Starting phenix.real_space_refine on Fri Apr 5 19:02:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjx_10514/04_2024/6tjx_10514.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjx_10514/04_2024/6tjx_10514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjx_10514/04_2024/6tjx_10514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjx_10514/04_2024/6tjx_10514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjx_10514/04_2024/6tjx_10514.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjx_10514/04_2024/6tjx_10514.pdb" } resolution = 3.0 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= 0.001 sd= 0.004 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 12 5.16 5 C 3042 2.51 5 N 906 2.21 5 O 918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 4878 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "B" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "D" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "F" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Time building chain proxies: 2.83, per 1000 atoms: 0.58 Number of scatterers: 4878 At special positions: 0 Unit cell: (180.55, 141.45, 32.2, 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 12 16.00 O 918 8.00 N 906 7.00 C 3042 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 - 3.50 Amino acid : False - 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: 1.74 Conformation dependent library (CDL) restraints added in 826.3 milliseconds 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 279 removed outlier: 6.280A pdb=" N GLN A 276 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN E 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ILE A 278 " --> pdb=" O ASN E 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 286 through 289 removed outlier: 6.204A pdb=" N VAL A 287 " --> pdb=" O GLN C 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.427A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL C 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 318 through 319 removed outlier: 6.663A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 327 through 330 removed outlier: 6.823A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 336 through 339 removed outlier: 6.259A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.519A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.208A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LYS C 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER A 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.659A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 377 removed outlier: 6.597A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N THR C 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLU A 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LYS C 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N HIS A 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N THR C 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 275 through 279 removed outlier: 6.240A pdb=" N GLN B 276 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASN F 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE B 278 " --> pdb=" O ASN F 279 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 286 through 289 removed outlier: 6.191A pdb=" N VAL B 287 " --> pdb=" O GLN D 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.382A pdb=" N VAL B 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL D 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 318 through 319 removed outlier: 6.645A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 327 through 330 removed outlier: 6.825A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 336 through 339 removed outlier: 6.294A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.514A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.231A pdb=" N VAL B 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LYS D 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER B 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 360 through 362 Processing sheet with id=AC2, first strand: chain 'D' and resid 369 through 377 removed outlier: 6.684A pdb=" N LYS B 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N THR D 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU B 372 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LYS D 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N HIS B 374 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N THR D 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU B 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) 68 hydrogen bonds defined for protein. 204 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1006 1.32 - 1.44: 926 1.44 - 1.55: 3000 1.55 - 1.67: 0 1.67 - 1.78: 12 Bond restraints: 4944 Sorted by residual: bond pdb=" CD LYS E 311 " pdb=" CE LYS E 311 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 4.00e+00 bond pdb=" CD LYS A 311 " pdb=" CE LYS A 311 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 3.96e+00 bond pdb=" CD LYS C 311 " pdb=" CE LYS C 311 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 3.94e+00 bond pdb=" CD LYS F 311 " pdb=" CE LYS F 311 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.93e+00 bond pdb=" CD LYS D 311 " pdb=" CE LYS D 311 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.89e+00 ... (remaining 4939 not shown) Histogram of bond angle deviations from ideal: 102.80 - 108.50: 505 108.50 - 114.21: 2715 114.21 - 119.91: 1166 119.91 - 125.61: 2154 125.61 - 131.31: 66 Bond angle restraints: 6606 Sorted by residual: angle pdb=" N ASP B 348 " pdb=" CA ASP B 348 " pdb=" C ASP B 348 " ideal model delta sigma weight residual 108.45 112.68 -4.23 1.26e+00 6.30e-01 1.13e+01 angle pdb=" N ASP C 348 " pdb=" CA ASP C 348 " pdb=" C ASP C 348 " ideal model delta sigma weight residual 108.45 112.68 -4.23 1.26e+00 6.30e-01 1.13e+01 angle pdb=" N ASP D 348 " pdb=" CA ASP D 348 " pdb=" C ASP D 348 " ideal model delta sigma weight residual 108.45 112.67 -4.22 1.26e+00 6.30e-01 1.12e+01 angle pdb=" N ASP A 348 " pdb=" CA ASP A 348 " pdb=" C ASP A 348 " ideal model delta sigma weight residual 108.45 112.67 -4.22 1.26e+00 6.30e-01 1.12e+01 angle pdb=" N ASP F 348 " pdb=" CA ASP F 348 " pdb=" C ASP F 348 " ideal model delta sigma weight residual 108.45 112.65 -4.20 1.26e+00 6.30e-01 1.11e+01 ... (remaining 6601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.32: 2437 8.32 - 16.65: 436 16.65 - 24.97: 121 24.97 - 33.29: 42 33.29 - 41.61: 18 Dihedral angle restraints: 3054 sinusoidal: 1284 harmonic: 1770 Sorted by residual: dihedral pdb=" CA GLY D 323 " pdb=" C GLY D 323 " pdb=" N SER D 324 " pdb=" CA SER D 324 " ideal model delta harmonic sigma weight residual 180.00 150.27 29.73 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA GLY B 323 " pdb=" C GLY B 323 " pdb=" N SER B 324 " pdb=" CA SER B 324 " ideal model delta harmonic sigma weight residual 180.00 150.31 29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA GLY A 323 " pdb=" C GLY A 323 " pdb=" N SER A 324 " pdb=" CA SER A 324 " ideal model delta harmonic sigma weight residual 180.00 150.32 29.68 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 3051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 525 0.068 - 0.135: 200 0.135 - 0.203: 7 0.203 - 0.270: 6 0.270 - 0.338: 6 Chirality restraints: 744 Sorted by residual: chirality pdb=" CB ILE D 360 " pdb=" CA ILE D 360 " pdb=" CG1 ILE D 360 " pdb=" CG2 ILE D 360 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CB ILE A 360 " pdb=" CA ILE A 360 " pdb=" CG1 ILE A 360 " pdb=" CG2 ILE A 360 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB ILE F 360 " pdb=" CA ILE F 360 " pdb=" CG1 ILE F 360 " pdb=" CG2 ILE F 360 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 741 not shown) Planarity restraints: 846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 331 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.75e+00 pdb=" N PRO D 332 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 332 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 332 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 331 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO E 332 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 332 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 332 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 331 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO A 332 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " -0.036 5.00e-02 4.00e+02 ... (remaining 843 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1238 2.83 - 3.35: 3672 3.35 - 3.86: 8108 3.86 - 4.38: 8233 4.38 - 4.90: 16275 Nonbonded interactions: 37526 Sorted by model distance: nonbonded pdb=" OD2 ASP A 348 " pdb=" NZ LYS B 347 " model vdw 2.312 2.520 nonbonded pdb=" OD2 ASP E 348 " pdb=" NZ LYS F 347 " model vdw 2.320 2.520 nonbonded pdb=" N ASP E 295 " pdb=" OD1 ASP E 295 " model vdw 2.393 2.520 nonbonded pdb=" N ASP C 295 " pdb=" OD1 ASP C 295 " model vdw 2.394 2.520 nonbonded pdb=" N ASP B 295 " pdb=" OD1 ASP B 295 " model vdw 2.394 2.520 ... (remaining 37521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 2.440 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: 7.400 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.420 Find NCS groups from input model: 0.320 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:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 0.094 4944 Z= 0.785 Angle : 1.098 9.474 6606 Z= 0.572 Chirality : 0.068 0.338 744 Planarity : 0.009 0.065 846 Dihedral : 9.926 41.614 1926 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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: -3.93 (0.25), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.19), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS C 329 PHE 0.009 0.003 PHE D 346 TYR 0.012 0.004 TYR E 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8612 (mttt) cc_final: 0.8312 (mtpm) REVERT: A 369 LYS cc_start: 0.9012 (mttt) cc_final: 0.8731 (mttp) REVERT: A 371 ILE cc_start: 0.8522 (mt) cc_final: 0.8241 (pp) REVERT: B 343 LYS cc_start: 0.8711 (mttt) cc_final: 0.8468 (mtpm) REVERT: C 343 LYS cc_start: 0.8639 (mttt) cc_final: 0.8280 (mtpp) REVERT: D 343 LYS cc_start: 0.8718 (mttt) cc_final: 0.8439 (mtpp) REVERT: D 360 ILE cc_start: 0.8497 (tt) cc_final: 0.7961 (mt) REVERT: D 371 ILE cc_start: 0.8645 (mt) cc_final: 0.8293 (pp) REVERT: E 343 LYS cc_start: 0.8866 (mttt) cc_final: 0.8610 (mtpm) REVERT: F 279 ASN cc_start: 0.7680 (t0) cc_final: 0.7468 (t0) REVERT: F 316 SER cc_start: 0.8797 (m) cc_final: 0.8514 (t) REVERT: F 343 LYS cc_start: 0.8830 (mttt) cc_final: 0.8608 (mtpm) REVERT: F 368 ASN cc_start: 0.7736 (m-40) cc_final: 0.7040 (m110) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.8757 time to fit residues: 117.8934 Evaluate side-chains 84 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 362 HIS ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN B 362 HIS C 276 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS E 362 HIS F 362 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4944 Z= 0.181 Angle : 0.651 12.198 6606 Z= 0.312 Chirality : 0.053 0.235 744 Planarity : 0.005 0.036 846 Dihedral : 6.458 25.031 654 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.55 % Allowed : 10.28 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.25), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.19), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.004 0.001 PHE C 346 TYR 0.011 0.002 TYR D 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.571 Fit side-chains REVERT: A 343 LYS cc_start: 0.8594 (mttt) cc_final: 0.8315 (mtpm) REVERT: A 349 ARG cc_start: 0.7885 (mtt180) cc_final: 0.7623 (mtp85) REVERT: A 368 ASN cc_start: 0.8869 (m-40) cc_final: 0.8645 (m-40) REVERT: A 371 ILE cc_start: 0.8730 (mt) cc_final: 0.8405 (pp) REVERT: C 343 LYS cc_start: 0.8699 (mttt) cc_final: 0.8384 (mtpp) REVERT: C 349 ARG cc_start: 0.7734 (mtt180) cc_final: 0.6710 (mmp-170) REVERT: D 343 LYS cc_start: 0.8761 (mttt) cc_final: 0.8517 (mtpp) REVERT: D 356 SER cc_start: 0.8702 (t) cc_final: 0.8497 (p) REVERT: E 343 LYS cc_start: 0.8721 (mttt) cc_final: 0.8473 (mtpm) REVERT: E 349 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7835 (mtt180) REVERT: F 343 LYS cc_start: 0.8680 (mttt) cc_final: 0.8472 (mtpm) REVERT: F 351 GLN cc_start: 0.7801 (tt0) cc_final: 0.7600 (mt0) REVERT: F 368 ASN cc_start: 0.7380 (m-40) cc_final: 0.6800 (m110) outliers start: 20 outliers final: 5 residues processed: 111 average time/residue: 0.7498 time to fit residues: 88.5309 Evaluate side-chains 80 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 358 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 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 296 ASN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS C 276 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN F 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4944 Z= 0.261 Angle : 0.701 12.015 6606 Z= 0.334 Chirality : 0.054 0.273 744 Planarity : 0.004 0.034 846 Dihedral : 6.519 26.447 654 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.90 % Allowed : 14.89 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.26), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.006 0.001 PHE C 346 TYR 0.020 0.004 TYR F 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 0.630 Fit side-chains REVERT: A 343 LYS cc_start: 0.8630 (mttt) cc_final: 0.8393 (mtpm) REVERT: A 371 ILE cc_start: 0.8735 (mt) cc_final: 0.8421 (pp) REVERT: A 379 ARG cc_start: 0.5726 (mmm-85) cc_final: 0.3826 (ptm160) REVERT: C 274 LYS cc_start: 0.5704 (mtpt) cc_final: 0.4746 (pmtt) REVERT: C 343 LYS cc_start: 0.8775 (mttt) cc_final: 0.8482 (mtpp) REVERT: D 343 LYS cc_start: 0.8797 (mttt) cc_final: 0.8587 (mtpp) REVERT: D 356 SER cc_start: 0.8720 (t) cc_final: 0.8510 (p) REVERT: E 325 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8158 (tm) REVERT: E 343 LYS cc_start: 0.8728 (mttt) cc_final: 0.8479 (mtpm) REVERT: E 351 GLN cc_start: 0.7911 (tt0) cc_final: 0.7608 (mt0) REVERT: F 368 ASN cc_start: 0.7586 (m-40) cc_final: 0.6985 (m110) outliers start: 22 outliers final: 13 residues processed: 96 average time/residue: 0.7837 time to fit residues: 79.8998 Evaluate side-chains 86 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 360 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 4944 Z= 0.434 Angle : 0.752 10.401 6606 Z= 0.368 Chirality : 0.056 0.212 744 Planarity : 0.004 0.030 846 Dihedral : 7.066 27.853 654 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 6.03 % Allowed : 15.25 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.25), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.19), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.007 0.002 PHE C 346 TYR 0.028 0.005 TYR F 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 77 time to evaluate : 0.605 Fit side-chains REVERT: A 343 LYS cc_start: 0.8691 (mttt) cc_final: 0.8444 (mtpm) REVERT: A 351 GLN cc_start: 0.7151 (tt0) cc_final: 0.6733 (mt0) REVERT: A 371 ILE cc_start: 0.8751 (mt) cc_final: 0.8411 (pp) REVERT: B 351 GLN cc_start: 0.7148 (tt0) cc_final: 0.6799 (mt0) REVERT: B 360 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7085 (mt) REVERT: C 295 ASP cc_start: 0.8769 (p0) cc_final: 0.8546 (p0) REVERT: C 343 LYS cc_start: 0.8779 (mttt) cc_final: 0.8452 (mtpp) REVERT: C 353 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7996 (tttp) REVERT: D 343 LYS cc_start: 0.8802 (mttt) cc_final: 0.8555 (mtpp) REVERT: D 353 LYS cc_start: 0.8386 (ttpt) cc_final: 0.8134 (tttp) REVERT: D 356 SER cc_start: 0.8761 (t) cc_final: 0.8487 (p) REVERT: D 358 ASP cc_start: 0.6869 (OUTLIER) cc_final: 0.6411 (t0) REVERT: E 343 LYS cc_start: 0.8772 (mttt) cc_final: 0.8521 (mtpm) REVERT: E 351 GLN cc_start: 0.7968 (tt0) cc_final: 0.7644 (mt0) REVERT: F 368 ASN cc_start: 0.7559 (m-40) cc_final: 0.6935 (m110) outliers start: 34 outliers final: 22 residues processed: 97 average time/residue: 0.7238 time to fit residues: 74.8714 Evaluate side-chains 95 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 71 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 30.0000 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4944 Z= 0.358 Angle : 0.717 11.187 6606 Z= 0.344 Chirality : 0.055 0.220 744 Planarity : 0.003 0.029 846 Dihedral : 6.826 27.231 654 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 5.67 % Allowed : 15.25 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.25), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.19), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.005 0.001 PHE B 346 TYR 0.019 0.004 TYR E 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 74 time to evaluate : 0.620 Fit side-chains REVERT: A 343 LYS cc_start: 0.8695 (mttt) cc_final: 0.8444 (mtpm) REVERT: A 371 ILE cc_start: 0.8757 (mt) cc_final: 0.8408 (pp) REVERT: B 351 GLN cc_start: 0.7203 (tt0) cc_final: 0.6852 (mt0) REVERT: B 360 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.6968 (mt) REVERT: C 295 ASP cc_start: 0.8673 (p0) cc_final: 0.8458 (p0) REVERT: C 343 LYS cc_start: 0.8801 (mttt) cc_final: 0.8496 (mtpp) REVERT: C 353 LYS cc_start: 0.8302 (ttpt) cc_final: 0.8057 (tttp) REVERT: D 274 LYS cc_start: 0.5821 (mtpt) cc_final: 0.5178 (pmtt) REVERT: D 295 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8451 (p0) REVERT: D 343 LYS cc_start: 0.8808 (mttt) cc_final: 0.8565 (mtpp) REVERT: D 353 LYS cc_start: 0.8312 (ttpt) cc_final: 0.8079 (tttp) REVERT: D 356 SER cc_start: 0.8698 (t) cc_final: 0.8483 (p) REVERT: D 358 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.6127 (t0) REVERT: D 360 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7953 (mt) REVERT: E 343 LYS cc_start: 0.8767 (mttt) cc_final: 0.8510 (mtpm) REVERT: E 351 GLN cc_start: 0.7924 (tt0) cc_final: 0.7647 (mt0) REVERT: E 369 LYS cc_start: 0.4415 (pmtt) cc_final: 0.4141 (pptt) REVERT: F 368 ASN cc_start: 0.7611 (m-40) cc_final: 0.6960 (m-40) outliers start: 32 outliers final: 24 residues processed: 93 average time/residue: 0.6731 time to fit residues: 67.0829 Evaluate side-chains 98 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 70 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 359 ASN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4944 Z= 0.271 Angle : 0.684 11.304 6606 Z= 0.324 Chirality : 0.054 0.218 744 Planarity : 0.003 0.028 846 Dihedral : 6.469 26.400 654 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 6.03 % Allowed : 15.78 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.25), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.19), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.004 0.001 PHE D 346 TYR 0.020 0.004 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 75 time to evaluate : 0.600 Fit side-chains REVERT: A 343 LYS cc_start: 0.8693 (mttt) cc_final: 0.8436 (mtpm) REVERT: A 371 ILE cc_start: 0.8751 (mt) cc_final: 0.8400 (pp) REVERT: B 360 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.6982 (mt) REVERT: B 371 ILE cc_start: 0.8855 (mt) cc_final: 0.8591 (pp) REVERT: C 343 LYS cc_start: 0.8803 (mttt) cc_final: 0.8496 (mtpp) REVERT: C 353 LYS cc_start: 0.8297 (ttpt) cc_final: 0.8063 (tttp) REVERT: D 274 LYS cc_start: 0.5969 (mtpt) cc_final: 0.5226 (pmtt) REVERT: D 295 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8409 (p0) REVERT: D 343 LYS cc_start: 0.8801 (mttt) cc_final: 0.8550 (mtpp) REVERT: D 353 LYS cc_start: 0.8298 (ttpt) cc_final: 0.8086 (tttp) REVERT: D 356 SER cc_start: 0.8731 (t) cc_final: 0.8502 (p) REVERT: D 358 ASP cc_start: 0.6807 (OUTLIER) cc_final: 0.6068 (t0) REVERT: D 360 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7960 (mt) REVERT: D 371 ILE cc_start: 0.8739 (mt) cc_final: 0.8518 (pp) REVERT: E 343 LYS cc_start: 0.8743 (mttt) cc_final: 0.8475 (mtpm) REVERT: E 351 GLN cc_start: 0.7921 (tt0) cc_final: 0.7680 (mt0) REVERT: E 369 LYS cc_start: 0.4476 (pmtt) cc_final: 0.4171 (pptt) REVERT: F 368 ASN cc_start: 0.7471 (m-40) cc_final: 0.6848 (m-40) outliers start: 34 outliers final: 20 residues processed: 95 average time/residue: 0.6320 time to fit residues: 64.6454 Evaluate side-chains 94 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 70 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 10.0000 chunk 48 optimal weight: 0.0010 chunk 57 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4944 Z= 0.196 Angle : 0.664 11.901 6606 Z= 0.310 Chirality : 0.053 0.222 744 Planarity : 0.003 0.027 846 Dihedral : 6.096 25.047 654 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.32 % Allowed : 16.84 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.26), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.003 0.000 PHE D 346 TYR 0.026 0.005 TYR F 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8662 (mttt) cc_final: 0.8417 (mtpm) REVERT: A 371 ILE cc_start: 0.8789 (mt) cc_final: 0.8473 (pp) REVERT: B 351 GLN cc_start: 0.7194 (tt0) cc_final: 0.6921 (mt0) REVERT: B 371 ILE cc_start: 0.8833 (mt) cc_final: 0.8578 (pp) REVERT: C 274 LYS cc_start: 0.5939 (mtpt) cc_final: 0.4923 (pmtt) REVERT: C 343 LYS cc_start: 0.8785 (mttt) cc_final: 0.8467 (mtpp) REVERT: C 349 ARG cc_start: 0.7821 (mtt180) cc_final: 0.6678 (mmp-170) REVERT: C 353 LYS cc_start: 0.8316 (ttpt) cc_final: 0.8041 (tttp) REVERT: C 358 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6757 (t0) REVERT: D 274 LYS cc_start: 0.6039 (mtpt) cc_final: 0.5055 (pmtt) REVERT: D 295 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8298 (p0) REVERT: D 343 LYS cc_start: 0.8787 (mttt) cc_final: 0.8551 (mtpp) REVERT: D 353 LYS cc_start: 0.8244 (ttpt) cc_final: 0.8032 (tttp) REVERT: E 343 LYS cc_start: 0.8717 (mttt) cc_final: 0.8461 (mtpm) REVERT: E 369 LYS cc_start: 0.4412 (pmtt) cc_final: 0.4128 (pptt) REVERT: F 274 LYS cc_start: 0.6954 (mtpt) cc_final: 0.6748 (ttpp) REVERT: F 368 ASN cc_start: 0.7445 (m-40) cc_final: 0.6886 (m-40) outliers start: 30 outliers final: 22 residues processed: 103 average time/residue: 0.7179 time to fit residues: 78.7971 Evaluate side-chains 99 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 75 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 359 ASN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 50 optimal weight: 0.0370 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 0.0470 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4944 Z= 0.164 Angle : 0.688 13.390 6606 Z= 0.316 Chirality : 0.055 0.325 744 Planarity : 0.003 0.027 846 Dihedral : 5.895 24.069 654 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.61 % Allowed : 18.62 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.26), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.002 0.000 PHE D 346 TYR 0.027 0.005 TYR F 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8643 (mttt) cc_final: 0.8410 (mtpm) REVERT: A 371 ILE cc_start: 0.8709 (mt) cc_final: 0.8427 (pp) REVERT: B 351 GLN cc_start: 0.7160 (tt0) cc_final: 0.6930 (mt0) REVERT: C 274 LYS cc_start: 0.5990 (mtpt) cc_final: 0.4757 (pmtt) REVERT: C 343 LYS cc_start: 0.8766 (mttt) cc_final: 0.8465 (mtpp) REVERT: C 349 ARG cc_start: 0.7838 (mtt180) cc_final: 0.6648 (mmp-170) REVERT: C 353 LYS cc_start: 0.8330 (ttpt) cc_final: 0.8074 (tttp) REVERT: C 358 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6674 (t0) REVERT: D 274 LYS cc_start: 0.6094 (mtpt) cc_final: 0.5096 (pmtt) REVERT: D 343 LYS cc_start: 0.8766 (mttt) cc_final: 0.8542 (mtpp) REVERT: D 349 ARG cc_start: 0.7759 (mtt180) cc_final: 0.6717 (mmp-170) REVERT: D 353 LYS cc_start: 0.8235 (ttpt) cc_final: 0.8021 (tttp) REVERT: E 343 LYS cc_start: 0.8658 (mttt) cc_final: 0.8407 (mtpm) REVERT: F 274 LYS cc_start: 0.6920 (mtpt) cc_final: 0.6718 (ttpp) REVERT: F 325 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.6013 (pt) REVERT: F 368 ASN cc_start: 0.7892 (m-40) cc_final: 0.7309 (m-40) outliers start: 26 outliers final: 20 residues processed: 103 average time/residue: 0.8515 time to fit residues: 92.6064 Evaluate side-chains 104 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 360 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 0.0070 chunk 56 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4944 Z= 0.287 Angle : 0.724 12.162 6606 Z= 0.341 Chirality : 0.057 0.282 744 Planarity : 0.003 0.027 846 Dihedral : 6.315 25.144 654 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.26 % Allowed : 20.04 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.26), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.005 0.001 PHE D 346 TYR 0.029 0.006 TYR E 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 78 time to evaluate : 0.543 Fit side-chains REVERT: A 343 LYS cc_start: 0.8665 (mttt) cc_final: 0.8416 (mtpm) REVERT: A 371 ILE cc_start: 0.8799 (mt) cc_final: 0.8503 (pp) REVERT: B 351 GLN cc_start: 0.7101 (tt0) cc_final: 0.6891 (mt0) REVERT: C 274 LYS cc_start: 0.6046 (mtpt) cc_final: 0.4749 (pmtt) REVERT: C 343 LYS cc_start: 0.8714 (mttt) cc_final: 0.8409 (mtpp) REVERT: C 353 LYS cc_start: 0.8319 (ttpt) cc_final: 0.8059 (tttp) REVERT: C 358 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.6859 (t0) REVERT: D 274 LYS cc_start: 0.6358 (mtpt) cc_final: 0.5150 (pmtt) REVERT: D 295 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.8469 (p0) REVERT: D 343 LYS cc_start: 0.8744 (mttt) cc_final: 0.8507 (mtpp) REVERT: D 353 LYS cc_start: 0.8244 (ttpt) cc_final: 0.8044 (tttp) REVERT: E 343 LYS cc_start: 0.8716 (mttt) cc_final: 0.8461 (mtpm) REVERT: E 369 LYS cc_start: 0.4511 (pmtt) cc_final: 0.4131 (pptt) REVERT: F 368 ASN cc_start: 0.7913 (m-40) cc_final: 0.7332 (m-40) outliers start: 24 outliers final: 18 residues processed: 93 average time/residue: 0.7971 time to fit residues: 78.7775 Evaluate side-chains 94 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 0.0270 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 overall best weight: 1.0238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4944 Z= 0.161 Angle : 0.692 12.916 6606 Z= 0.318 Chirality : 0.054 0.253 744 Planarity : 0.003 0.027 846 Dihedral : 5.852 23.874 654 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.72 % Allowed : 20.92 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.26), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.002 0.000 PHE B 346 TYR 0.026 0.006 TYR A 310 ARG 0.001 0.000 ARG F 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8624 (mttt) cc_final: 0.8396 (mtpm) REVERT: A 368 ASN cc_start: 0.9065 (m110) cc_final: 0.8803 (m-40) REVERT: A 371 ILE cc_start: 0.8661 (mt) cc_final: 0.8423 (pp) REVERT: C 274 LYS cc_start: 0.6081 (mtpt) cc_final: 0.4769 (pmtt) REVERT: C 343 LYS cc_start: 0.8738 (mttt) cc_final: 0.8462 (mtpp) REVERT: C 349 ARG cc_start: 0.7780 (mtt180) cc_final: 0.6518 (mmp-170) REVERT: C 353 LYS cc_start: 0.8316 (ttpt) cc_final: 0.8061 (tttp) REVERT: C 358 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.6697 (t0) REVERT: D 274 LYS cc_start: 0.6383 (mtpt) cc_final: 0.5145 (pmtt) REVERT: D 349 ARG cc_start: 0.7742 (mtt180) cc_final: 0.6476 (mmp-170) REVERT: E 325 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.6163 (pt) REVERT: E 343 LYS cc_start: 0.8610 (mttt) cc_final: 0.8359 (mtpm) REVERT: E 349 ARG cc_start: 0.8062 (mtt180) cc_final: 0.7805 (mtt180) REVERT: F 325 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.6119 (pt) REVERT: F 368 ASN cc_start: 0.7876 (m-40) cc_final: 0.7279 (m-40) outliers start: 21 outliers final: 17 residues processed: 96 average time/residue: 0.8763 time to fit residues: 88.6538 Evaluate side-chains 98 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.167622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.122048 restraints weight = 5341.164| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.39 r_work: 0.4167 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4049 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 4944 Z= 0.418 Angle : 0.792 13.524 6606 Z= 0.373 Chirality : 0.059 0.302 744 Planarity : 0.004 0.025 846 Dihedral : 6.704 26.534 654 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.26 % Allowed : 20.74 % Favored : 75.00 % 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: -3.42 (0.26), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.007 0.001 PHE E 346 TYR 0.029 0.007 TYR E 310 ARG 0.002 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2094.06 seconds wall clock time: 38 minutes 26.20 seconds (2306.20 seconds total)