Starting phenix.real_space_refine on Thu Nov 14 02:56:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwl_60532/11_2024/8zwl_60532.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwl_60532/11_2024/8zwl_60532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwl_60532/11_2024/8zwl_60532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwl_60532/11_2024/8zwl_60532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwl_60532/11_2024/8zwl_60532.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwl_60532/11_2024/8zwl_60532.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3468 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 3.06, per 1000 atoms: 0.88 Number of scatterers: 3468 At special positions: 0 Unit cell: (133.63, 87.15, 39.01, 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 6 16.00 O 648 8.00 N 642 7.00 C 2172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 406.8 milliseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.583A pdb=" N GLN C 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYR E 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL C 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 343 through 345 removed outlier: 6.386A pdb=" N LEU C 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.529A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 370 through 371 removed outlier: 6.348A pdb=" N LYS C 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 374 through 376 removed outlier: 6.177A pdb=" N LYS C 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.583A pdb=" N GLN F 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYR B 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL F 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 345 removed outlier: 6.386A pdb=" N LEU F 344 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 362 removed outlier: 6.529A pdb=" N THR F 361 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 370 through 371 removed outlier: 6.348A pdb=" N LYS F 370 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 376 removed outlier: 6.177A pdb=" N LYS F 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) 22 hydrogen bonds defined for protein. 66 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.65 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1146 1.34 - 1.45: 508 1.45 - 1.57: 1862 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 3522 Sorted by residual: bond pdb=" CB ASP B 345 " pdb=" CG ASP B 345 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.44e+00 bond pdb=" CB ASP C 345 " pdb=" CG ASP C 345 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.41e+00 bond pdb=" CB ASP E 345 " pdb=" CG ASP E 345 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.38e+00 bond pdb=" CB ASP F 345 " pdb=" CG ASP F 345 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.36e+00 bond pdb=" CB ASP D 345 " pdb=" CG ASP D 345 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.34e+00 ... (remaining 3517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 4285 1.36 - 2.72: 306 2.72 - 4.07: 100 4.07 - 5.43: 7 5.43 - 6.79: 12 Bond angle restraints: 4710 Sorted by residual: angle pdb=" N GLN A 336 " pdb=" CA GLN A 336 " pdb=" C GLN A 336 " ideal model delta sigma weight residual 108.46 112.55 -4.09 1.51e+00 4.39e-01 7.34e+00 angle pdb=" N GLN B 336 " pdb=" CA GLN B 336 " pdb=" C GLN B 336 " ideal model delta sigma weight residual 108.46 112.52 -4.06 1.51e+00 4.39e-01 7.24e+00 angle pdb=" N GLN C 336 " pdb=" CA GLN C 336 " pdb=" C GLN C 336 " ideal model delta sigma weight residual 108.46 112.51 -4.05 1.51e+00 4.39e-01 7.20e+00 angle pdb=" N GLN D 336 " pdb=" CA GLN D 336 " pdb=" C GLN D 336 " ideal model delta sigma weight residual 108.46 112.50 -4.04 1.51e+00 4.39e-01 7.16e+00 angle pdb=" N GLN F 336 " pdb=" CA GLN F 336 " pdb=" C GLN F 336 " ideal model delta sigma weight residual 108.46 112.49 -4.03 1.51e+00 4.39e-01 7.13e+00 ... (remaining 4705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.98: 1722 8.98 - 17.96: 246 17.96 - 26.94: 126 26.94 - 35.92: 42 35.92 - 44.90: 6 Dihedral angle restraints: 2142 sinusoidal: 894 harmonic: 1248 Sorted by residual: dihedral pdb=" CA ASP C 358 " pdb=" C ASP C 358 " pdb=" N ASN C 359 " pdb=" CA ASN C 359 " ideal model delta harmonic sigma weight residual 180.00 160.88 19.12 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ASP F 358 " pdb=" C ASP F 358 " pdb=" N ASN F 359 " pdb=" CA ASN F 359 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ASP D 358 " pdb=" C ASP D 358 " pdb=" N ASN D 359 " pdb=" CA ASN D 359 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 2139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 396 0.062 - 0.123: 123 0.123 - 0.185: 3 0.185 - 0.247: 0 0.247 - 0.308: 6 Chirality restraints: 528 Sorted by residual: chirality pdb=" CG LEU B 344 " pdb=" CB LEU B 344 " pdb=" CD1 LEU B 344 " pdb=" CD2 LEU B 344 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CG LEU C 344 " pdb=" CB LEU C 344 " pdb=" CD1 LEU C 344 " pdb=" CD2 LEU C 344 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CG LEU E 344 " pdb=" CB LEU E 344 " pdb=" CD1 LEU E 344 " pdb=" CD2 LEU E 344 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 525 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 346 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C PHE D 346 " -0.020 2.00e-02 2.50e+03 pdb=" O PHE D 346 " 0.008 2.00e-02 2.50e+03 pdb=" N LYS D 347 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 346 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C PHE F 346 " 0.020 2.00e-02 2.50e+03 pdb=" O PHE F 346 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS F 347 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 346 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.33e+00 pdb=" C PHE B 346 " 0.020 2.00e-02 2.50e+03 pdb=" O PHE B 346 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS B 347 " -0.007 2.00e-02 2.50e+03 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 901 2.80 - 3.32: 2772 3.32 - 3.85: 5115 3.85 - 4.37: 5522 4.37 - 4.90: 11775 Nonbonded interactions: 26085 Sorted by model distance: nonbonded pdb=" NZ LYS D 343 " pdb=" OD1 ASP D 345 " model vdw 2.273 3.120 nonbonded pdb=" NZ LYS B 343 " pdb=" OD1 ASP B 345 " model vdw 2.273 3.120 nonbonded pdb=" NZ LYS E 343 " pdb=" OD1 ASP E 345 " model vdw 2.273 3.120 nonbonded pdb=" NZ LYS A 343 " pdb=" OD1 ASP A 345 " model vdw 2.273 3.120 nonbonded pdb=" NZ LYS F 343 " pdb=" OD1 ASP F 345 " model vdw 2.274 3.120 ... (remaining 26080 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: 2.100 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.970 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.008 0.038 3522 Z= 0.575 Angle : 0.918 6.791 4710 Z= 0.496 Chirality : 0.063 0.308 528 Planarity : 0.004 0.017 600 Dihedral : 11.351 44.902 1350 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % 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: -4.31 (0.24), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.19), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 330 PHE 0.008 0.004 PHE A 378 TYR 0.015 0.004 TYR D 310 ARG 0.006 0.002 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 379 ARG cc_start: 0.6382 (mtt180) cc_final: 0.5998 (tpt90) REVERT: D 311 LYS cc_start: 0.8082 (ttmt) cc_final: 0.7804 (mtmt) REVERT: D 379 ARG cc_start: 0.6320 (mtt180) cc_final: 0.5904 (tpt90) REVERT: E 311 LYS cc_start: 0.8277 (ttmt) cc_final: 0.8049 (mtmt) REVERT: E 357 LEU cc_start: 0.8515 (tt) cc_final: 0.8301 (tt) REVERT: E 379 ARG cc_start: 0.6416 (mtt180) cc_final: 0.5931 (tpt90) REVERT: A 379 ARG cc_start: 0.6600 (mtt180) cc_final: 0.6005 (tpt90) REVERT: B 379 ARG cc_start: 0.6428 (mtt180) cc_final: 0.5932 (tpt90) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2782 time to fit residues: 12.8779 Evaluate side-chains 29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.0980 overall best weight: 4.0188 ------------------------------------------------------------------------------- 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: 0.7848 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3522 Z= 0.400 Angle : 0.725 7.009 4710 Z= 0.384 Chirality : 0.053 0.121 528 Planarity : 0.004 0.027 600 Dihedral : 5.718 17.632 468 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 1.01 % Allowed : 5.56 % Favored : 93.43 % 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: -3.82 (0.25), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.19), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 329 PHE 0.011 0.002 PHE D 378 TYR 0.020 0.004 TYR F 310 ARG 0.004 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 379 ARG cc_start: 0.6422 (mtt180) cc_final: 0.6080 (tpt90) REVERT: D 311 LYS cc_start: 0.7931 (ttmt) cc_final: 0.7646 (mtmt) REVERT: D 379 ARG cc_start: 0.6166 (mtt180) cc_final: 0.5856 (tpt90) REVERT: E 342 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7366 (mp0) REVERT: E 379 ARG cc_start: 0.6452 (mtt180) cc_final: 0.5977 (tpt90) REVERT: F 344 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7533 (mt) REVERT: F 378 PHE cc_start: 0.8206 (t80) cc_final: 0.7680 (t80) REVERT: A 379 ARG cc_start: 0.6672 (mtt180) cc_final: 0.6218 (tpt90) REVERT: B 342 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7443 (mp0) REVERT: B 348 ASP cc_start: 0.7719 (t0) cc_final: 0.7378 (m-30) REVERT: B 379 ARG cc_start: 0.6501 (mtt180) cc_final: 0.6106 (tpt90) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.2139 time to fit residues: 9.3712 Evaluate side-chains 33 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 319 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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: 0.7884 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 3522 Z= 0.467 Angle : 0.754 5.389 4710 Z= 0.398 Chirality : 0.052 0.120 528 Planarity : 0.004 0.020 600 Dihedral : 5.995 18.943 468 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.28 % Allowed : 7.07 % Favored : 89.65 % 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: -3.68 (0.26), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.20), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.011 0.002 PHE D 378 TYR 0.024 0.005 TYR E 310 ARG 0.004 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.444 Fit side-chains REVERT: C 379 ARG cc_start: 0.6390 (mtt180) cc_final: 0.6083 (tpt90) REVERT: D 311 LYS cc_start: 0.7972 (ttmt) cc_final: 0.7656 (mtmt) REVERT: D 379 ARG cc_start: 0.6296 (mtt180) cc_final: 0.5972 (tpt90) REVERT: E 379 ARG cc_start: 0.6644 (mtt180) cc_final: 0.6031 (tpt90) REVERT: A 338 GLU cc_start: 0.7516 (tt0) cc_final: 0.6818 (mt-10) REVERT: A 379 ARG cc_start: 0.6792 (mtt180) cc_final: 0.6280 (tpt90) REVERT: B 379 ARG cc_start: 0.6616 (mtt180) cc_final: 0.6245 (tpt90) outliers start: 13 outliers final: 7 residues processed: 39 average time/residue: 0.2159 time to fit residues: 10.1193 Evaluate side-chains 34 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 356 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3522 Z= 0.240 Angle : 0.583 4.602 4710 Z= 0.302 Chirality : 0.050 0.124 528 Planarity : 0.002 0.018 600 Dihedral : 5.186 14.693 468 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.27 % Allowed : 9.85 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.28), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.21), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.007 0.002 PHE D 378 TYR 0.014 0.003 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.375 Fit side-chains REVERT: C 379 ARG cc_start: 0.6304 (mtt180) cc_final: 0.6033 (tpt90) REVERT: D 379 ARG cc_start: 0.6141 (mtt180) cc_final: 0.5872 (tpt90) REVERT: E 379 ARG cc_start: 0.6566 (mtt180) cc_final: 0.6066 (tpt90) REVERT: A 379 ARG cc_start: 0.6743 (mtt180) cc_final: 0.6231 (tpt90) REVERT: B 379 ARG cc_start: 0.6558 (mtt180) cc_final: 0.6221 (tpt90) outliers start: 9 outliers final: 8 residues processed: 36 average time/residue: 0.2151 time to fit residues: 9.3677 Evaluate side-chains 30 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 0.0370 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3522 Z= 0.257 Angle : 0.578 4.422 4710 Z= 0.301 Chirality : 0.050 0.122 528 Planarity : 0.003 0.019 600 Dihedral : 5.118 15.498 468 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.53 % Allowed : 11.87 % Favored : 85.61 % 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: -3.23 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.007 0.002 PHE A 378 TYR 0.017 0.004 TYR F 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.416 Fit side-chains REVERT: C 379 ARG cc_start: 0.6281 (mtt180) cc_final: 0.6021 (tpt90) REVERT: D 379 ARG cc_start: 0.6146 (mtt180) cc_final: 0.5866 (tpt90) REVERT: E 379 ARG cc_start: 0.6604 (mtt180) cc_final: 0.6047 (tpt90) REVERT: A 338 GLU cc_start: 0.7505 (tt0) cc_final: 0.6806 (mt-10) REVERT: A 379 ARG cc_start: 0.6731 (mtt180) cc_final: 0.6214 (tpt90) REVERT: B 379 ARG cc_start: 0.6588 (mtt180) cc_final: 0.6276 (tpt90) outliers start: 10 outliers final: 9 residues processed: 30 average time/residue: 0.2239 time to fit residues: 8.2149 Evaluate side-chains 30 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 356 SER 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: 9.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3522 Z= 0.398 Angle : 0.653 4.406 4710 Z= 0.348 Chirality : 0.051 0.122 528 Planarity : 0.003 0.020 600 Dihedral : 5.547 16.773 468 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.03 % Allowed : 12.12 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.010 0.002 PHE D 378 TYR 0.020 0.005 TYR F 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.320 Fit side-chains REVERT: C 379 ARG cc_start: 0.6317 (mtt180) cc_final: 0.6058 (tpt90) REVERT: D 379 ARG cc_start: 0.6230 (mtt180) cc_final: 0.5926 (tpt90) REVERT: E 342 GLU cc_start: 0.4002 (OUTLIER) cc_final: 0.2209 (mp0) REVERT: E 379 ARG cc_start: 0.6642 (mtt180) cc_final: 0.6114 (tpt90) REVERT: A 338 GLU cc_start: 0.7542 (tt0) cc_final: 0.6836 (mt-10) REVERT: A 379 ARG cc_start: 0.6796 (mtt180) cc_final: 0.6275 (tpt90) REVERT: B 342 GLU cc_start: 0.3977 (OUTLIER) cc_final: 0.2247 (mp0) REVERT: B 379 ARG cc_start: 0.6597 (mtt180) cc_final: 0.6288 (tpt90) outliers start: 12 outliers final: 7 residues processed: 39 average time/residue: 0.1731 time to fit residues: 8.3574 Evaluate side-chains 37 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 342 GLU 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: 5.9990 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3522 Z= 0.263 Angle : 0.582 4.094 4710 Z= 0.306 Chirality : 0.050 0.121 528 Planarity : 0.003 0.018 600 Dihedral : 5.230 14.748 468 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.78 % Allowed : 13.13 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.16 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.007 0.002 PHE D 378 TYR 0.017 0.004 TYR F 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 0.422 Fit side-chains REVERT: C 379 ARG cc_start: 0.6284 (mtt180) cc_final: 0.6034 (tpt90) REVERT: D 379 ARG cc_start: 0.6217 (mtt180) cc_final: 0.5889 (tpt90) REVERT: E 342 GLU cc_start: 0.4162 (OUTLIER) cc_final: 0.2381 (mp0) REVERT: E 357 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8297 (tt) REVERT: E 379 ARG cc_start: 0.6659 (mtt180) cc_final: 0.6163 (tpt90) REVERT: A 338 GLU cc_start: 0.7481 (tt0) cc_final: 0.6824 (mt-10) REVERT: A 379 ARG cc_start: 0.6763 (mtt180) cc_final: 0.6272 (tpt90) REVERT: B 342 GLU cc_start: 0.4245 (OUTLIER) cc_final: 0.2531 (mp0) REVERT: B 357 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8181 (tt) REVERT: B 379 ARG cc_start: 0.6589 (mtt180) cc_final: 0.6314 (tpt90) outliers start: 11 outliers final: 7 residues processed: 33 average time/residue: 0.1981 time to fit residues: 8.1769 Evaluate side-chains 33 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3522 Z= 0.334 Angle : 0.610 4.004 4710 Z= 0.324 Chirality : 0.050 0.120 528 Planarity : 0.003 0.019 600 Dihedral : 5.380 15.655 468 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.03 % Allowed : 12.88 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.20 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 329 PHE 0.009 0.002 PHE D 378 TYR 0.019 0.004 TYR F 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.432 Fit side-chains REVERT: C 379 ARG cc_start: 0.6293 (mtt180) cc_final: 0.6036 (tpt90) REVERT: D 379 ARG cc_start: 0.6227 (mtt180) cc_final: 0.5920 (tpt90) REVERT: E 342 GLU cc_start: 0.4172 (OUTLIER) cc_final: 0.2448 (mp0) REVERT: E 379 ARG cc_start: 0.6673 (mtt180) cc_final: 0.6188 (tpt90) REVERT: A 338 GLU cc_start: 0.7503 (tt0) cc_final: 0.6836 (mt-10) REVERT: A 379 ARG cc_start: 0.6770 (mtt180) cc_final: 0.6313 (tpt90) REVERT: B 342 GLU cc_start: 0.4230 (OUTLIER) cc_final: 0.2548 (mp0) REVERT: B 379 ARG cc_start: 0.6598 (mtt180) cc_final: 0.6321 (tpt90) outliers start: 12 outliers final: 7 residues processed: 35 average time/residue: 0.1946 time to fit residues: 8.4596 Evaluate side-chains 32 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 342 GLU 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: 0.3980 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3522 Z= 0.223 Angle : 0.574 5.745 4710 Z= 0.293 Chirality : 0.049 0.121 528 Planarity : 0.003 0.018 600 Dihedral : 5.053 13.383 468 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.78 % Allowed : 12.63 % Favored : 84.60 % 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: -3.14 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.006 0.002 PHE D 378 TYR 0.016 0.004 TYR F 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.426 Fit side-chains REVERT: C 379 ARG cc_start: 0.6376 (mtt180) cc_final: 0.6055 (tpt90) REVERT: D 379 ARG cc_start: 0.6210 (mtt180) cc_final: 0.5887 (tpt90) REVERT: E 342 GLU cc_start: 0.4145 (OUTLIER) cc_final: 0.2424 (mp0) REVERT: E 379 ARG cc_start: 0.6627 (mtt180) cc_final: 0.6191 (tpt90) REVERT: A 379 ARG cc_start: 0.6726 (mtt180) cc_final: 0.6297 (tpt90) REVERT: B 342 GLU cc_start: 0.4151 (OUTLIER) cc_final: 0.2474 (mp0) REVERT: B 379 ARG cc_start: 0.6593 (mtt180) cc_final: 0.6322 (tpt90) outliers start: 11 outliers final: 7 residues processed: 34 average time/residue: 0.2035 time to fit residues: 8.5712 Evaluate side-chains 31 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 342 GLU 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: 4.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3522 Z= 0.230 Angle : 0.576 7.093 4710 Z= 0.293 Chirality : 0.049 0.121 528 Planarity : 0.003 0.019 600 Dihedral : 4.992 13.672 468 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.27 % Allowed : 13.89 % Favored : 83.84 % 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: -3.15 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.006 0.002 PHE D 378 TYR 0.017 0.004 TYR F 310 ARG 0.001 0.000 ARG F 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.408 Fit side-chains REVERT: C 379 ARG cc_start: 0.6371 (mtt180) cc_final: 0.6081 (tpt90) REVERT: D 379 ARG cc_start: 0.6191 (mtt180) cc_final: 0.5890 (tpt90) REVERT: E 342 GLU cc_start: 0.4186 (OUTLIER) cc_final: 0.2472 (mp0) REVERT: E 379 ARG cc_start: 0.6649 (mtt180) cc_final: 0.6226 (tpt90) REVERT: A 379 ARG cc_start: 0.6725 (mtt180) cc_final: 0.6296 (tpt90) REVERT: B 342 GLU cc_start: 0.4173 (OUTLIER) cc_final: 0.2496 (mp0) REVERT: B 379 ARG cc_start: 0.6559 (mtt180) cc_final: 0.6311 (tpt90) outliers start: 9 outliers final: 7 residues processed: 30 average time/residue: 0.2097 time to fit residues: 7.8567 Evaluate side-chains 30 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 342 GLU 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: 8.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.134391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.117469 restraints weight = 4630.038| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.55 r_work: 0.3851 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3522 Z= 0.379 Angle : 0.653 6.187 4710 Z= 0.342 Chirality : 0.050 0.120 528 Planarity : 0.003 0.019 600 Dihedral : 5.431 15.859 468 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.53 % Allowed : 13.89 % Favored : 83.59 % 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: -3.25 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 329 PHE 0.010 0.002 PHE D 378 TYR 0.019 0.004 TYR F 310 ARG 0.002 0.001 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1190.00 seconds wall clock time: 22 minutes 41.01 seconds (1361.01 seconds total)