Starting phenix.real_space_refine on Thu Oct 10 08:04:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgx_45588/10_2024/9cgx_45588.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgx_45588/10_2024/9cgx_45588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgx_45588/10_2024/9cgx_45588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgx_45588/10_2024/9cgx_45588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgx_45588/10_2024/9cgx_45588.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cgx_45588/10_2024/9cgx_45588.cif" } resolution = 2.97 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2142 2.51 5 N 630 2.21 5 O 642 1.98 5 H 3540 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 6960 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1160 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1160 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1160 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1160 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "E" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1160 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "F" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1160 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Time building chain proxies: 4.41, per 1000 atoms: 0.63 Number of scatterers: 6960 At special positions: 0 Unit cell: (149.46, 76.32, 33.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 642 8.00 N 630 7.00 C 2142 6.00 H 3540 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 660.3 milliseconds 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 310 removed outlier: 6.762A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322 Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.649A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LYS E 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 356 removed outlier: 6.844A pdb=" N SER A 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER C 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.444A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AB2, first strand: chain 'B' and resid 308 through 310 removed outlier: 6.680A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE D 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AB4, first strand: chain 'B' and resid 317 through 322 Processing sheet with id=AB5, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AB6, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.545A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL D 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LYS F 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL D 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 343 through 347 removed outlier: 6.325A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS D 347 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE B 346 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU D 344 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LYS F 347 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE D 346 " --> pdb=" O LYS F 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 351 through 356 removed outlier: 6.819A pdb=" N SER B 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER D 356 " --> pdb=" O GLY F 355 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 359 through 362 Processing sheet with id=AC1, first strand: chain 'B' and resid 369 through 371 Processing sheet with id=AC2, first strand: chain 'B' and resid 369 through 371 90 hydrogen bonds defined for protein. 267 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: 2.15 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3534 1.12 - 1.29: 576 1.29 - 1.47: 1061 1.47 - 1.64: 1837 1.64 - 1.81: 6 Bond restraints: 7014 Sorted by residual: bond pdb=" N VAL B 363 " pdb=" H VAL B 363 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N GLY A 366 " pdb=" H GLY A 366 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N VAL B 339 " pdb=" H VAL B 339 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N LYS D 347 " pdb=" H LYS D 347 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N SER E 324 " pdb=" H SER E 324 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 7009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 10618 2.54 - 5.07: 1645 5.07 - 7.61: 487 7.61 - 10.14: 24 10.14 - 12.68: 6 Bond angle restraints: 12780 Sorted by residual: angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 121.32 -7.52 1.00e+00 1.00e+00 5.66e+01 angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 118.57 -5.97 1.00e+00 1.00e+00 3.57e+01 angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 118.55 -5.95 1.00e+00 1.00e+00 3.54e+01 angle pdb=" CA ASP B 345 " pdb=" CB ASP B 345 " pdb=" CG ASP B 345 " ideal model delta sigma weight residual 112.60 118.51 -5.91 1.00e+00 1.00e+00 3.49e+01 angle pdb=" CA ASP C 345 " pdb=" CB ASP C 345 " pdb=" CG ASP C 345 " ideal model delta sigma weight residual 112.60 118.35 -5.75 1.00e+00 1.00e+00 3.30e+01 ... (remaining 12775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 2851 17.63 - 35.25: 204 35.25 - 52.88: 85 52.88 - 70.50: 84 70.50 - 88.13: 4 Dihedral angle restraints: 3228 sinusoidal: 1848 harmonic: 1380 Sorted by residual: dihedral pdb=" CA LEU B 325 " pdb=" C LEU B 325 " pdb=" N GLY B 326 " pdb=" CA GLY B 326 " ideal model delta harmonic sigma weight residual -180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA LEU E 325 " pdb=" C LEU E 325 " pdb=" N GLY E 326 " pdb=" CA GLY E 326 " ideal model delta harmonic sigma weight residual -180.00 -150.80 -29.20 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA LEU D 325 " pdb=" C LEU D 325 " pdb=" N GLY D 326 " pdb=" CA GLY D 326 " ideal model delta harmonic sigma weight residual -180.00 -150.89 -29.11 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 3225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 230 0.056 - 0.113: 169 0.113 - 0.169: 73 0.169 - 0.225: 34 0.225 - 0.282: 10 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA ARG C 379 " pdb=" N ARG C 379 " pdb=" C ARG C 379 " pdb=" CB ARG C 379 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA ARG F 349 " pdb=" N ARG F 349 " pdb=" C ARG F 349 " pdb=" CB ARG F 349 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ARG D 379 " pdb=" N ARG D 379 " pdb=" C ARG D 379 " pdb=" CB ARG D 379 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 513 not shown) Planarity restraints: 1014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 346 " -0.168 2.00e-02 2.50e+03 1.18e-01 4.15e+02 pdb=" CG PHE E 346 " 0.167 2.00e-02 2.50e+03 pdb=" CD1 PHE E 346 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE E 346 " 0.147 2.00e-02 2.50e+03 pdb=" CE1 PHE E 346 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 PHE E 346 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 346 " 0.030 2.00e-02 2.50e+03 pdb=" HD1 PHE E 346 " -0.134 2.00e-02 2.50e+03 pdb=" HD2 PHE E 346 " 0.107 2.00e-02 2.50e+03 pdb=" HE1 PHE E 346 " 0.083 2.00e-02 2.50e+03 pdb=" HE2 PHE E 346 " -0.208 2.00e-02 2.50e+03 pdb=" HZ PHE E 346 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 346 " -0.101 2.00e-02 2.50e+03 5.35e-02 8.57e+01 pdb=" CG PHE B 346 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 346 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE B 346 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE B 346 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 346 " 0.028 2.00e-02 2.50e+03 pdb=" CZ PHE B 346 " -0.027 2.00e-02 2.50e+03 pdb=" HD1 PHE B 346 " 0.107 2.00e-02 2.50e+03 pdb=" HD2 PHE B 346 " 0.033 2.00e-02 2.50e+03 pdb=" HE1 PHE B 346 " -0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE B 346 " 0.046 2.00e-02 2.50e+03 pdb=" HZ PHE B 346 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 330 " -0.106 2.00e-02 2.50e+03 5.93e-02 7.91e+01 pdb=" CG HIS D 330 " 0.069 2.00e-02 2.50e+03 pdb=" ND1 HIS D 330 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 HIS D 330 " 0.066 2.00e-02 2.50e+03 pdb=" CE1 HIS D 330 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS D 330 " 0.037 2.00e-02 2.50e+03 pdb=" HD2 HIS D 330 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 HIS D 330 " -0.047 2.00e-02 2.50e+03 pdb=" HE2 HIS D 330 " -0.077 2.00e-02 2.50e+03 ... (remaining 1011 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 517 2.17 - 2.77: 11836 2.77 - 3.38: 18315 3.38 - 3.99: 24527 3.99 - 4.60: 34690 Nonbonded interactions: 89885 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.556 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.568 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.585 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.593 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.605 2.450 ... (remaining 89880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 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: 0.110 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.990 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.037 3474 Z= 0.722 Angle : 2.027 12.677 4644 Z= 1.311 Chirality : 0.094 0.282 516 Planarity : 0.012 0.098 594 Dihedral : 13.192 88.128 1344 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 2.78 % Allowed : 4.86 % Favored : 92.36 % Rotamer: Outliers : 2.82 % Allowed : 3.08 % Favored : 94.10 % 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: -2.56 (0.32), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.004 HIS E 362 PHE 0.164 0.019 PHE E 346 TYR 0.060 0.020 TYR E 310 ARG 0.010 0.002 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 0.550 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8129 (tttt) cc_final: 0.7598 (ttmm) REVERT: A 331 LYS cc_start: 0.8052 (mttt) cc_final: 0.7781 (mttp) REVERT: A 338 GLU cc_start: 0.7369 (tt0) cc_final: 0.6876 (mm-30) REVERT: A 342 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6872 (mp0) REVERT: A 369 LYS cc_start: 0.7903 (mttt) cc_final: 0.7614 (mmtp) REVERT: B 321 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7873 (mtpt) REVERT: B 338 GLU cc_start: 0.7849 (tt0) cc_final: 0.7341 (mp0) REVERT: B 342 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6638 (mp0) REVERT: B 348 ASP cc_start: 0.7879 (t0) cc_final: 0.7648 (t0) REVERT: B 351 GLN cc_start: 0.7893 (mt0) cc_final: 0.7691 (mt0) REVERT: B 373 THR cc_start: 0.7127 (m) cc_final: 0.6817 (p) REVERT: B 379 ARG cc_start: 0.6423 (ttt180) cc_final: 0.5833 (ttp-110) REVERT: C 315 LEU cc_start: 0.8292 (mt) cc_final: 0.8069 (mm) REVERT: C 321 LYS cc_start: 0.7320 (mtmt) cc_final: 0.7071 (mtpt) REVERT: C 338 GLU cc_start: 0.7060 (tt0) cc_final: 0.6805 (tt0) REVERT: C 340 LYS cc_start: 0.7668 (mtmt) cc_final: 0.7024 (tptp) REVERT: C 345 ASP cc_start: 0.7836 (m-30) cc_final: 0.7597 (m-30) REVERT: C 349 ARG cc_start: 0.6841 (mtm180) cc_final: 0.6505 (mtp85) REVERT: C 369 LYS cc_start: 0.7169 (mttt) cc_final: 0.6521 (mtpt) REVERT: D 315 LEU cc_start: 0.8368 (mt) cc_final: 0.7936 (mm) REVERT: D 317 LYS cc_start: 0.6758 (mttp) cc_final: 0.6283 (ttmt) REVERT: D 321 LYS cc_start: 0.7159 (ttmt) cc_final: 0.6203 (tmtt) REVERT: D 338 GLU cc_start: 0.7010 (tt0) cc_final: 0.6116 (mt-10) REVERT: D 340 LYS cc_start: 0.6788 (mttt) cc_final: 0.6460 (mtpt) REVERT: E 311 LYS cc_start: 0.7346 (tttt) cc_final: 0.6449 (tppt) REVERT: E 317 LYS cc_start: 0.6759 (mttt) cc_final: 0.6460 (ttpt) REVERT: E 321 LYS cc_start: 0.7212 (mtmt) cc_final: 0.6021 (mmtm) REVERT: E 327 ASN cc_start: 0.7408 (t0) cc_final: 0.7195 (t0) REVERT: E 343 LYS cc_start: 0.7732 (mttt) cc_final: 0.6382 (mmpt) REVERT: E 353 LYS cc_start: 0.7912 (tttt) cc_final: 0.7571 (tttm) REVERT: E 370 LYS cc_start: 0.7962 (tttt) cc_final: 0.5911 (mttt) REVERT: F 311 LYS cc_start: 0.7423 (tttt) cc_final: 0.6566 (tppt) REVERT: F 327 ASN cc_start: 0.7434 (m-40) cc_final: 0.7180 (m-40) REVERT: F 331 LYS cc_start: 0.7292 (mttt) cc_final: 0.5391 (tmtt) REVERT: F 338 GLU cc_start: 0.7201 (tt0) cc_final: 0.6440 (mp0) REVERT: F 343 LYS cc_start: 0.7277 (mptt) cc_final: 0.6524 (mmtm) REVERT: F 358 ASP cc_start: 0.7483 (m-30) cc_final: 0.7216 (m-30) outliers start: 11 outliers final: 3 residues processed: 138 average time/residue: 2.9104 time to fit residues: 410.9129 Evaluate side-chains 104 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3474 Z= 0.244 Angle : 0.771 6.999 4644 Z= 0.393 Chirality : 0.054 0.141 516 Planarity : 0.004 0.024 594 Dihedral : 8.000 24.518 459 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.18 % Favored : 92.59 % Rotamer: Outliers : 1.54 % Allowed : 11.54 % Favored : 86.92 % 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: -2.35 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.018 0.002 PHE E 346 TYR 0.012 0.002 TYR C 310 ARG 0.004 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8090 (mttt) cc_final: 0.7780 (mtmt) REVERT: A 338 GLU cc_start: 0.7750 (tt0) cc_final: 0.6875 (mp0) REVERT: A 342 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7014 (mp0) REVERT: A 351 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7737 (mt0) REVERT: A 356 SER cc_start: 0.8794 (p) cc_final: 0.8444 (p) REVERT: A 379 ARG cc_start: 0.5970 (ttt180) cc_final: 0.5170 (ttp80) REVERT: B 321 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7850 (mtpt) REVERT: B 338 GLU cc_start: 0.7967 (tt0) cc_final: 0.7101 (mp0) REVERT: B 342 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6674 (mp0) REVERT: B 343 LYS cc_start: 0.8013 (mptt) cc_final: 0.7477 (mppt) REVERT: B 348 ASP cc_start: 0.7788 (t0) cc_final: 0.7345 (t0) REVERT: B 351 GLN cc_start: 0.7956 (mt0) cc_final: 0.7632 (mt0) REVERT: B 379 ARG cc_start: 0.6331 (ttt180) cc_final: 0.5735 (ttp-110) REVERT: C 321 LYS cc_start: 0.7460 (mtmt) cc_final: 0.7116 (mtpt) REVERT: C 331 LYS cc_start: 0.7776 (mttt) cc_final: 0.7401 (mtpp) REVERT: C 338 GLU cc_start: 0.7346 (tt0) cc_final: 0.6418 (tm-30) REVERT: C 340 LYS cc_start: 0.7797 (mtmt) cc_final: 0.6838 (tptp) REVERT: C 349 ARG cc_start: 0.7134 (mtm180) cc_final: 0.6524 (mtp85) REVERT: D 317 LYS cc_start: 0.6822 (mttp) cc_final: 0.6240 (ptmt) REVERT: D 321 LYS cc_start: 0.7052 (ttmt) cc_final: 0.5940 (tmmt) REVERT: D 340 LYS cc_start: 0.6964 (mttt) cc_final: 0.6591 (mtpt) REVERT: D 342 GLU cc_start: 0.7560 (mm-30) cc_final: 0.6748 (mm-30) REVERT: D 343 LYS cc_start: 0.7812 (mptp) cc_final: 0.7511 (mmtt) REVERT: D 348 ASP cc_start: 0.7722 (t70) cc_final: 0.7397 (t70) REVERT: E 311 LYS cc_start: 0.7276 (tttt) cc_final: 0.6341 (tppt) REVERT: E 317 LYS cc_start: 0.6622 (mttt) cc_final: 0.6347 (ptmt) REVERT: E 321 LYS cc_start: 0.7320 (mtmt) cc_final: 0.6920 (mttp) REVERT: E 327 ASN cc_start: 0.7223 (t0) cc_final: 0.6860 (m-40) REVERT: E 338 GLU cc_start: 0.6905 (tt0) cc_final: 0.6534 (tt0) REVERT: F 311 LYS cc_start: 0.7571 (tttt) cc_final: 0.6513 (tppt) REVERT: F 331 LYS cc_start: 0.7428 (mttt) cc_final: 0.5388 (tmtt) REVERT: F 343 LYS cc_start: 0.7453 (mptt) cc_final: 0.7082 (mmtm) REVERT: F 348 ASP cc_start: 0.7524 (t0) cc_final: 0.7067 (t0) outliers start: 6 outliers final: 2 residues processed: 104 average time/residue: 3.0337 time to fit residues: 322.8571 Evaluate side-chains 93 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain B residue 341 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3474 Z= 0.175 Angle : 0.597 4.204 4644 Z= 0.306 Chirality : 0.052 0.141 516 Planarity : 0.003 0.025 594 Dihedral : 6.976 20.096 456 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.71 % Favored : 93.06 % Rotamer: Outliers : 1.28 % Allowed : 15.90 % Favored : 82.82 % 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: -2.34 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.013 0.002 PHE E 346 TYR 0.010 0.002 TYR C 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8247 (mtmt) cc_final: 0.8034 (mtpp) REVERT: A 331 LYS cc_start: 0.8081 (mttt) cc_final: 0.7793 (mtmt) REVERT: A 342 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6804 (mp0) REVERT: A 356 SER cc_start: 0.8793 (p) cc_final: 0.8476 (p) REVERT: A 369 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7047 (mttm) REVERT: A 379 ARG cc_start: 0.5733 (ttt180) cc_final: 0.3724 (mmp-170) REVERT: B 342 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6771 (mp0) REVERT: B 343 LYS cc_start: 0.8077 (mptt) cc_final: 0.7583 (mppt) REVERT: B 351 GLN cc_start: 0.7854 (mt0) cc_final: 0.7566 (mt0) REVERT: B 379 ARG cc_start: 0.6178 (ttt180) cc_final: 0.5610 (ttp-110) REVERT: C 321 LYS cc_start: 0.7576 (mtmt) cc_final: 0.7304 (mtpt) REVERT: C 331 LYS cc_start: 0.7671 (mttt) cc_final: 0.7210 (mtpp) REVERT: C 338 GLU cc_start: 0.7076 (tt0) cc_final: 0.6808 (tt0) REVERT: C 349 ARG cc_start: 0.7280 (mtm180) cc_final: 0.6537 (mtp85) REVERT: D 317 LYS cc_start: 0.6875 (mttp) cc_final: 0.6257 (ptmt) REVERT: D 340 LYS cc_start: 0.7060 (mttt) cc_final: 0.6635 (mtpt) REVERT: D 342 GLU cc_start: 0.7624 (mm-30) cc_final: 0.6970 (mt-10) REVERT: D 343 LYS cc_start: 0.7864 (mptp) cc_final: 0.7575 (mmtt) REVERT: E 311 LYS cc_start: 0.7341 (tttt) cc_final: 0.6341 (tppt) REVERT: E 317 LYS cc_start: 0.6516 (mttt) cc_final: 0.6302 (ptmt) REVERT: E 321 LYS cc_start: 0.7356 (mtmt) cc_final: 0.7002 (mttp) REVERT: E 327 ASN cc_start: 0.7134 (t0) cc_final: 0.6898 (m-40) REVERT: E 343 LYS cc_start: 0.7841 (mtpt) cc_final: 0.6485 (mmpt) REVERT: E 376 LEU cc_start: 0.8044 (tp) cc_final: 0.7802 (tm) REVERT: F 311 LYS cc_start: 0.7611 (tttt) cc_final: 0.6632 (tppt) REVERT: F 331 LYS cc_start: 0.7412 (mttt) cc_final: 0.5391 (tmtt) outliers start: 5 outliers final: 1 residues processed: 87 average time/residue: 3.3119 time to fit residues: 294.3881 Evaluate side-chains 79 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3474 Z= 0.244 Angle : 0.605 4.674 4644 Z= 0.305 Chirality : 0.051 0.128 516 Planarity : 0.003 0.025 594 Dihedral : 6.932 21.098 456 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.87 % Favored : 91.90 % Rotamer: Outliers : 1.79 % Allowed : 16.15 % Favored : 82.05 % 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: -2.51 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.010 0.002 PHE D 346 TYR 0.011 0.003 TYR E 310 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8121 (mttt) cc_final: 0.7883 (mtmt) REVERT: A 342 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6844 (mp0) REVERT: A 349 ARG cc_start: 0.7248 (mtp180) cc_final: 0.7028 (mtm180) REVERT: A 369 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7380 (mttm) REVERT: A 379 ARG cc_start: 0.5917 (ttt180) cc_final: 0.3921 (mmp-170) REVERT: B 311 LYS cc_start: 0.7793 (tttt) cc_final: 0.6938 (tmmt) REVERT: B 331 LYS cc_start: 0.8213 (mttt) cc_final: 0.7754 (mtpt) REVERT: B 340 LYS cc_start: 0.8079 (mttt) cc_final: 0.7847 (mttt) REVERT: B 342 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6800 (mp0) REVERT: B 343 LYS cc_start: 0.8104 (mptt) cc_final: 0.7556 (mppt) REVERT: B 351 GLN cc_start: 0.7952 (mt0) cc_final: 0.7632 (mt0) REVERT: B 379 ARG cc_start: 0.6256 (ttt180) cc_final: 0.5782 (ttp-110) REVERT: C 356 SER cc_start: 0.8592 (p) cc_final: 0.8359 (p) REVERT: D 317 LYS cc_start: 0.6869 (mttp) cc_final: 0.6270 (ttpt) REVERT: D 340 LYS cc_start: 0.7065 (mttt) cc_final: 0.6556 (mtpt) REVERT: D 342 GLU cc_start: 0.7673 (mm-30) cc_final: 0.6948 (tt0) REVERT: D 343 LYS cc_start: 0.8019 (mptp) cc_final: 0.7688 (mmtt) REVERT: E 314 ASP cc_start: 0.8074 (t0) cc_final: 0.7820 (t0) REVERT: E 317 LYS cc_start: 0.6588 (mttt) cc_final: 0.6275 (ptmt) REVERT: E 321 LYS cc_start: 0.7509 (mtmt) cc_final: 0.6936 (mttp) REVERT: E 327 ASN cc_start: 0.7180 (t0) cc_final: 0.6966 (t0) REVERT: E 343 LYS cc_start: 0.7799 (mtpt) cc_final: 0.6506 (mmpt) REVERT: F 343 LYS cc_start: 0.7782 (mptt) cc_final: 0.7247 (mppt) REVERT: F 353 LYS cc_start: 0.7783 (tttm) cc_final: 0.7482 (tttm) REVERT: F 370 LYS cc_start: 0.7815 (tttt) cc_final: 0.5851 (mttt) outliers start: 7 outliers final: 1 residues processed: 91 average time/residue: 3.2543 time to fit residues: 302.6843 Evaluate side-chains 79 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3474 Z= 0.180 Angle : 0.556 4.354 4644 Z= 0.282 Chirality : 0.050 0.138 516 Planarity : 0.003 0.025 594 Dihedral : 6.623 18.781 456 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.87 % Favored : 91.90 % Rotamer: Outliers : 2.56 % Allowed : 15.90 % Favored : 81.54 % 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: -2.56 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 362 PHE 0.007 0.001 PHE E 346 TYR 0.009 0.002 TYR E 310 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8121 (mttt) cc_final: 0.7893 (mtmt) REVERT: A 342 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6746 (mp0) REVERT: A 369 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7259 (mttm) REVERT: A 379 ARG cc_start: 0.6082 (ttt180) cc_final: 0.4033 (mmp-170) REVERT: B 331 LYS cc_start: 0.8218 (mttt) cc_final: 0.7766 (mtpt) REVERT: B 340 LYS cc_start: 0.8000 (mttt) cc_final: 0.7728 (mttt) REVERT: B 342 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6816 (mp0) REVERT: B 343 LYS cc_start: 0.8104 (mptt) cc_final: 0.7551 (mppt) REVERT: B 351 GLN cc_start: 0.7994 (mt0) cc_final: 0.7668 (mt0) REVERT: B 379 ARG cc_start: 0.6416 (ttt180) cc_final: 0.5631 (mpp80) REVERT: C 342 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6922 (mt-10) REVERT: C 356 SER cc_start: 0.8582 (p) cc_final: 0.8298 (p) REVERT: D 317 LYS cc_start: 0.6906 (mttp) cc_final: 0.6244 (ttmt) REVERT: D 340 LYS cc_start: 0.7124 (mttt) cc_final: 0.6643 (mtpt) REVERT: D 342 GLU cc_start: 0.7636 (mm-30) cc_final: 0.6955 (mt-10) REVERT: D 343 LYS cc_start: 0.7990 (mptp) cc_final: 0.7624 (mmtt) REVERT: E 314 ASP cc_start: 0.8016 (t0) cc_final: 0.7721 (t0) REVERT: E 317 LYS cc_start: 0.6675 (mttt) cc_final: 0.6303 (ttpt) REVERT: E 321 LYS cc_start: 0.7512 (mtmt) cc_final: 0.6946 (mttp) REVERT: F 311 LYS cc_start: 0.8294 (tttp) cc_final: 0.7170 (tppt) REVERT: F 340 LYS cc_start: 0.7223 (mtpt) cc_final: 0.6576 (mtmm) REVERT: F 343 LYS cc_start: 0.7811 (mptt) cc_final: 0.7331 (mppt) outliers start: 10 outliers final: 2 residues processed: 83 average time/residue: 2.8229 time to fit residues: 240.1604 Evaluate side-chains 75 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 356 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.0470 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3474 Z= 0.176 Angle : 0.534 4.156 4644 Z= 0.272 Chirality : 0.050 0.132 516 Planarity : 0.003 0.027 594 Dihedral : 6.456 18.553 456 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.10 % Favored : 91.67 % Rotamer: Outliers : 1.28 % Allowed : 16.92 % Favored : 81.79 % 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: -2.57 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 362 PHE 0.007 0.001 PHE E 346 TYR 0.008 0.002 TYR C 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8111 (mttt) cc_final: 0.7880 (mtmt) REVERT: A 342 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6755 (mp0) REVERT: A 369 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7241 (mttm) REVERT: A 379 ARG cc_start: 0.6065 (ttt180) cc_final: 0.3981 (mmp-170) REVERT: B 331 LYS cc_start: 0.8213 (mttt) cc_final: 0.7768 (mtpt) REVERT: B 340 LYS cc_start: 0.7980 (mttt) cc_final: 0.7718 (mttt) REVERT: B 342 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6826 (mp0) REVERT: B 343 LYS cc_start: 0.8116 (mptt) cc_final: 0.7562 (mppt) REVERT: B 351 GLN cc_start: 0.8020 (mt0) cc_final: 0.7682 (mt0) REVERT: B 353 LYS cc_start: 0.8027 (tttm) cc_final: 0.7753 (tttt) REVERT: B 379 ARG cc_start: 0.6300 (ttt180) cc_final: 0.5582 (mpp80) REVERT: C 342 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6951 (mt-10) REVERT: C 356 SER cc_start: 0.8587 (p) cc_final: 0.8314 (p) REVERT: D 317 LYS cc_start: 0.6929 (mttp) cc_final: 0.6245 (ttmt) REVERT: D 340 LYS cc_start: 0.7145 (mttt) cc_final: 0.6603 (mtpt) REVERT: D 342 GLU cc_start: 0.7621 (mm-30) cc_final: 0.6946 (mt-10) REVERT: D 343 LYS cc_start: 0.7986 (mptp) cc_final: 0.7590 (mmtt) REVERT: E 317 LYS cc_start: 0.6683 (mttt) cc_final: 0.6285 (ttpt) REVERT: E 321 LYS cc_start: 0.7462 (mtmt) cc_final: 0.6906 (mttp) REVERT: E 343 LYS cc_start: 0.7865 (mtpt) cc_final: 0.6506 (mmpt) REVERT: F 340 LYS cc_start: 0.7312 (mtpt) cc_final: 0.7112 (mtpp) REVERT: F 343 LYS cc_start: 0.7807 (mptt) cc_final: 0.7297 (mppt) REVERT: F 379 ARG cc_start: 0.6367 (ttm170) cc_final: 0.5906 (ttp-110) outliers start: 5 outliers final: 2 residues processed: 76 average time/residue: 3.1303 time to fit residues: 243.4950 Evaluate side-chains 76 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3474 Z= 0.231 Angle : 0.560 4.293 4644 Z= 0.284 Chirality : 0.050 0.130 516 Planarity : 0.003 0.026 594 Dihedral : 6.617 19.443 456 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.10 % Favored : 91.67 % Rotamer: Outliers : 1.03 % Allowed : 17.18 % Favored : 81.79 % 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: -2.72 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 374 PHE 0.007 0.001 PHE F 346 TYR 0.011 0.002 TYR E 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8030 (tttt) cc_final: 0.7597 (ttmm) REVERT: A 331 LYS cc_start: 0.8081 (mttt) cc_final: 0.7866 (mtmt) REVERT: A 342 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6778 (mp0) REVERT: A 369 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7463 (mttm) REVERT: A 379 ARG cc_start: 0.5980 (ttt180) cc_final: 0.4140 (mmp-170) REVERT: B 311 LYS cc_start: 0.7583 (tttt) cc_final: 0.6790 (tmmt) REVERT: B 331 LYS cc_start: 0.8233 (mttt) cc_final: 0.7789 (mtpt) REVERT: B 340 LYS cc_start: 0.8000 (mttt) cc_final: 0.7740 (mttt) REVERT: B 342 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6802 (mp0) REVERT: B 343 LYS cc_start: 0.8108 (mptt) cc_final: 0.7584 (mppt) REVERT: B 351 GLN cc_start: 0.8069 (mt0) cc_final: 0.7706 (mt0) REVERT: B 379 ARG cc_start: 0.6431 (ttt180) cc_final: 0.5531 (mpp80) REVERT: C 342 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6962 (mt-10) REVERT: C 356 SER cc_start: 0.8584 (p) cc_final: 0.8307 (p) REVERT: D 317 LYS cc_start: 0.6795 (mttp) cc_final: 0.6222 (ttmt) REVERT: D 340 LYS cc_start: 0.7175 (mttt) cc_final: 0.6590 (mtpt) REVERT: D 342 GLU cc_start: 0.7642 (mm-30) cc_final: 0.6952 (mt-10) REVERT: D 343 LYS cc_start: 0.7988 (mptp) cc_final: 0.7564 (mmtt) REVERT: E 317 LYS cc_start: 0.6500 (mttt) cc_final: 0.6117 (ttpt) REVERT: E 321 LYS cc_start: 0.7447 (mtmt) cc_final: 0.6840 (mttp) REVERT: F 311 LYS cc_start: 0.8250 (tttp) cc_final: 0.7192 (tppt) REVERT: F 340 LYS cc_start: 0.7302 (mtpt) cc_final: 0.7075 (mtpp) REVERT: F 343 LYS cc_start: 0.7893 (mptt) cc_final: 0.7363 (mppt) REVERT: F 370 LYS cc_start: 0.7810 (tttt) cc_final: 0.5864 (mttt) outliers start: 4 outliers final: 2 residues processed: 82 average time/residue: 2.9570 time to fit residues: 248.4360 Evaluate side-chains 80 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 0.0270 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3474 Z= 0.162 Angle : 0.524 4.156 4644 Z= 0.267 Chirality : 0.050 0.134 516 Planarity : 0.003 0.029 594 Dihedral : 6.372 18.449 456 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.64 % Favored : 92.13 % Rotamer: Outliers : 0.77 % Allowed : 17.95 % Favored : 81.28 % 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: -2.71 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 362 PHE 0.006 0.001 PHE E 346 TYR 0.007 0.001 TYR E 310 ARG 0.002 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8417 (mtpt) cc_final: 0.7876 (mtpp) REVERT: A 331 LYS cc_start: 0.8070 (mttt) cc_final: 0.7865 (mtmt) REVERT: A 342 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6768 (mp0) REVERT: A 369 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7268 (mttm) REVERT: B 311 LYS cc_start: 0.7529 (tttt) cc_final: 0.6683 (tmmt) REVERT: B 331 LYS cc_start: 0.8227 (mttt) cc_final: 0.7788 (mtpt) REVERT: B 342 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6812 (mp0) REVERT: B 343 LYS cc_start: 0.8109 (mptt) cc_final: 0.7577 (mppt) REVERT: B 351 GLN cc_start: 0.8046 (mt0) cc_final: 0.7680 (mt0) REVERT: B 353 LYS cc_start: 0.7948 (tttm) cc_final: 0.7662 (tttt) REVERT: B 379 ARG cc_start: 0.6199 (ttt180) cc_final: 0.5442 (mpp80) REVERT: C 342 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6983 (mt-10) REVERT: C 356 SER cc_start: 0.8588 (p) cc_final: 0.8315 (p) REVERT: D 317 LYS cc_start: 0.6824 (mttp) cc_final: 0.6247 (ttmt) REVERT: D 340 LYS cc_start: 0.7203 (mttt) cc_final: 0.6584 (mtpt) REVERT: D 342 GLU cc_start: 0.7617 (mm-30) cc_final: 0.6945 (mt-10) REVERT: D 343 LYS cc_start: 0.7947 (mptp) cc_final: 0.7620 (mmtt) REVERT: E 317 LYS cc_start: 0.6458 (mttt) cc_final: 0.6113 (ttpt) REVERT: E 321 LYS cc_start: 0.7520 (mtmt) cc_final: 0.6883 (mttp) REVERT: E 379 ARG cc_start: 0.7391 (mtp-110) cc_final: 0.6097 (mtt180) REVERT: F 311 LYS cc_start: 0.8277 (tttp) cc_final: 0.7175 (tppt) REVERT: F 340 LYS cc_start: 0.7303 (mtpt) cc_final: 0.7074 (mtpp) REVERT: F 343 LYS cc_start: 0.7850 (mptt) cc_final: 0.7350 (mppt) REVERT: F 370 LYS cc_start: 0.7793 (tttt) cc_final: 0.5882 (mttt) REVERT: F 379 ARG cc_start: 0.6426 (ttm170) cc_final: 0.5997 (ttp-110) outliers start: 3 outliers final: 2 residues processed: 75 average time/residue: 3.0511 time to fit residues: 234.3174 Evaluate side-chains 76 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3474 Z= 0.219 Angle : 0.543 4.231 4644 Z= 0.276 Chirality : 0.050 0.133 516 Planarity : 0.003 0.029 594 Dihedral : 6.476 19.008 456 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.33 % Favored : 91.44 % Rotamer: Outliers : 0.77 % Allowed : 19.23 % Favored : 80.00 % 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: -2.79 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 374 PHE 0.006 0.001 PHE D 346 TYR 0.011 0.002 TYR E 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7945 (tttt) cc_final: 0.7549 (ttmm) REVERT: A 321 LYS cc_start: 0.8432 (mtpt) cc_final: 0.7908 (mtpp) REVERT: A 331 LYS cc_start: 0.8061 (mttt) cc_final: 0.7851 (mtmt) REVERT: A 342 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6770 (mp0) REVERT: A 369 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7425 (mttm) REVERT: B 311 LYS cc_start: 0.7612 (tttt) cc_final: 0.6805 (tmmt) REVERT: B 331 LYS cc_start: 0.8226 (mttt) cc_final: 0.7788 (mtpt) REVERT: B 342 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6825 (mp0) REVERT: B 343 LYS cc_start: 0.8186 (mptt) cc_final: 0.7651 (mppt) REVERT: B 351 GLN cc_start: 0.8067 (mt0) cc_final: 0.7700 (mt0) REVERT: B 353 LYS cc_start: 0.7968 (tttm) cc_final: 0.7767 (tttt) REVERT: B 379 ARG cc_start: 0.6409 (ttt180) cc_final: 0.5552 (mpp80) REVERT: C 316 SER cc_start: 0.8794 (p) cc_final: 0.8453 (p) REVERT: C 342 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6923 (mt-10) REVERT: C 356 SER cc_start: 0.8592 (p) cc_final: 0.8318 (p) REVERT: D 317 LYS cc_start: 0.6784 (mttp) cc_final: 0.6187 (ttmt) REVERT: D 340 LYS cc_start: 0.7169 (mttt) cc_final: 0.6562 (mtpt) REVERT: D 342 GLU cc_start: 0.7626 (mm-30) cc_final: 0.6955 (mt-10) REVERT: D 343 LYS cc_start: 0.7946 (mptp) cc_final: 0.7584 (mmtt) REVERT: E 317 LYS cc_start: 0.6444 (mttt) cc_final: 0.6030 (ttpt) REVERT: E 321 LYS cc_start: 0.7564 (mtmt) cc_final: 0.6833 (mttp) REVERT: E 379 ARG cc_start: 0.7478 (mtp-110) cc_final: 0.6140 (mtt180) REVERT: F 311 LYS cc_start: 0.8280 (tttp) cc_final: 0.7202 (tppt) REVERT: F 340 LYS cc_start: 0.7265 (mtpt) cc_final: 0.7013 (mtpp) REVERT: F 343 LYS cc_start: 0.7895 (mptt) cc_final: 0.7395 (mppt) REVERT: F 370 LYS cc_start: 0.7814 (tttt) cc_final: 0.5868 (mttt) REVERT: F 375 LYS cc_start: 0.5965 (mttt) cc_final: 0.5577 (mmmm) outliers start: 3 outliers final: 2 residues processed: 81 average time/residue: 3.0799 time to fit residues: 255.8600 Evaluate side-chains 82 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3474 Z= 0.180 Angle : 0.525 4.215 4644 Z= 0.267 Chirality : 0.050 0.133 516 Planarity : 0.003 0.030 594 Dihedral : 6.350 18.471 456 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.87 % Favored : 91.90 % Rotamer: Outliers : 0.77 % Allowed : 18.97 % Favored : 80.26 % 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: -2.78 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 374 PHE 0.005 0.001 PHE E 346 TYR 0.007 0.002 TYR E 310 ARG 0.002 0.000 ARG E 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8435 (mtpt) cc_final: 0.7913 (mtpp) REVERT: A 342 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6687 (mp0) REVERT: A 343 LYS cc_start: 0.7679 (mptt) cc_final: 0.7367 (mmtp) REVERT: A 369 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7466 (mttm) REVERT: B 311 LYS cc_start: 0.7631 (tttt) cc_final: 0.6735 (tmmt) REVERT: B 331 LYS cc_start: 0.8221 (mttt) cc_final: 0.7783 (mtpt) REVERT: B 342 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6830 (mp0) REVERT: B 343 LYS cc_start: 0.8136 (mptt) cc_final: 0.7613 (mppt) REVERT: B 351 GLN cc_start: 0.8061 (mt0) cc_final: 0.7683 (mt0) REVERT: B 353 LYS cc_start: 0.7885 (tttm) cc_final: 0.7568 (tttt) REVERT: B 379 ARG cc_start: 0.6334 (ttt180) cc_final: 0.5494 (mpp80) REVERT: C 316 SER cc_start: 0.8808 (p) cc_final: 0.8471 (p) REVERT: C 342 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6992 (mt-10) REVERT: C 356 SER cc_start: 0.8594 (p) cc_final: 0.8303 (p) REVERT: D 317 LYS cc_start: 0.6799 (mttp) cc_final: 0.6188 (ttmt) REVERT: D 340 LYS cc_start: 0.7180 (mttt) cc_final: 0.6563 (mtpt) REVERT: D 342 GLU cc_start: 0.7621 (mm-30) cc_final: 0.6949 (mt-10) REVERT: D 343 LYS cc_start: 0.7948 (mptp) cc_final: 0.7587 (mmtt) REVERT: E 317 LYS cc_start: 0.6539 (mttt) cc_final: 0.6078 (ttpt) REVERT: E 321 LYS cc_start: 0.7557 (mtmt) cc_final: 0.6820 (mttp) REVERT: F 311 LYS cc_start: 0.8288 (tttp) cc_final: 0.7191 (tppt) REVERT: F 340 LYS cc_start: 0.7321 (mtpt) cc_final: 0.7070 (mtpp) REVERT: F 343 LYS cc_start: 0.7874 (mptt) cc_final: 0.7367 (mppt) REVERT: F 370 LYS cc_start: 0.7810 (tttt) cc_final: 0.5872 (mttt) REVERT: F 375 LYS cc_start: 0.5925 (mttt) cc_final: 0.5568 (mmmm) REVERT: F 379 ARG cc_start: 0.6455 (ttm170) cc_final: 0.6034 (ttp-110) outliers start: 3 outliers final: 2 residues processed: 81 average time/residue: 3.1504 time to fit residues: 261.2365 Evaluate side-chains 82 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 24 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.157397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.131801 restraints weight = 10631.773| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.90 r_work: 0.3902 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.6479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3474 Z= 0.157 Angle : 0.515 4.202 4644 Z= 0.262 Chirality : 0.050 0.133 516 Planarity : 0.003 0.030 594 Dihedral : 6.176 18.234 456 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.10 % Favored : 91.67 % Rotamer: Outliers : 1.03 % Allowed : 19.23 % Favored : 79.74 % 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: -2.75 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 374 PHE 0.005 0.001 PHE E 346 TYR 0.006 0.001 TYR E 310 ARG 0.002 0.000 ARG E 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5544.46 seconds wall clock time: 98 minutes 16.93 seconds (5896.93 seconds total)