49 -7.35 1.60e+00 3.91e-01 2.11e+01 angle pdb=" C LEU B 376 " pdb=" CA LEU B 376 " pdb=" CB LEU B 376 " ideal model delta sigma weight residual 110.14 117.47 -7.33 1.60e+00 3.91e-01 2.10e+01 angle pdb=" C LEU C 376 " pdb=" CA LEU C 376 " pdb=" CB LEU C 376 " ideal model delta sigma weight residual 110.14 117.46 -7.32 1.60e+00 3.91e-01 2.09e+01 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.64: 1510 10.64 - 21.28: 210 21.28 - 31.92: 40 31.92 - 42.56: 5 42.56 - 53.20: 15 Dihedral angle restraints: 1780 sinusoidal: 745 harmonic: 1035 Sorted by residual: dihedral pdb=" CA ILE E 360 " pdb=" C ILE E 360 " pdb=" N THR E 361 " pdb=" CA THR E 361 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ILE A 360 " pdb=" C ILE A 360 " pdb=" N THR A 361 " pdb=" CA THR A 361 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ILE C 360 " pdb=" C ILE C 360 " pdb=" N THR C 361 " pdb=" CA THR C 361 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 1777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 170 0.056 - 0.111: 206 0.111 - 0.167: 45 0.167 - 0.223: 14 0.223 - 0.278: 5 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA LYS C 317 " pdb=" N LYS C 317 " pdb=" C LYS C 317 " pdb=" CB LYS C 317 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA LYS A 317 " pdb=" N LYS A 317 " pdb=" C LYS A 317 " pdb=" CB LYS A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA LYS E 317 " pdb=" N LYS E 317 " pdb=" C LYS E 317 " pdb=" CB LYS E 317 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 437 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 370 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.15e+00 pdb=" C LYS C 370 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS C 370 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE C 371 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 370 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C LYS A 370 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS A 370 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 371 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 370 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" C LYS D 370 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS D 370 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE D 371 " 0.010 2.00e-02 2.50e+03 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 1721 3.09 - 3.54: 2610 3.54 - 4.00: 4102 4.00 - 4.45: 4278 4.45 - 4.90: 8165 Nonbonded interactions: 20876 Sorted by model distance: nonbonded pdb=" N ASP C 348 " pdb=" O ASP C 348 " model vdw 2.641 2.496 nonbonded pdb=" N ASP A 348 " pdb=" O ASP A 348 " model vdw 2.642 2.496 nonbonded pdb=" N ASP E 348 " pdb=" O ASP E 348 " model vdw 2.642 2.496 nonbonded pdb=" N ASP B 348 " pdb=" O ASP B 348 " model vdw 2.642 2.496 nonbonded pdb=" N ASP D 348 " pdb=" O ASP D 348 " model vdw 2.642 2.496 ... (remaining 20871 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' selection = chain 'D' selection = chain 'E' } 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: 4.250 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.520 Find NCS groups from input model: 0.030 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 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 : 0.009 0.055 2915 Z= 0.579 Angle : 1.427 7.377 3900 Z= 0.908 Chirality : 0.088 0.278 440 Planarity : 0.010 0.056 495 Dihedral : 11.153 53.196 1120 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.03 % Allowed : 6.06 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.04 (0.34), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.26), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.003 ARG C 349 TYR 0.012 0.006 TYR E 310 PHE 0.007 0.002 PHE D 378 HIS 0.005 0.002 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00901 ( 2915) covalent geometry : angle 1.42696 ( 3900) hydrogen bonds : bond 0.16487 ( 49) hydrogen bonds : angle 7.40708 ( 147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8336 (mt0) cc_final: 0.7876 (tt0) REVERT: A 317 LYS cc_start: 0.8806 (pttt) cc_final: 0.8524 (ptpp) REVERT: A 331 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8832 (mtpp) REVERT: A 340 LYS cc_start: 0.8874 (mtpm) cc_final: 0.8290 (mttm) REVERT: A 376 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8714 (tp) REVERT: B 307 GLN cc_start: 0.8600 (mt0) cc_final: 0.8196 (tt0) REVERT: B 317 LYS cc_start: 0.8897 (pttt) cc_final: 0.8634 (ptpp) REVERT: B 331 LYS cc_start: 0.9171 (mtmt) cc_final: 0.8949 (mtpp) REVERT: C 307 GLN cc_start: 0.8628 (mt0) cc_final: 0.8194 (tt0) REVERT: C 317 LYS cc_start: 0.8902 (pttt) cc_final: 0.8626 (ptpp) REVERT: C 331 LYS cc_start: 0.9161 (mtmt) cc_final: 0.8950 (mtpp) REVERT: C 376 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8901 (tp) REVERT: D 311 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8323 (mttt) REVERT: D 317 LYS cc_start: 0.8846 (pttt) cc_final: 0.8508 (ptpt) REVERT: D 331 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8826 (mtpp) REVERT: D 376 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8819 (tp) REVERT: E 307 GLN cc_start: 0.8403 (mt0) cc_final: 0.7944 (tt0) REVERT: E 311 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8426 (mttt) REVERT: E 317 LYS cc_start: 0.8817 (pttt) cc_final: 0.8479 (ptpt) REVERT: E 331 LYS cc_start: 0.9097 (mtmt) cc_final: 0.8864 (mtpp) REVERT: E 376 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8852 (tp) outliers start: 10 outliers final: 1 residues processed: 152 average time/residue: 0.7010 time to fit residues: 108.4016 Evaluate side-chains 132 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 376 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 336 GLN B 327 ASN B 330 HIS B 336 GLN C 327 ASN C 336 GLN D 327 ASN D 336 GLN E 327 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.118510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.098135 restraints weight = 3032.296| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.58 r_work: 0.3278 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2915 Z= 0.176 Angle : 0.706 6.818 3900 Z= 0.351 Chirality : 0.052 0.144 440 Planarity : 0.003 0.019 495 Dihedral : 6.192 33.347 395 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.24 % Allowed : 13.33 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 379 TYR 0.004 0.001 TYR B 310 PHE 0.005 0.001 PHE C 378 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 2915) covalent geometry : angle 0.70610 ( 3900) hydrogen bonds : bond 0.03269 ( 49) hydrogen bonds : angle 5.90530 ( 147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8049 (mt0) cc_final: 0.7781 (tt0) REVERT: A 317 LYS cc_start: 0.8609 (pttt) cc_final: 0.8304 (ptpp) REVERT: A 331 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8656 (mtpp) REVERT: A 340 LYS cc_start: 0.8569 (mtpm) cc_final: 0.7833 (mttm) REVERT: B 307 GLN cc_start: 0.8368 (mt0) cc_final: 0.8111 (tt0) REVERT: B 317 LYS cc_start: 0.8734 (pttt) cc_final: 0.8445 (ptpp) REVERT: B 325 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9024 (tt) REVERT: B 331 LYS cc_start: 0.8977 (mtmt) cc_final: 0.8757 (mtpp) REVERT: C 307 GLN cc_start: 0.8330 (mt0) cc_final: 0.8038 (tt0) REVERT: C 317 LYS cc_start: 0.8788 (pttt) cc_final: 0.8513 (ptpp) REVERT: C 325 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8925 (tt) REVERT: D 311 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8195 (mttt) REVERT: D 317 LYS cc_start: 0.8671 (pttt) cc_final: 0.8332 (ptpt) REVERT: D 340 LYS cc_start: 0.8543 (mtpm) cc_final: 0.7865 (mttm) REVERT: E 307 GLN cc_start: 0.7975 (mt0) cc_final: 0.7681 (tt0) REVERT: E 311 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8350 (mttt) REVERT: E 317 LYS cc_start: 0.8690 (pttt) cc_final: 0.8311 (ptpt) REVERT: E 331 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8660 (mtpp) REVERT: E 369 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8553 (ttmt) outliers start: 14 outliers final: 0 residues processed: 126 average time/residue: 0.8229 time to fit residues: 105.1890 Evaluate side-chains 117 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 369 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN C 336 GLN E 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.117666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.097891 restraints weight = 3066.340| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.55 r_work: 0.3286 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2915 Z= 0.158 Angle : 0.696 7.191 3900 Z= 0.332 Chirality : 0.051 0.138 440 Planarity : 0.003 0.017 495 Dihedral : 5.062 16.694 385 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.33 % Allowed : 17.88 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 379 TYR 0.006 0.001 TYR B 310 PHE 0.004 0.001 PHE C 378 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 2915) covalent geometry : angle 0.69579 ( 3900) hydrogen bonds : bond 0.02881 ( 49) hydrogen bonds : angle 5.59257 ( 147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8607 (pttt) cc_final: 0.8319 (ptpp) REVERT: A 331 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8635 (mtpp) REVERT: A 340 LYS cc_start: 0.8555 (mtpm) cc_final: 0.7805 (mttm) REVERT: B 307 GLN cc_start: 0.8319 (mt0) cc_final: 0.8112 (tt0) REVERT: B 317 LYS cc_start: 0.8721 (pttt) cc_final: 0.8442 (ptpp) REVERT: B 331 LYS cc_start: 0.8952 (mtmt) cc_final: 0.8730 (mtpp) REVERT: C 317 LYS cc_start: 0.8746 (pttt) cc_final: 0.8485 (ptpp) REVERT: C 325 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8957 (tt) REVERT: D 317 LYS cc_start: 0.8676 (pttt) cc_final: 0.8341 (ptpt) REVERT: D 369 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8736 (mtmt) REVERT: E 307 GLN cc_start: 0.7980 (mt0) cc_final: 0.7712 (tt0) REVERT: E 311 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8317 (mttt) REVERT: E 317 LYS cc_start: 0.8643 (pttt) cc_final: 0.8264 (ptpt) REVERT: E 331 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8667 (mtpp) REVERT: E 340 LYS cc_start: 0.8546 (mtpm) cc_final: 0.7905 (mttm) outliers start: 11 outliers final: 1 residues processed: 124 average time/residue: 0.8478 time to fit residues: 106.6498 Evaluate side-chains 119 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain D residue 369 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN C 307 GLN C 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.117585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.097866 restraints weight = 3041.651| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.52 r_work: 0.3293 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2915 Z= 0.152 Angle : 0.659 7.362 3900 Z= 0.317 Chirality : 0.050 0.136 440 Planarity : 0.003 0.022 495 Dihedral : 4.980 16.698 385 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.73 % Allowed : 18.18 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 379 TYR 0.006 0.001 TYR A 310 PHE 0.004 0.001 PHE C 378 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 2915) covalent geometry : angle 0.65893 ( 3900) hydrogen bonds : bond 0.02635 ( 49) hydrogen bonds : angle 5.44827 ( 147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8580 (pttt) cc_final: 0.8244 (ptpp) REVERT: A 331 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8627 (mtpp) REVERT: B 317 LYS cc_start: 0.8651 (pttt) cc_final: 0.8371 (ptpp) REVERT: B 331 LYS cc_start: 0.8985 (mtmt) cc_final: 0.8746 (mtpp) REVERT: C 317 LYS cc_start: 0.8747 (pttt) cc_final: 0.8479 (ptpp) REVERT: C 325 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8920 (tt) REVERT: D 317 LYS cc_start: 0.8662 (pttt) cc_final: 0.8325 (ptpt) REVERT: D 369 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8702 (mtmt) REVERT: E 311 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8302 (mttt) REVERT: E 317 LYS cc_start: 0.8642 (pttt) cc_final: 0.8247 (ptpt) REVERT: E 331 LYS cc_start: 0.8914 (mtmt) cc_final: 0.8671 (mtpp) REVERT: E 340 LYS cc_start: 0.8548 (mtpm) cc_final: 0.7898 (mttm) outliers start: 9 outliers final: 2 residues processed: 119 average time/residue: 0.8510 time to fit residues: 102.6995 Evaluate side-chains 119 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain D residue 369 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 26 optimal weight: 0.0000 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN C 336 GLN E 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.120031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.100581 restraints weight = 3015.274| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.52 r_work: 0.3332 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2915 Z= 0.105 Angle : 0.608 8.096 3900 Z= 0.285 Chirality : 0.049 0.128 440 Planarity : 0.002 0.019 495 Dihedral : 4.692 16.391 385 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.42 % Allowed : 19.39 % Favored : 78.18 % 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: -1.28 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 379 TYR 0.006 0.001 TYR A 310 PHE 0.004 0.001 PHE C 378 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 2915) covalent geometry : angle 0.60786 ( 3900) hydrogen bonds : bond 0.02146 ( 49) hydrogen bonds : angle 5.16097 ( 147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8544 (pttt) cc_final: 0.8247 (ptpp) REVERT: A 331 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8618 (mtpp) REVERT: A 340 LYS cc_start: 0.8448 (mtpm) cc_final: 0.7711 (mttm) REVERT: B 317 LYS cc_start: 0.8598 (pttt) cc_final: 0.8321 (ptpp) REVERT: B 331 LYS cc_start: 0.8962 (mtmt) cc_final: 0.8735 (mtpp) REVERT: B 369 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8754 (mtmt) REVERT: C 317 LYS cc_start: 0.8713 (pttt) cc_final: 0.8456 (ptpp) REVERT: D 317 LYS cc_start: 0.8633 (pttt) cc_final: 0.8289 (ptpt) REVERT: E 311 LYS cc_start: 0.8772 (mtmt) cc_final: 0.8293 (mttt) REVERT: E 317 LYS cc_start: 0.8626 (pttt) cc_final: 0.8218 (ptpt) REVERT: E 331 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8647 (mtpp) REVERT: E 340 LYS cc_start: 0.8527 (mtpm) cc_final: 0.7875 (mttm) outliers start: 8 outliers final: 1 residues processed: 121 average time/residue: 0.8115 time to fit residues: 99.6808 Evaluate side-chains 118 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 369 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 34 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 21 optimal weight: 0.3980 chunk 26 optimal weight: 0.0570 chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 0.0270 overall best weight: 1.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN C 336 GLN E 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.121302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.101463 restraints weight = 3018.351| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.55 r_work: 0.3340 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2915 Z= 0.096 Angle : 0.596 8.420 3900 Z= 0.278 Chirality : 0.049 0.127 440 Planarity : 0.002 0.014 495 Dihedral : 4.594 16.241 385 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.42 % Allowed : 19.39 % Favored : 78.18 % 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: -1.28 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 379 TYR 0.007 0.001 TYR A 310 PHE 0.003 0.001 PHE D 378 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 2915) covalent geometry : angle 0.59623 ( 3900) hydrogen bonds : bond 0.01990 ( 49) hydrogen bonds : angle 5.02231 ( 147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8535 (pttt) cc_final: 0.8220 (ptpt) REVERT: A 331 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8627 (mtpp) REVERT: A 340 LYS cc_start: 0.8469 (mtpm) cc_final: 0.7725 (mttm) REVERT: B 317 LYS cc_start: 0.8597 (pttt) cc_final: 0.8317 (ptpp) REVERT: B 331 LYS cc_start: 0.8977 (mtmt) cc_final: 0.8744 (mtpp) REVERT: B 369 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8754 (mtmt) REVERT: C 311 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8456 (mtmt) REVERT: C 317 LYS cc_start: 0.8727 (pttt) cc_final: 0.8457 (ptpp) REVERT: C 379 ARG cc_start: 0.7355 (mtp85) cc_final: 0.7090 (mtt90) REVERT: D 317 LYS cc_start: 0.8629 (pttt) cc_final: 0.8286 (ptpt) REVERT: E 311 LYS cc_start: 0.8774 (mtmt) cc_final: 0.8293 (mttt) REVERT: E 317 LYS cc_start: 0.8610 (pttt) cc_final: 0.8257 (ptpt) REVERT: E 331 LYS cc_start: 0.8895 (mtmt) cc_final: 0.8651 (mtpp) REVERT: E 340 LYS cc_start: 0.8532 (mtpm) cc_final: 0.7884 (mttm) outliers start: 8 outliers final: 2 residues processed: 119 average time/residue: 0.8552 time to fit residues: 103.2251 Evaluate side-chains 119 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 369 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 330 HIS B 336 GLN C 336 GLN E 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.115949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.096181 restraints weight = 3049.414| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.51 r_work: 0.3273 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2915 Z= 0.209 Angle : 0.708 8.612 3900 Z= 0.344 Chirality : 0.052 0.141 440 Planarity : 0.003 0.016 495 Dihedral : 5.002 16.939 385 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.82 % Allowed : 19.09 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 379 TYR 0.009 0.002 TYR B 310 PHE 0.006 0.001 PHE C 378 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 2915) covalent geometry : angle 0.70844 ( 3900) hydrogen bonds : bond 0.02945 ( 49) hydrogen bonds : angle 5.42401 ( 147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8559 (pttt) cc_final: 0.8244 (ptpp) REVERT: A 331 LYS cc_start: 0.8867 (mtmt) cc_final: 0.8641 (mtpp) REVERT: A 340 LYS cc_start: 0.8550 (mtpm) cc_final: 0.7788 (mttm) REVERT: B 317 LYS cc_start: 0.8656 (pttt) cc_final: 0.8372 (ptpp) REVERT: B 331 LYS cc_start: 0.8981 (mtmt) cc_final: 0.8744 (mtpp) REVERT: C 311 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8469 (mtmt) REVERT: C 317 LYS cc_start: 0.8738 (pttt) cc_final: 0.8485 (ptpp) REVERT: C 325 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.8965 (tt) REVERT: C 379 ARG cc_start: 0.7469 (mtp85) cc_final: 0.7236 (mtt90) REVERT: D 317 LYS cc_start: 0.8683 (pttt) cc_final: 0.8344 (ptpt) REVERT: E 311 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8314 (mttt) REVERT: E 317 LYS cc_start: 0.8640 (pttt) cc_final: 0.8226 (ptpt) REVERT: E 331 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8667 (mtpp) REVERT: E 340 LYS cc_start: 0.8536 (mtpm) cc_final: 0.7889 (mttm) outliers start: 6 outliers final: 2 residues processed: 114 average time/residue: 0.9096 time to fit residues: 105.1900 Evaluate side-chains 117 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 369 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 336 GLN C 336 GLN E 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.117388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.097698 restraints weight = 3109.146| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.54 r_work: 0.3290 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2915 Z= 0.161 Angle : 0.666 8.520 3900 Z= 0.317 Chirality : 0.050 0.136 440 Planarity : 0.002 0.012 495 Dihedral : 4.879 16.875 385 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.82 % Allowed : 19.70 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 379 TYR 0.009 0.002 TYR B 310 PHE 0.005 0.001 PHE C 378 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 2915) covalent geometry : angle 0.66630 ( 3900) hydrogen bonds : bond 0.02663 ( 49) hydrogen bonds : angle 5.29759 ( 147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8536 (pttt) cc_final: 0.8200 (ptpp) REVERT: A 331 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8623 (mtpp) REVERT: B 317 LYS cc_start: 0.8698 (pttt) cc_final: 0.8407 (ptpp) REVERT: B 331 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8717 (mtpp) REVERT: C 311 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8465 (mtmt) REVERT: C 317 LYS cc_start: 0.8738 (pttt) cc_final: 0.8475 (ptpp) REVERT: C 325 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8967 (tt) REVERT: C 379 ARG cc_start: 0.7414 (mtp85) cc_final: 0.7102 (mtt90) REVERT: D 317 LYS cc_start: 0.8666 (pttt) cc_final: 0.8314 (ptpt) REVERT: D 340 LYS cc_start: 0.8452 (mtpm) cc_final: 0.7763 (mttp) REVERT: E 311 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8294 (mttt) REVERT: E 317 LYS cc_start: 0.8659 (pttt) cc_final: 0.8218 (ptpt) REVERT: E 331 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8655 (mtpp) REVERT: E 340 LYS cc_start: 0.8517 (mtpm) cc_final: 0.7858 (mttm) outliers start: 6 outliers final: 2 residues processed: 116 average time/residue: 0.8931 time to fit residues: 105.1169 Evaluate side-chains 116 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 369 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 0.3980 chunk 29 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN B 336 GLN C 336 GLN E 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.118996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.099439 restraints weight = 3088.303| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.54 r_work: 0.3321 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2915 Z= 0.114 Angle : 0.622 8.328 3900 Z= 0.293 Chirality : 0.049 0.130 440 Planarity : 0.002 0.013 495 Dihedral : 4.716 16.675 385 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.21 % Allowed : 20.91 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 379 TYR 0.007 0.002 TYR A 310 PHE 0.004 0.001 PHE C 378 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 2915) covalent geometry : angle 0.62241 ( 3900) hydrogen bonds : bond 0.02217 ( 49) hydrogen bonds : angle 5.12827 ( 147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8522 (pttt) cc_final: 0.8192 (ptpp) REVERT: A 331 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8623 (mtpp) REVERT: A 340 LYS cc_start: 0.8444 (mtpp) cc_final: 0.7710 (mttm) REVERT: B 317 LYS cc_start: 0.8632 (pttt) cc_final: 0.8346 (ptpp) REVERT: B 331 LYS cc_start: 0.8958 (mtmt) cc_final: 0.8733 (mtpp) REVERT: B 369 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8759 (mtmt) REVERT: C 311 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8458 (mtmt) REVERT: C 317 LYS cc_start: 0.8732 (pttt) cc_final: 0.8470 (ptpp) REVERT: C 379 ARG cc_start: 0.7415 (mtp85) cc_final: 0.7122 (mtt90) REVERT: D 317 LYS cc_start: 0.8627 (pttt) cc_final: 0.8289 (ptpt) REVERT: E 311 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8287 (mttt) REVERT: E 317 LYS cc_start: 0.8647 (pttt) cc_final: 0.8209 (ptpt) REVERT: E 331 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8651 (mtpp) REVERT: E 340 LYS cc_start: 0.8530 (mtpm) cc_final: 0.7872 (mttm) outliers start: 4 outliers final: 2 residues processed: 113 average time/residue: 0.9300 time to fit residues: 106.5976 Evaluate side-chains 116 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 369 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN B 336 GLN C 336 GLN E 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.116758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.096998 restraints weight = 3053.493| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.53 r_work: 0.3283 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2915 Z= 0.174 Angle : 0.687 8.312 3900 Z= 0.328 Chirality : 0.051 0.136 440 Planarity : 0.002 0.018 495 Dihedral : 4.885 16.815 385 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.52 % Allowed : 20.91 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 379 TYR 0.008 0.002 TYR A 310 PHE 0.007 0.001 PHE C 378 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 2915) covalent geometry : angle 0.68702 ( 3900) hydrogen bonds : bond 0.02743 ( 49) hydrogen bonds : angle 5.31130 ( 147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8530 (pttt) cc_final: 0.8189 (ptpp) REVERT: A 331 LYS cc_start: 0.8855 (mtmt) cc_final: 0.8618 (mtpp) REVERT: A 340 LYS cc_start: 0.8465 (mtpp) cc_final: 0.7717 (mttm) REVERT: B 317 LYS cc_start: 0.8656 (pttt) cc_final: 0.8359 (ptpp) REVERT: B 331 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8736 (mtpp) REVERT: B 340 LYS cc_start: 0.8694 (mtpm) cc_final: 0.7962 (mttm) REVERT: B 369 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8800 (mtmt) REVERT: C 311 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8443 (mtmt) REVERT: C 317 LYS cc_start: 0.8736 (pttt) cc_final: 0.8473 (ptpp) REVERT: C 379 ARG cc_start: 0.7430 (mtp85) cc_final: 0.7230 (mtt90) REVERT: D 317 LYS cc_start: 0.8685 (pttt) cc_final: 0.8312 (ptpt) REVERT: E 311 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8303 (mttt) REVERT: E 317 LYS cc_start: 0.8657 (pttt) cc_final: 0.8212 (ptpt) REVERT: E 331 LYS cc_start: 0.8904 (mtmt) cc_final: 0.8643 (mtpp) REVERT: E 340 LYS cc_start: 0.8513 (mtpm) cc_final: 0.7850 (mttm) outliers start: 5 outliers final: 2 residues processed: 113 average time/residue: 0.9004 time to fit residues: 103.2425 Evaluate side-chains 116 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 369 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 27 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN B 336 GLN C 336 GLN E 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.117378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.097817 restraints weight = 3035.950| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.52 r_work: 0.3293 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2915 Z= 0.161 Angle : 0.676 8.163 3900 Z= 0.321 Chirality : 0.051 0.135 440 Planarity : 0.002 0.016 495 Dihedral : 4.857 16.894 385 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.52 % Allowed : 21.21 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 379 TYR 0.009 0.002 TYR B 310 PHE 0.006 0.001 PHE C 378 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 2915) covalent geometry : angle 0.67559 ( 3900) hydrogen bonds : bond 0.02632 ( 49) hydrogen bonds : angle 5.26581 ( 147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2278.14 seconds wall clock time: 39 minutes 32.25 seconds (2372.25 seconds total)