Starting phenix.real_space_refine on Mon Jan 13 15:00:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9erm_19926/01_2025/9erm_19926.cif Found real_map, /net/cci-nas-00/data/ceres_data/9erm_19926/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9erm_19926/01_2025/9erm_19926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9erm_19926/01_2025/9erm_19926.map" model { file = "/net/cci-nas-00/data/ceres_data/9erm_19926/01_2025/9erm_19926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9erm_19926/01_2025/9erm_19926.cif" } resolution = 2.3 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= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: C, B, E, D Time building chain proxies: 2.85, per 1000 atoms: 0.99 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: 0.66 Conformation dependent library (CDL) restraints added in 393.7 milliseconds 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: 0.44 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: 0.64 Time building geometry restraints manager: 0.76 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 2.660 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.490 Find NCS groups from input model: 0.060 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:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.450 ------------------------------------------------------------------------------- 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= 0.634 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 (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: -2.04 (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 HIS 0.005 0.002 HIS D 374 PHE 0.007 0.002 PHE D 378 TYR 0.012 0.006 TYR E 310 ARG 0.010 0.003 ARG C 349 *********************** 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 : 0.371 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: 1.5084 time to fit residues: 233.3724 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 : 0.445 ------------------------------------------------------------------------------- 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 29 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 336 GLN C 327 ASN C 336 GLN D 327 ASN D 336 GLN E 327 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.123054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.103279 restraints weight = 3005.736| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.56 r_work: 0.3357 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.2093 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= 0.162 Angle : 0.592 5.770 3900 Z= 0.293 Chirality : 0.050 0.134 440 Planarity : 0.003 0.018 495 Dihedral : 6.122 35.247 395 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.24 % Allowed : 13.64 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.004 0.001 PHE C 378 TYR 0.003 0.001 TYR B 310 ARG 0.003 0.001 ARG B 379 *********************** 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 140 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8036 (mt0) cc_final: 0.7821 (tt0) REVERT: A 317 LYS cc_start: 0.8554 (pttt) cc_final: 0.8293 (ptpp) REVERT: A 340 LYS cc_start: 0.8538 (mtpm) cc_final: 0.7820 (mttm) REVERT: B 307 GLN cc_start: 0.8316 (mt0) cc_final: 0.8102 (tt0) REVERT: B 317 LYS cc_start: 0.8655 (pttt) cc_final: 0.8388 (ptpp) REVERT: B 331 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8722 (mtpp) REVERT: C 307 GLN cc_start: 0.8261 (mt0) cc_final: 0.8005 (tt0) REVERT: C 317 LYS cc_start: 0.8696 (pttt) cc_final: 0.8434 (ptpp) REVERT: D 317 LYS cc_start: 0.8624 (pttt) cc_final: 0.8335 (ptpt) REVERT: E 307 GLN cc_start: 0.7911 (mt0) cc_final: 0.7644 (tt0) REVERT: E 311 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8308 (mttt) REVERT: E 317 LYS cc_start: 0.8625 (pttt) cc_final: 0.8310 (ptpt) REVERT: E 331 LYS cc_start: 0.8863 (mtmt) cc_final: 0.8657 (mtpp) REVERT: E 340 LYS cc_start: 0.8550 (mtpm) cc_final: 0.7933 (mttm) outliers start: 14 outliers final: 0 residues processed: 133 average time/residue: 1.5932 time to fit residues: 215.5034 Evaluate side-chains 120 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 25 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS B 330 HIS B 336 GLN C 336 GLN E 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.114195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.094258 restraints weight = 3008.948| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.52 r_work: 0.3216 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 2915 Z= 0.656 Angle : 0.862 7.247 3900 Z= 0.428 Chirality : 0.058 0.154 440 Planarity : 0.004 0.020 495 Dihedral : 5.426 16.943 385 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.55 % Allowed : 18.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 374 PHE 0.008 0.001 PHE C 378 TYR 0.008 0.002 TYR B 310 ARG 0.004 0.001 ARG B 379 *********************** 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 132 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8672 (pttt) cc_final: 0.8327 (ptpp) REVERT: B 307 GLN cc_start: 0.8380 (mt0) cc_final: 0.8117 (tt0) REVERT: B 317 LYS cc_start: 0.8739 (pttt) cc_final: 0.8453 (ptpt) REVERT: B 325 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9075 (tt) REVERT: B 331 LYS cc_start: 0.8947 (mtmt) cc_final: 0.8742 (mtpp) REVERT: C 307 GLN cc_start: 0.8345 (mt0) cc_final: 0.8127 (tt0) REVERT: C 317 LYS cc_start: 0.8778 (pttt) cc_final: 0.8519 (ptpp) REVERT: D 317 LYS cc_start: 0.8693 (pttt) cc_final: 0.8369 (ptpt) REVERT: D 369 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8693 (mtmt) REVERT: E 307 GLN cc_start: 0.7989 (mt0) cc_final: 0.7699 (tt0) REVERT: E 311 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8333 (mttt) REVERT: E 317 LYS cc_start: 0.8675 (pttt) cc_final: 0.8280 (ptpt) REVERT: E 331 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8675 (mtpp) REVERT: E 340 LYS cc_start: 0.8584 (mtpm) cc_final: 0.7930 (mttm) outliers start: 15 outliers final: 2 residues processed: 125 average time/residue: 1.8206 time to fit residues: 231.4271 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 : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain D residue 319 THR 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 13 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.118348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.098462 restraints weight = 3047.386| |-----------------------------------------------------------------------------| r_work (start): 0.3411 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: 0.9077 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2915 Z= 0.242 Angle : 0.657 7.917 3900 Z= 0.311 Chirality : 0.050 0.133 440 Planarity : 0.002 0.014 495 Dihedral : 4.992 16.815 385 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 374 PHE 0.004 0.001 PHE C 378 TYR 0.005 0.001 TYR D 310 ARG 0.003 0.001 ARG B 379 *********************** 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 126 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8582 (pttt) cc_final: 0.8246 (ptpp) REVERT: A 340 LYS cc_start: 0.8508 (mtpm) cc_final: 0.7770 (mttm) REVERT: B 317 LYS cc_start: 0.8670 (pttt) cc_final: 0.8385 (ptpp) REVERT: B 331 LYS cc_start: 0.8951 (mtmt) cc_final: 0.8728 (mtpp) REVERT: C 317 LYS cc_start: 0.8751 (pttt) cc_final: 0.8491 (ptpp) REVERT: C 325 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8937 (tt) REVERT: D 317 LYS cc_start: 0.8654 (pttt) cc_final: 0.8323 (ptpt) REVERT: D 369 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8707 (mtmt) REVERT: E 307 GLN cc_start: 0.7971 (mt0) cc_final: 0.7703 (tt0) REVERT: E 311 LYS cc_start: 0.8857 (mtmt) cc_final: 0.8348 (mttt) REVERT: E 317 LYS cc_start: 0.8630 (pttt) cc_final: 0.8225 (ptpt) REVERT: E 331 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8661 (mtpp) REVERT: E 340 LYS cc_start: 0.8550 (mtpm) cc_final: 0.7904 (mttm) outliers start: 11 outliers final: 2 residues processed: 121 average time/residue: 1.8141 time to fit residues: 222.8857 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 : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 345 ASP 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 28 optimal weight: 0.0010 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 C 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.121175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.101477 restraints weight = 3005.072| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.54 r_work: 0.3339 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2915 Z= 0.156 Angle : 0.591 8.067 3900 Z= 0.274 Chirality : 0.048 0.123 440 Planarity : 0.002 0.026 495 Dihedral : 4.650 16.084 385 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.03 % Allowed : 18.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.002 0.001 PHE B 378 TYR 0.006 0.001 TYR A 310 ARG 0.003 0.001 ARG C 379 *********************** 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 125 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8540 (pttt) cc_final: 0.8239 (ptpp) REVERT: B 317 LYS cc_start: 0.8594 (pttt) cc_final: 0.8313 (ptpp) REVERT: B 331 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8721 (mtpp) REVERT: C 317 LYS cc_start: 0.8719 (pttt) cc_final: 0.8457 (ptpp) REVERT: D 317 LYS cc_start: 0.8603 (pttt) cc_final: 0.8271 (ptpt) REVERT: E 311 LYS cc_start: 0.8783 (mtmt) cc_final: 0.8301 (mttt) REVERT: E 317 LYS cc_start: 0.8617 (pttt) cc_final: 0.8262 (ptpt) REVERT: E 331 LYS cc_start: 0.8880 (mtmt) cc_final: 0.8652 (mtpp) REVERT: E 340 LYS cc_start: 0.8560 (mtpm) cc_final: 0.7909 (mttm) outliers start: 10 outliers final: 3 residues processed: 120 average time/residue: 1.7853 time to fit residues: 217.6923 Evaluate side-chains 116 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 345 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.116019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.095586 restraints weight = 3023.491| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.54 r_work: 0.3249 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2915 Z= 0.396 Angle : 0.724 7.605 3900 Z= 0.350 Chirality : 0.052 0.142 440 Planarity : 0.003 0.021 495 Dihedral : 5.069 16.847 385 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.42 % Allowed : 20.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 374 PHE 0.006 0.001 PHE C 378 TYR 0.009 0.002 TYR B 310 ARG 0.005 0.001 ARG C 379 *********************** 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 : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8583 (pttt) cc_final: 0.8223 (ptpp) REVERT: B 317 LYS cc_start: 0.8691 (pttt) cc_final: 0.8391 (ptpp) REVERT: B 331 LYS cc_start: 0.8970 (mtmt) cc_final: 0.8741 (mtpp) REVERT: C 317 LYS cc_start: 0.8767 (pttt) cc_final: 0.8506 (ptpp) REVERT: C 325 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8949 (tt) REVERT: D 317 LYS cc_start: 0.8677 (pttt) cc_final: 0.8347 (ptpt) REVERT: E 311 LYS cc_start: 0.8823 (mtmt) cc_final: 0.8314 (mttt) REVERT: E 317 LYS cc_start: 0.8641 (pttt) cc_final: 0.8222 (ptpt) REVERT: E 331 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8680 (mtpp) REVERT: E 340 LYS cc_start: 0.8567 (mtpm) cc_final: 0.7917 (mttm) outliers start: 8 outliers final: 3 residues processed: 120 average time/residue: 1.7410 time to fit residues: 212.2376 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 : 0.385 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain C residue 345 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 0.0170 chunk 34 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.5222 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.119985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099646 restraints weight = 3035.738| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.56 r_work: 0.3314 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.2915 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= 0.189 Angle : 0.624 8.006 3900 Z= 0.291 Chirality : 0.049 0.128 440 Planarity : 0.002 0.017 495 Dihedral : 4.758 16.552 385 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.52 % Allowed : 21.52 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (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 HIS 0.003 0.001 HIS C 374 PHE 0.003 0.001 PHE C 378 TYR 0.007 0.002 TYR B 310 ARG 0.004 0.001 ARG A 379 *********************** 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 118 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8552 (pttt) cc_final: 0.8235 (ptpp) REVERT: B 317 LYS cc_start: 0.8677 (pttt) cc_final: 0.8386 (ptpp) REVERT: B 331 LYS cc_start: 0.8950 (mtmt) cc_final: 0.8727 (mtpp) REVERT: C 317 LYS cc_start: 0.8752 (pttt) cc_final: 0.8487 (ptpp) REVERT: D 317 LYS cc_start: 0.8628 (pttt) cc_final: 0.8294 (ptpt) REVERT: E 311 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8319 (mttt) REVERT: E 317 LYS cc_start: 0.8623 (pttt) cc_final: 0.8258 (ptpt) REVERT: E 331 LYS cc_start: 0.8904 (mtmt) cc_final: 0.8666 (mtpp) REVERT: E 340 LYS cc_start: 0.8567 (mtpm) cc_final: 0.7926 (mttm) outliers start: 5 outliers final: 3 residues processed: 115 average time/residue: 1.8653 time to fit residues: 217.7564 Evaluate side-chains 114 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 27 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 0.0170 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.2024 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.118927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098657 restraints weight = 3046.100| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.56 r_work: 0.3295 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.2874 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= 0.241 Angle : 0.643 7.077 3900 Z= 0.304 Chirality : 0.050 0.133 440 Planarity : 0.003 0.029 495 Dihedral : 4.808 16.630 385 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.12 % Allowed : 19.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (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 HIS 0.003 0.001 HIS D 374 PHE 0.004 0.001 PHE D 378 TYR 0.007 0.002 TYR A 310 ARG 0.004 0.000 ARG A 379 *********************** 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 115 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8557 (pttt) cc_final: 0.8239 (ptpp) REVERT: B 317 LYS cc_start: 0.8665 (pttt) cc_final: 0.8352 (ptpt) REVERT: B 331 LYS cc_start: 0.8963 (mtmt) cc_final: 0.8739 (mtpp) REVERT: C 317 LYS cc_start: 0.8765 (pttt) cc_final: 0.8503 (ptpp) REVERT: C 325 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8941 (tt) REVERT: C 379 ARG cc_start: 0.7342 (mtp85) cc_final: 0.6669 (mtm110) REVERT: D 317 LYS cc_start: 0.8654 (pttt) cc_final: 0.8324 (ptpt) REVERT: E 311 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8324 (mttt) REVERT: E 317 LYS cc_start: 0.8639 (pttt) cc_final: 0.8273 (ptpt) REVERT: E 331 LYS cc_start: 0.8903 (mtmt) cc_final: 0.8668 (mtpp) REVERT: E 340 LYS cc_start: 0.8572 (mtpm) cc_final: 0.7935 (mttm) outliers start: 7 outliers final: 2 residues processed: 112 average time/residue: 1.7711 time to fit residues: 201.4733 Evaluate side-chains 111 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.0050 chunk 26 optimal weight: 0.0470 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.9096 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.122178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.102362 restraints weight = 3017.485| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.55 r_work: 0.3355 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.3038 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= 0.147 Angle : 0.586 6.810 3900 Z= 0.270 Chirality : 0.048 0.123 440 Planarity : 0.002 0.014 495 Dihedral : 4.494 15.981 385 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.93 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS C 374 PHE 0.003 0.001 PHE C 378 TYR 0.006 0.001 TYR A 310 ARG 0.003 0.000 ARG A 379 *********************** 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 111 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8520 (pttt) cc_final: 0.8177 (ptpt) REVERT: B 317 LYS cc_start: 0.8618 (pttt) cc_final: 0.8314 (ptpt) REVERT: B 331 LYS cc_start: 0.8940 (mtmt) cc_final: 0.8731 (mtpp) REVERT: C 317 LYS cc_start: 0.8737 (pttt) cc_final: 0.8456 (ptpp) REVERT: C 379 ARG cc_start: 0.7219 (mtp85) cc_final: 0.6615 (mtm110) REVERT: D 317 LYS cc_start: 0.8593 (pttt) cc_final: 0.8255 (ptpt) REVERT: E 311 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8299 (mttt) REVERT: E 317 LYS cc_start: 0.8576 (pttt) cc_final: 0.8226 (ptpt) REVERT: E 331 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8652 (mtpp) REVERT: E 340 LYS cc_start: 0.8564 (mtpm) cc_final: 0.7930 (mttm) outliers start: 4 outliers final: 2 residues processed: 110 average time/residue: 1.7538 time to fit residues: 196.0970 Evaluate side-chains 109 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.115545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.095286 restraints weight = 3062.022| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.54 r_work: 0.3235 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 2915 Z= 0.492 Angle : 0.763 7.396 3900 Z= 0.372 Chirality : 0.054 0.143 440 Planarity : 0.003 0.016 495 Dihedral : 5.097 16.938 385 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 2.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (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 HIS 0.004 0.001 HIS A 374 PHE 0.009 0.001 PHE C 378 TYR 0.011 0.003 TYR B 310 ARG 0.004 0.001 ARG A 379 ********************** 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 111 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8704 (pttt) cc_final: 0.8404 (ptpp) REVERT: B 325 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9095 (tt) REVERT: B 331 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8749 (mtpp) REVERT: C 317 LYS cc_start: 0.8767 (pttt) cc_final: 0.8499 (ptpp) REVERT: C 379 ARG cc_start: 0.7423 (mtp85) cc_final: 0.6708 (mtm110) REVERT: D 317 LYS cc_start: 0.8697 (pttt) cc_final: 0.8342 (ptpt) REVERT: E 311 LYS cc_start: 0.8840 (mtmt) cc_final: 0.8335 (mttt) REVERT: E 317 LYS cc_start: 0.8672 (pttt) cc_final: 0.8266 (ptpt) REVERT: E 331 LYS cc_start: 0.8912 (mtmt) cc_final: 0.8668 (mtpp) REVERT: E 340 LYS cc_start: 0.8586 (mtpm) cc_final: 0.7935 (mttm) outliers start: 4 outliers final: 3 residues processed: 109 average time/residue: 1.7982 time to fit residues: 199.1439 Evaluate side-chains 111 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.118925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.098676 restraints weight = 2961.526| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.54 r_work: 0.3298 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.2921 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= 0.235 Angle : 0.656 7.828 3900 Z= 0.308 Chirality : 0.050 0.131 440 Planarity : 0.002 0.012 495 Dihedral : 4.819 16.721 385 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.42 % Allowed : 20.91 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.38), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.006 0.001 PHE A 378 TYR 0.008 0.002 TYR B 310 ARG 0.004 0.001 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4283.04 seconds wall clock time: 76 minutes 12.59 seconds (4572.59 seconds total)