Starting phenix.real_space_refine on Fri Aug 22 13:45:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwl_60532/08_2025/8zwl_60532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwl_60532/08_2025/8zwl_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/cci-nas-00/data/ceres_data/8zwl_60532/08_2025/8zwl_60532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwl_60532/08_2025/8zwl_60532.map" model { file = "/net/cci-nas-00/data/ceres_data/8zwl_60532/08_2025/8zwl_60532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwl_60532/08_2025/8zwl_60532.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3468 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: D, E, F, A, B Time building chain proxies: 0.72, per 1000 atoms: 0.21 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: 0.26 Conformation dependent library (CDL) restraints added in 154.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.12 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: 0.32 Time building geometry restraints manager: 0.37 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: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'A' selection = chain 'B' } 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: 4.830 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.880 Find NCS groups from input model: 0.030 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.000 ------------------------------------------------------------------------------- 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= 0.383 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.002 ARG B 349 TYR 0.015 0.004 TYR D 310 PHE 0.008 0.004 PHE A 378 HIS 0.003 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00829 ( 3522) covalent geometry : angle 0.91781 ( 4710) hydrogen bonds : bond 0.14685 ( 22) hydrogen bonds : angle 5.17429 ( 66) *********************** 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 : 0.150 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: 0.1323 time to fit residues: 5.9997 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 : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.143632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.126557 restraints weight = 4599.362| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.53 r_work: 0.3982 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 3522 Z= 0.120 Angle : 0.575 5.176 4710 Z= 0.300 Chirality : 0.050 0.122 528 Planarity : 0.002 0.015 600 Dihedral : 5.050 14.031 468 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.76 % Allowed : 5.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.70 (0.26), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.20), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 379 TYR 0.014 0.003 TYR F 310 PHE 0.006 0.001 PHE D 378 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3522) covalent geometry : angle 0.57517 ( 4710) hydrogen bonds : bond 0.01444 ( 22) hydrogen bonds : angle 3.70985 ( 66) *********************** 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 41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.149 Fit side-chains REVERT: C 348 ASP cc_start: 0.7579 (t0) cc_final: 0.7129 (m-30) REVERT: C 379 ARG cc_start: 0.7044 (mtt180) cc_final: 0.6180 (tpt90) REVERT: D 348 ASP cc_start: 0.7615 (t0) cc_final: 0.7206 (m-30) REVERT: D 379 ARG cc_start: 0.6832 (mtt180) cc_final: 0.6074 (tpt90) REVERT: E 348 ASP cc_start: 0.7763 (t0) cc_final: 0.7392 (m-30) REVERT: E 379 ARG cc_start: 0.7026 (mtt180) cc_final: 0.6123 (tpt90) REVERT: F 348 ASP cc_start: 0.7543 (t0) cc_final: 0.6949 (m-30) REVERT: A 348 ASP cc_start: 0.7603 (t0) cc_final: 0.7207 (m-30) REVERT: A 379 ARG cc_start: 0.6884 (mtt180) cc_final: 0.6226 (tpt90) REVERT: B 348 ASP cc_start: 0.7699 (t0) cc_final: 0.7497 (m-30) REVERT: B 379 ARG cc_start: 0.6829 (mtt180) cc_final: 0.6203 (tpt90) outliers start: 3 outliers final: 1 residues processed: 39 average time/residue: 0.1090 time to fit residues: 5.0308 Evaluate side-chains 27 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 0.0170 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 368 ASN F 368 ASN B 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.142491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.124914 restraints weight = 4606.503| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.54 r_work: 0.3961 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3853 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3522 Z= 0.146 Angle : 0.568 4.902 4710 Z= 0.295 Chirality : 0.049 0.119 528 Planarity : 0.003 0.017 600 Dihedral : 4.887 15.089 468 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.78 % Allowed : 5.30 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.37 (0.26), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.20), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 379 TYR 0.016 0.004 TYR F 310 PHE 0.007 0.002 PHE A 378 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 3522) covalent geometry : angle 0.56808 ( 4710) hydrogen bonds : bond 0.01531 ( 22) hydrogen bonds : angle 3.37621 ( 66) *********************** 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 28 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 17 time to evaluate : 0.147 Fit side-chains REVERT: C 379 ARG cc_start: 0.7005 (mtt180) cc_final: 0.6218 (tpt90) REVERT: D 379 ARG cc_start: 0.6751 (mtt180) cc_final: 0.6014 (tpt90) REVERT: E 311 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8093 (mtmm) REVERT: E 342 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7674 (mp0) REVERT: E 379 ARG cc_start: 0.6968 (mtt180) cc_final: 0.6101 (tpt90) REVERT: F 344 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8045 (mt) REVERT: A 379 ARG cc_start: 0.7097 (mtt180) cc_final: 0.6280 (tpt90) REVERT: B 342 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7758 (mp0) REVERT: B 357 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8548 (tt) REVERT: B 379 ARG cc_start: 0.6896 (mtt180) cc_final: 0.6285 (tpt90) outliers start: 11 outliers final: 5 residues processed: 27 average time/residue: 0.1279 time to fit residues: 4.0294 Evaluate side-chains 24 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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 357 LEU Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 0.1980 chunk 7 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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** F 368 ASN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.138642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.121529 restraints weight = 4621.069| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.50 r_work: 0.3912 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3522 Z= 0.178 Angle : 0.585 5.705 4710 Z= 0.305 Chirality : 0.049 0.119 528 Planarity : 0.003 0.019 600 Dihedral : 5.116 15.385 468 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.78 % Allowed : 6.31 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.17 (0.27), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.21), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 349 TYR 0.017 0.004 TYR F 310 PHE 0.010 0.002 PHE F 378 HIS 0.003 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 3522) covalent geometry : angle 0.58492 ( 4710) hydrogen bonds : bond 0.01189 ( 22) hydrogen bonds : angle 3.32689 ( 66) *********************** 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 33 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 0.147 Fit side-chains REVERT: C 379 ARG cc_start: 0.7048 (mtt180) cc_final: 0.6268 (tpt90) REVERT: D 379 ARG cc_start: 0.6803 (mtt180) cc_final: 0.6046 (tpt90) REVERT: E 342 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7638 (mp0) REVERT: E 379 ARG cc_start: 0.7085 (mtt180) cc_final: 0.6111 (tpt90) REVERT: F 344 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8023 (mt) REVERT: F 378 PHE cc_start: 0.8364 (t80) cc_final: 0.7987 (t80) REVERT: A 379 ARG cc_start: 0.7205 (mtt180) cc_final: 0.6364 (tpt90) REVERT: B 342 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7787 (mp0) REVERT: B 379 ARG cc_start: 0.6929 (mtt180) cc_final: 0.6362 (tpt90) outliers start: 11 outliers final: 8 residues processed: 31 average time/residue: 0.1067 time to fit residues: 3.9601 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 : 0.141 ------------------------------------------------------------------------------- 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 344 LEU 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 28 optimal weight: 0.0000 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 3 optimal weight: 0.2980 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.143181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.125864 restraints weight = 4545.903| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.52 r_work: 0.3959 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3850 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2523 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= 0.107 Angle : 0.502 4.656 4710 Z= 0.260 Chirality : 0.048 0.126 528 Planarity : 0.002 0.021 600 Dihedral : 4.707 12.468 468 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.54 % Allowed : 5.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 379 TYR 0.013 0.003 TYR F 310 PHE 0.008 0.001 PHE F 378 HIS 0.002 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 3522) covalent geometry : angle 0.50232 ( 4710) hydrogen bonds : bond 0.01052 ( 22) hydrogen bonds : angle 3.37104 ( 66) *********************** 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 29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 15 time to evaluate : 0.137 Fit side-chains REVERT: C 344 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8187 (mt) REVERT: C 379 ARG cc_start: 0.7043 (mtt180) cc_final: 0.6298 (tpt90) REVERT: D 379 ARG cc_start: 0.6955 (mtt180) cc_final: 0.6100 (tpt90) REVERT: E 379 ARG cc_start: 0.7171 (mtt180) cc_final: 0.6227 (tpt90) REVERT: F 344 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8081 (mt) REVERT: A 379 ARG cc_start: 0.7121 (mtt180) cc_final: 0.6341 (tpt90) REVERT: B 357 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8533 (tt) REVERT: B 379 ARG cc_start: 0.6960 (mtt180) cc_final: 0.6342 (tpt90) outliers start: 14 outliers final: 9 residues processed: 25 average time/residue: 0.1188 time to fit residues: 3.5575 Evaluate side-chains 26 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 14 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 344 LEU 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 348 ASP Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 0.0570 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 overall best weight: 2.7504 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.139002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.122169 restraints weight = 4583.745| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.52 r_work: 0.3910 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3522 Z= 0.173 Angle : 0.559 5.288 4710 Z= 0.291 Chirality : 0.048 0.119 528 Planarity : 0.003 0.021 600 Dihedral : 4.962 14.912 468 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.54 % Allowed : 7.83 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.04 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 349 TYR 0.017 0.004 TYR F 310 PHE 0.008 0.002 PHE F 378 HIS 0.003 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 3522) covalent geometry : angle 0.55935 ( 4710) hydrogen bonds : bond 0.01170 ( 22) hydrogen bonds : angle 3.39847 ( 66) *********************** 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 35 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 21 time to evaluate : 0.151 Fit side-chains REVERT: C 344 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8067 (mt) REVERT: C 379 ARG cc_start: 0.6962 (mtt180) cc_final: 0.6246 (tpt90) REVERT: D 379 ARG cc_start: 0.6912 (mtt180) cc_final: 0.6052 (tpt90) REVERT: E 342 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7675 (mp0) REVERT: E 379 ARG cc_start: 0.7198 (mtt180) cc_final: 0.6197 (tpt90) REVERT: F 344 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7946 (mt) REVERT: A 379 ARG cc_start: 0.7164 (mtt180) cc_final: 0.6313 (tpt90) REVERT: B 342 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7764 (mp0) REVERT: B 357 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8514 (tt) REVERT: B 379 ARG cc_start: 0.6972 (mtt180) cc_final: 0.6321 (tpt90) outliers start: 14 outliers final: 9 residues processed: 33 average time/residue: 0.0812 time to fit residues: 3.2812 Evaluate side-chains 33 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 21 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 344 LEU 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 344 LEU 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 348 ASP Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4228 r_free = 0.4228 target = 0.140602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.123367 restraints weight = 4558.894| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.53 r_work: 0.3926 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 3522 Z= 0.134 Angle : 0.527 4.697 4710 Z= 0.271 Chirality : 0.048 0.121 528 Planarity : 0.003 0.020 600 Dihedral : 4.788 12.654 468 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.28 % Allowed : 9.60 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.07 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.014 0.003 TYR F 310 PHE 0.008 0.002 PHE F 378 HIS 0.003 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 3522) covalent geometry : angle 0.52681 ( 4710) hydrogen bonds : bond 0.01040 ( 22) hydrogen bonds : angle 3.39551 ( 66) *********************** 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 26 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 13 time to evaluate : 0.084 Fit side-chains REVERT: C 344 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8114 (mt) REVERT: C 379 ARG cc_start: 0.7096 (mtt180) cc_final: 0.6316 (tpt90) REVERT: D 379 ARG cc_start: 0.6925 (mtt180) cc_final: 0.6068 (tpt90) REVERT: E 379 ARG cc_start: 0.7213 (mtt180) cc_final: 0.6284 (tpt90) REVERT: F 344 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.7988 (mt) REVERT: A 379 ARG cc_start: 0.7121 (mtt180) cc_final: 0.6331 (tpt90) REVERT: B 342 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7861 (mp0) REVERT: B 357 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8511 (tt) REVERT: B 379 ARG cc_start: 0.7040 (mtt180) cc_final: 0.6392 (tpt90) outliers start: 13 outliers final: 9 residues processed: 25 average time/residue: 0.0786 time to fit residues: 2.4433 Evaluate side-chains 25 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 13 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 344 LEU 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 344 LEU 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 348 ASP 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 39 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 overall best weight: 2.6784 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.138298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.121441 restraints weight = 4630.988| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.54 r_work: 0.3900 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3522 Z= 0.168 Angle : 0.548 4.937 4710 Z= 0.285 Chirality : 0.048 0.118 528 Planarity : 0.003 0.021 600 Dihedral : 4.912 13.920 468 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.28 % Allowed : 9.85 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.08 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.016 0.004 TYR F 310 PHE 0.008 0.002 PHE F 378 HIS 0.003 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 3522) covalent geometry : angle 0.54840 ( 4710) hydrogen bonds : bond 0.01197 ( 22) hydrogen bonds : angle 3.52045 ( 66) *********************** 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 37 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.141 Fit side-chains REVERT: C 344 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8105 (mt) REVERT: C 379 ARG cc_start: 0.7102 (mtt180) cc_final: 0.6331 (tpt90) REVERT: D 379 ARG cc_start: 0.6977 (mtt180) cc_final: 0.6106 (tpt90) REVERT: E 342 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7736 (mp0) REVERT: E 379 ARG cc_start: 0.7213 (mtt180) cc_final: 0.6304 (tpt90) REVERT: F 344 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8073 (mt) REVERT: A 379 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6343 (tpt90) REVERT: B 342 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7833 (mp0) REVERT: B 357 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8569 (tt) REVERT: B 379 ARG cc_start: 0.7045 (mtt180) cc_final: 0.6430 (tpt90) outliers start: 13 outliers final: 9 residues processed: 36 average time/residue: 0.0740 time to fit residues: 3.3024 Evaluate side-chains 36 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 344 LEU 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 344 LEU 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 348 ASP Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.4249 r_free = 0.4249 target = 0.142143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.124800 restraints weight = 4459.003| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.52 r_work: 0.3950 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 3522 Z= 0.113 Angle : 0.507 4.430 4710 Z= 0.259 Chirality : 0.048 0.119 528 Planarity : 0.003 0.020 600 Dihedral : 4.645 11.779 468 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.03 % Allowed : 11.11 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.01 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.014 0.003 TYR F 310 PHE 0.008 0.002 PHE F 378 HIS 0.003 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 3522) covalent geometry : angle 0.50731 ( 4710) hydrogen bonds : bond 0.01020 ( 22) hydrogen bonds : angle 3.53832 ( 66) *********************** 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 27 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 15 time to evaluate : 0.124 Fit side-chains REVERT: C 344 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8170 (mt) REVERT: C 379 ARG cc_start: 0.7148 (mtt180) cc_final: 0.6348 (tpt90) REVERT: D 379 ARG cc_start: 0.6992 (mtt180) cc_final: 0.6093 (tpt90) REVERT: E 379 ARG cc_start: 0.7189 (mtt180) cc_final: 0.6289 (tpt90) REVERT: F 344 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8091 (mt) REVERT: A 379 ARG cc_start: 0.7083 (mtt180) cc_final: 0.6313 (tpt90) REVERT: B 357 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8536 (tt) REVERT: B 379 ARG cc_start: 0.7038 (mtt180) cc_final: 0.6456 (tpt90) outliers start: 12 outliers final: 9 residues processed: 26 average time/residue: 0.0996 time to fit residues: 3.1099 Evaluate side-chains 27 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 15 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 344 LEU 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 344 LEU 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 348 ASP Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 0.0870 chunk 11 optimal weight: 0.0020 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.2172 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.140617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.123573 restraints weight = 4502.290| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.53 r_work: 0.3932 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3522 Z= 0.140 Angle : 0.519 4.699 4710 Z= 0.268 Chirality : 0.048 0.118 528 Planarity : 0.003 0.020 600 Dihedral : 4.690 12.481 468 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.03 % Allowed : 11.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.00 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.015 0.003 TYR F 310 PHE 0.008 0.002 PHE F 378 HIS 0.003 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3522) covalent geometry : angle 0.51929 ( 4710) hydrogen bonds : bond 0.01104 ( 22) hydrogen bonds : angle 3.57496 ( 66) ********************** 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 34 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 22 time to evaluate : 0.090 Fit side-chains REVERT: C 344 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8162 (mt) REVERT: C 379 ARG cc_start: 0.7141 (mtt180) cc_final: 0.6349 (tpt90) REVERT: D 379 ARG cc_start: 0.6995 (mtt180) cc_final: 0.6104 (tpt90) REVERT: E 342 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7739 (mp0) REVERT: E 379 ARG cc_start: 0.7150 (mtt180) cc_final: 0.6326 (tpt90) REVERT: F 344 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8069 (mt) REVERT: A 379 ARG cc_start: 0.7074 (mtt180) cc_final: 0.6333 (tpt90) REVERT: B 342 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7847 (mp0) REVERT: B 357 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8567 (tt) REVERT: B 379 ARG cc_start: 0.7055 (mtt180) cc_final: 0.6467 (tpt90) outliers start: 12 outliers final: 9 residues processed: 33 average time/residue: 0.0743 time to fit residues: 2.9683 Evaluate side-chains 34 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 22 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 344 LEU 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 344 LEU 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 348 ASP Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 0.0970 chunk 5 optimal weight: 8.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.136373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.119696 restraints weight = 4636.165| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.52 r_work: 0.3875 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3522 Z= 0.234 Angle : 0.612 5.222 4710 Z= 0.323 Chirality : 0.049 0.116 528 Planarity : 0.003 0.021 600 Dihedral : 5.207 14.688 468 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.03 % Allowed : 12.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.08 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.019 0.004 TYR F 310 PHE 0.010 0.002 PHE D 378 HIS 0.004 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 3522) covalent geometry : angle 0.61190 ( 4710) hydrogen bonds : bond 0.01412 ( 22) hydrogen bonds : angle 3.51535 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1026.34 seconds wall clock time: 18 minutes 30.02 seconds (1110.02 seconds total)