Starting phenix.real_space_refine on Fri Aug 2 16:06:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwl_60532/08_2024/8zwl_60532.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwl_60532/08_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_60532/08_2024/8zwl_60532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwl_60532/08_2024/8zwl_60532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwl_60532/08_2024/8zwl_60532.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwl_60532/08_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 Residue "C GLU 342": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3468 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "D" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} 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} Chain: "B" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 3.24, per 1000 atoms: 0.93 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 - 3.50 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: 1.22 Conformation dependent library (CDL) restraints added in 593.2 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: 0.38 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: 0.66 Time building geometry restraints manager: 1.35 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: 101.90 - 107.82: 246 107.82 - 113.74: 1950 113.74 - 119.66: 830 119.66 - 125.58: 1642 125.58 - 131.49: 42 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.360 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.550 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.407 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: 0.2677 time to fit residues: 12.4066 Evaluate side-chains 29 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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: 9.9990 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 fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.411 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: 0.2140 time to fit residues: 9.3320 Evaluate side-chains 33 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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: 8.9990 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.7876 moved from start: 0.2208 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= 0.428 Angle : 0.722 5.120 4710 Z= 0.381 Chirality : 0.051 0.119 528 Planarity : 0.003 0.020 600 Dihedral : 5.833 18.049 468 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.28 % Allowed : 6.06 % Favored : 90.66 % 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: -3.64 (0.26), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.20), 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 0.024 0.005 TYR E 310 ARG 0.003 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 38 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 25 time to evaluate : 0.400 Fit side-chains REVERT: C 379 ARG cc_start: 0.6347 (mtt180) cc_final: 0.6029 (tpt90) REVERT: D 311 LYS cc_start: 0.7926 (ttmt) cc_final: 0.7625 (mtmt) REVERT: D 379 ARG cc_start: 0.6256 (mtt180) cc_final: 0.5930 (tpt90) REVERT: E 379 ARG cc_start: 0.6610 (mtt180) cc_final: 0.6012 (tpt90) REVERT: A 338 GLU cc_start: 0.7507 (tt0) cc_final: 0.6810 (mt-10) REVERT: A 379 ARG cc_start: 0.6775 (mtt180) cc_final: 0.6250 (tpt90) REVERT: B 379 ARG cc_start: 0.6595 (mtt180) cc_final: 0.6267 (tpt90) outliers start: 13 outliers final: 7 residues processed: 36 average time/residue: 0.2035 time to fit residues: 8.9365 Evaluate side-chains 30 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 23 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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: 5.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.6182 ------------------------------------------------------------------------------- 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: 0.7817 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3522 Z= 0.171 Angle : 0.547 4.358 4710 Z= 0.279 Chirality : 0.049 0.123 528 Planarity : 0.002 0.018 600 Dihedral : 4.967 13.338 468 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.77 % Allowed : 9.34 % Favored : 88.89 % 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: -3.36 (0.28), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.21), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.005 0.001 PHE D 378 TYR 0.012 0.003 TYR C 310 ARG 0.001 0.000 ARG C 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 34 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.415 Fit side-chains REVERT: C 379 ARG cc_start: 0.6284 (mtt180) cc_final: 0.6019 (tpt90) REVERT: D 379 ARG cc_start: 0.6063 (mtt180) cc_final: 0.5816 (tpt90) REVERT: E 379 ARG cc_start: 0.6516 (mtt180) cc_final: 0.6011 (tpt90) REVERT: A 379 ARG cc_start: 0.6714 (mtt180) cc_final: 0.6192 (tpt90) REVERT: B 379 ARG cc_start: 0.6497 (mtt180) cc_final: 0.6223 (tpt90) outliers start: 7 outliers final: 7 residues processed: 33 average time/residue: 0.2530 time to fit residues: 9.9038 Evaluate side-chains 26 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 19 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C 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: 9.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** B 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 3522 Z= 0.548 Angle : 0.754 5.014 4710 Z= 0.405 Chirality : 0.053 0.129 528 Planarity : 0.004 0.021 600 Dihedral : 5.971 19.280 468 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % 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: -3.42 (0.28), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 329 PHE 0.012 0.003 PHE D 378 TYR 0.024 0.006 TYR F 310 ARG 0.004 0.001 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 46 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.416 Fit side-chains REVERT: C 379 ARG cc_start: 0.6382 (mtt180) cc_final: 0.6076 (tpt90) REVERT: D 379 ARG cc_start: 0.6251 (mtt180) cc_final: 0.5938 (tpt90) REVERT: E 379 ARG cc_start: 0.6633 (mtt180) cc_final: 0.6094 (tpt90) REVERT: A 379 ARG cc_start: 0.6848 (mtt180) cc_final: 0.6242 (tpt90) REVERT: B 342 GLU cc_start: 0.4057 (OUTLIER) cc_final: 0.2304 (mp0) REVERT: B 379 ARG cc_start: 0.6643 (mtt180) cc_final: 0.6282 (tpt90) outliers start: 11 outliers final: 7 residues processed: 43 average time/residue: 0.1669 time to fit residues: 9.0930 Evaluate side-chains 42 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 342 GLU 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: 6.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 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** B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3522 Z= 0.231 Angle : 0.576 4.075 4710 Z= 0.302 Chirality : 0.050 0.122 528 Planarity : 0.002 0.018 600 Dihedral : 5.272 13.906 468 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.78 % Allowed : 13.38 % 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: -3.22 (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 0.003 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 B 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 32 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 21 time to evaluate : 0.402 Fit side-chains REVERT: C 379 ARG cc_start: 0.6319 (mtt180) cc_final: 0.6064 (tpt90) REVERT: D 379 ARG cc_start: 0.6229 (mtt180) cc_final: 0.5888 (tpt90) REVERT: E 342 GLU cc_start: 0.4141 (OUTLIER) cc_final: 0.2314 (mp0) REVERT: E 379 ARG cc_start: 0.6656 (mtt180) cc_final: 0.6123 (tpt90) REVERT: A 338 GLU cc_start: 0.7603 (tt0) cc_final: 0.6947 (mt-10) REVERT: A 379 ARG cc_start: 0.6739 (mtt180) cc_final: 0.6251 (tpt90) REVERT: B 379 ARG cc_start: 0.6580 (mtt180) cc_final: 0.6308 (tpt90) outliers start: 11 outliers final: 7 residues processed: 30 average time/residue: 0.1917 time to fit residues: 7.1876 Evaluate side-chains 29 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 21 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 0.4980 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- 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: 0.7877 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3522 Z= 0.388 Angle : 0.655 4.310 4710 Z= 0.349 Chirality : 0.051 0.122 528 Planarity : 0.003 0.019 600 Dihedral : 5.565 16.344 468 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % 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: -3.23 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (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 F 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 41 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 29 time to evaluate : 0.400 Fit side-chains REVERT: C 379 ARG cc_start: 0.6328 (mtt180) cc_final: 0.6072 (tpt90) REVERT: D 379 ARG cc_start: 0.6259 (mtt180) cc_final: 0.5922 (tpt90) REVERT: E 342 GLU cc_start: 0.4268 (OUTLIER) cc_final: 0.2510 (mp0) REVERT: E 379 ARG cc_start: 0.6642 (mtt180) cc_final: 0.6136 (tpt90) REVERT: A 338 GLU cc_start: 0.7626 (tt0) cc_final: 0.6974 (mt-10) REVERT: A 379 ARG cc_start: 0.6789 (mtt180) cc_final: 0.6314 (tpt90) REVERT: B 342 GLU cc_start: 0.4023 (OUTLIER) cc_final: 0.2320 (mp0) REVERT: B 379 ARG cc_start: 0.6575 (mtt180) cc_final: 0.6299 (tpt90) outliers start: 12 outliers final: 7 residues processed: 40 average time/residue: 0.1676 time to fit residues: 8.4505 Evaluate side-chains 37 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 28 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.0040 overall best weight: 2.3398 ------------------------------------------------------------------------------- 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: 0.7849 moved from start: 0.3128 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= 0.227 Angle : 0.581 5.109 4710 Z= 0.299 Chirality : 0.050 0.122 528 Planarity : 0.002 0.019 600 Dihedral : 5.165 13.282 468 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.02 % Allowed : 13.89 % 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: -3.15 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.23), 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 0.002 0.000 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 31 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 23 time to evaluate : 0.385 Fit side-chains REVERT: C 379 ARG cc_start: 0.6300 (mtt180) cc_final: 0.6028 (tpt90) REVERT: D 379 ARG cc_start: 0.6216 (mtt180) cc_final: 0.5890 (tpt90) REVERT: E 342 GLU cc_start: 0.4233 (OUTLIER) cc_final: 0.2478 (mp0) REVERT: E 379 ARG cc_start: 0.6642 (mtt180) cc_final: 0.6182 (tpt90) REVERT: A 338 GLU cc_start: 0.7583 (tt0) cc_final: 0.6946 (mt-10) REVERT: A 379 ARG cc_start: 0.6745 (mtt180) cc_final: 0.6300 (tpt90) REVERT: B 379 ARG cc_start: 0.6551 (mtt180) cc_final: 0.6308 (tpt90) outliers start: 8 outliers final: 7 residues processed: 31 average time/residue: 0.1950 time to fit residues: 7.5650 Evaluate side-chains 30 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 22 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.7863 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3522 Z= 0.304 Angle : 0.604 3.949 4710 Z= 0.317 Chirality : 0.050 0.120 528 Planarity : 0.003 0.019 600 Dihedral : 5.282 14.893 468 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % 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: -3.19 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.008 0.002 PHE D 378 TYR 0.018 0.004 TYR F 310 ARG 0.002 0.001 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 33 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 24 time to evaluate : 0.401 Fit side-chains REVERT: C 379 ARG cc_start: 0.6347 (mtt180) cc_final: 0.6037 (tpt90) REVERT: D 379 ARG cc_start: 0.6226 (mtt180) cc_final: 0.5913 (tpt90) REVERT: E 342 GLU cc_start: 0.4304 (OUTLIER) cc_final: 0.2577 (mp0) REVERT: E 379 ARG cc_start: 0.6690 (mtt180) cc_final: 0.6247 (tpt90) REVERT: A 338 GLU cc_start: 0.7567 (tt0) cc_final: 0.6927 (mt-10) REVERT: A 379 ARG cc_start: 0.6759 (mtt180) cc_final: 0.6312 (tpt90) REVERT: B 342 GLU cc_start: 0.4225 (OUTLIER) cc_final: 0.2607 (mp0) REVERT: B 379 ARG cc_start: 0.6586 (mtt180) cc_final: 0.6275 (tpt90) outliers start: 9 outliers final: 7 residues processed: 32 average time/residue: 0.1830 time to fit residues: 7.3511 Evaluate side-chains 33 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 24 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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: 5.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 0.0870 chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- 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: 0.7842 moved from start: 0.3241 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= 0.217 Angle : 0.558 4.568 4710 Z= 0.288 Chirality : 0.049 0.122 528 Planarity : 0.003 0.018 600 Dihedral : 5.033 12.936 468 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.27 % Allowed : 14.14 % 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: -3.12 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (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 0.003 TYR F 310 ARG 0.001 0.000 ARG D 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 31 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 22 time to evaluate : 0.416 Fit side-chains REVERT: C 379 ARG cc_start: 0.6368 (mtt180) cc_final: 0.6103 (tpt90) REVERT: D 379 ARG cc_start: 0.6206 (mtt180) cc_final: 0.5884 (tpt90) REVERT: E 342 GLU cc_start: 0.4271 (OUTLIER) cc_final: 0.2551 (mp0) REVERT: E 379 ARG cc_start: 0.6599 (mtt180) cc_final: 0.6259 (tpt90) REVERT: A 338 GLU cc_start: 0.7550 (tt0) cc_final: 0.6910 (mt-10) REVERT: A 379 ARG cc_start: 0.6731 (mtt180) cc_final: 0.6299 (tpt90) REVERT: B 342 GLU cc_start: 0.4339 (OUTLIER) cc_final: 0.2669 (mp0) REVERT: B 379 ARG cc_start: 0.6602 (mtt180) cc_final: 0.6309 (tpt90) outliers start: 9 outliers final: 7 residues processed: 31 average time/residue: 0.1963 time to fit residues: 7.5743 Evaluate side-chains 30 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 21 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.0030 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- 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 = 0.4211 r_free = 0.4211 target = 0.137814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.120475 restraints weight = 4577.223| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.55 r_work: 0.3899 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3522 Z= 0.251 Angle : 0.566 3.928 4710 Z= 0.295 Chirality : 0.049 0.121 528 Planarity : 0.003 0.020 600 Dihedral : 5.056 13.941 468 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.27 % Allowed : 14.39 % Favored : 83.33 % 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 0.007 0.002 PHE D 378 TYR 0.017 0.004 TYR F 310 ARG 0.001 0.000 ARG F 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1164.21 seconds wall clock time: 21 minutes 43.59 seconds (1303.59 seconds total)