Starting phenix.real_space_refine on Wed Mar 5 20:21:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwl_60532/03_2025/8zwl_60532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwl_60532/03_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_60532/03_2025/8zwl_60532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwl_60532/03_2025/8zwl_60532.map" model { file = "/net/cci-nas-00/data/ceres_data/8zwl_60532/03_2025/8zwl_60532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwl_60532/03_2025/8zwl_60532.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3468 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.30, per 1000 atoms: 0.66 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: 0.81 Conformation dependent library (CDL) restraints added in 429.4 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: 0.40 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: 0.74 Time building geometry restraints manager: 0.97 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.740 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.038 3522 Z= 0.575 Angle : 0.918 6.791 4710 Z= 0.496 Chirality : 0.063 0.308 528 Planarity : 0.004 0.017 600 Dihedral : 11.351 44.902 1350 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.24), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.19), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 330 PHE 0.008 0.004 PHE A 378 TYR 0.015 0.004 TYR D 310 ARG 0.006 0.002 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.425 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: 0.2843 time to fit residues: 13.1183 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 : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.0980 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.136053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.119181 restraints weight = 4553.531| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.56 r_work: 0.3883 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3522 Z= 0.400 Angle : 0.725 7.009 4710 Z= 0.384 Chirality : 0.053 0.121 528 Planarity : 0.004 0.027 600 Dihedral : 5.718 17.632 468 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 1.01 % Allowed : 5.56 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.25), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.19), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 329 PHE 0.011 0.002 PHE D 378 TYR 0.020 0.004 TYR F 310 ARG 0.004 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 379 ARG cc_start: 0.7065 (mtt180) cc_final: 0.6311 (tpt90) REVERT: D 311 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7931 (mtmt) REVERT: D 379 ARG cc_start: 0.6784 (mtt180) cc_final: 0.6057 (tpt90) REVERT: E 342 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7604 (mp0) REVERT: E 379 ARG cc_start: 0.7016 (mtt180) cc_final: 0.6125 (tpt90) REVERT: F 344 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8060 (mt) REVERT: F 378 PHE cc_start: 0.8442 (t80) cc_final: 0.7980 (t80) REVERT: A 379 ARG cc_start: 0.7038 (mtt180) cc_final: 0.6351 (tpt90) REVERT: B 342 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7712 (mp0) REVERT: B 348 ASP cc_start: 0.7895 (t0) cc_final: 0.7560 (m-30) REVERT: B 379 ARG cc_start: 0.6923 (mtt180) cc_final: 0.6246 (tpt90) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.2178 time to fit residues: 9.5158 Evaluate side-chains 33 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 25 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.139366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.121999 restraints weight = 4648.199| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.53 r_work: 0.3911 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2057 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= 0.259 Angle : 0.595 4.821 4710 Z= 0.309 Chirality : 0.049 0.120 528 Planarity : 0.003 0.018 600 Dihedral : 5.173 14.342 468 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.28 % Allowed : 4.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.26), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.007 0.002 PHE D 378 TYR 0.015 0.003 TYR E 310 ARG 0.002 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 36 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 23 time to evaluate : 0.377 Fit side-chains REVERT: C 379 ARG cc_start: 0.7070 (mtt180) cc_final: 0.6297 (tpt90) REVERT: D 379 ARG cc_start: 0.6803 (mtt180) cc_final: 0.6038 (tpt90) REVERT: E 379 ARG cc_start: 0.7119 (mtt180) cc_final: 0.6131 (tpt90) REVERT: F 378 PHE cc_start: 0.8450 (t80) cc_final: 0.8089 (t80) REVERT: A 379 ARG cc_start: 0.7052 (mtt180) cc_final: 0.6344 (tpt90) REVERT: B 342 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7812 (mp0) REVERT: B 357 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8539 (tt) REVERT: B 379 ARG cc_start: 0.6982 (mtt180) cc_final: 0.6390 (tpt90) outliers start: 13 outliers final: 8 residues processed: 34 average time/residue: 0.2029 time to fit residues: 8.4180 Evaluate side-chains 28 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B 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 25 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.140093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.122980 restraints weight = 4631.375| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.48 r_work: 0.3921 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3522 Z= 0.223 Angle : 0.556 4.187 4710 Z= 0.288 Chirality : 0.049 0.122 528 Planarity : 0.003 0.019 600 Dihedral : 4.942 14.318 468 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.02 % Allowed : 7.07 % 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 (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: -3.24 (0.28), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.21), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.006 0.002 PHE D 378 TYR 0.015 0.003 TYR F 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.416 Fit side-chains REVERT: C 379 ARG cc_start: 0.7112 (mtt180) cc_final: 0.6328 (tpt90) REVERT: D 379 ARG cc_start: 0.6819 (mtt180) cc_final: 0.6060 (tpt90) REVERT: E 342 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7698 (mp0) REVERT: E 379 ARG cc_start: 0.7116 (mtt180) cc_final: 0.6202 (tpt90) REVERT: F 378 PHE cc_start: 0.8399 (t80) cc_final: 0.8091 (t80) REVERT: A 379 ARG cc_start: 0.7161 (mtt180) cc_final: 0.6379 (tpt90) REVERT: B 342 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7838 (mp0) REVERT: B 379 ARG cc_start: 0.6968 (mtt180) cc_final: 0.6374 (tpt90) outliers start: 8 outliers final: 8 residues processed: 31 average time/residue: 0.2741 time to fit residues: 10.2272 Evaluate side-chains 29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain A residue 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 21 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.0170 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 0.0970 chunk 28 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- 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 = 0.4283 r_free = 0.4283 target = 0.145812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.127927 restraints weight = 4582.276| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.56 r_work: 0.3980 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3870 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3522 Z= 0.138 Angle : 0.486 3.701 4710 Z= 0.249 Chirality : 0.048 0.120 528 Planarity : 0.002 0.017 600 Dihedral : 4.535 12.013 468 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.53 % Allowed : 8.08 % Favored : 89.39 % 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: -3.08 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.004 0.001 PHE A 378 TYR 0.012 0.002 TYR F 310 ARG 0.001 0.000 ARG B 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 30 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.337 Fit side-chains REVERT: C 379 ARG cc_start: 0.7050 (mtt180) cc_final: 0.6283 (tpt90) REVERT: D 379 ARG cc_start: 0.6881 (mtt180) cc_final: 0.6100 (tpt90) REVERT: E 379 ARG cc_start: 0.7181 (mtt180) cc_final: 0.6222 (tpt90) REVERT: F 378 PHE cc_start: 0.8432 (t80) cc_final: 0.7968 (t80) REVERT: A 379 ARG cc_start: 0.7100 (mtt180) cc_final: 0.6328 (tpt90) REVERT: B 342 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7800 (mp0) REVERT: B 357 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8587 (tt) REVERT: B 379 ARG cc_start: 0.7013 (mtt180) cc_final: 0.6320 (tpt90) outliers start: 10 outliers final: 7 residues processed: 27 average time/residue: 0.2018 time to fit residues: 6.7221 Evaluate side-chains 26 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain A residue 319 THR 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 16 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.138421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.121368 restraints weight = 4638.781| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.52 r_work: 0.3899 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2664 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= 0.271 Angle : 0.551 3.967 4710 Z= 0.289 Chirality : 0.049 0.120 528 Planarity : 0.003 0.019 600 Dihedral : 4.915 15.130 468 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.78 % Allowed : 10.86 % Favored : 86.36 % 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: -3.07 (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 HIS 0.002 0.001 HIS D 329 PHE 0.008 0.002 PHE D 378 TYR 0.017 0.004 TYR F 310 ARG 0.002 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 35 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.368 Fit side-chains REVERT: C 379 ARG cc_start: 0.7035 (mtt180) cc_final: 0.6307 (tpt90) REVERT: D 379 ARG cc_start: 0.6876 (mtt180) cc_final: 0.6088 (tpt90) REVERT: E 342 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7679 (mp0) REVERT: E 379 ARG cc_start: 0.7244 (mtt180) cc_final: 0.6220 (tpt90) REVERT: F 378 PHE cc_start: 0.8429 (t80) cc_final: 0.8155 (t80) REVERT: A 379 ARG cc_start: 0.7108 (mtt180) cc_final: 0.6350 (tpt90) REVERT: B 342 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7815 (mp0) REVERT: B 357 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8611 (tt) REVERT: B 379 ARG cc_start: 0.6990 (mtt180) cc_final: 0.6330 (tpt90) outliers start: 11 outliers final: 8 residues processed: 32 average time/residue: 0.1923 time to fit residues: 7.6411 Evaluate side-chains 33 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 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 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 19 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.137096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.120193 restraints weight = 4628.762| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.53 r_work: 0.3882 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2809 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= 0.290 Angle : 0.575 3.947 4710 Z= 0.301 Chirality : 0.049 0.119 528 Planarity : 0.003 0.021 600 Dihedral : 5.076 13.901 468 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.78 % Allowed : 12.12 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 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 0.001 0.000 ARG D 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 32 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.410 Fit side-chains REVERT: C 379 ARG cc_start: 0.7060 (mtt180) cc_final: 0.6336 (tpt90) REVERT: D 379 ARG cc_start: 0.6966 (mtt180) cc_final: 0.6116 (tpt90) REVERT: E 357 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8688 (tt) REVERT: E 379 ARG cc_start: 0.7257 (mtt180) cc_final: 0.6268 (tpt90) REVERT: A 338 GLU cc_start: 0.8003 (tt0) cc_final: 0.7400 (mt-10) REVERT: A 379 ARG cc_start: 0.7195 (mtt180) cc_final: 0.6372 (tpt90) REVERT: B 342 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7792 (mp0) REVERT: B 357 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8524 (tt) REVERT: B 379 ARG cc_start: 0.7038 (mtt180) cc_final: 0.6382 (tpt90) outliers start: 11 outliers final: 8 residues processed: 31 average time/residue: 0.1968 time to fit residues: 7.6380 Evaluate side-chains 31 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 21 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 E residue 357 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 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 30 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.135442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.118800 restraints weight = 4665.253| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.50 r_work: 0.3857 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3522 Z= 0.346 Angle : 0.608 3.839 4710 Z= 0.322 Chirality : 0.050 0.119 528 Planarity : 0.003 0.021 600 Dihedral : 5.256 15.252 468 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.53 % Allowed : 13.64 % 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: -3.12 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 329 PHE 0.009 0.002 PHE D 378 TYR 0.019 0.004 TYR F 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.375 Fit side-chains REVERT: C 379 ARG cc_start: 0.7033 (mtt180) cc_final: 0.6291 (tpt90) REVERT: D 379 ARG cc_start: 0.6927 (mtt180) cc_final: 0.6062 (tpt90) REVERT: E 342 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7698 (mp0) REVERT: E 379 ARG cc_start: 0.7212 (mtt180) cc_final: 0.6291 (tpt90) REVERT: A 338 GLU cc_start: 0.8047 (tt0) cc_final: 0.7363 (mt-10) REVERT: A 379 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6334 (tpt90) REVERT: B 342 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7787 (mp0) REVERT: B 357 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8551 (tt) REVERT: B 379 ARG cc_start: 0.7072 (mtt180) cc_final: 0.6437 (tpt90) outliers start: 10 outliers final: 7 residues processed: 39 average time/residue: 0.1760 time to fit residues: 8.5532 Evaluate side-chains 38 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 22 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.140780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.123436 restraints weight = 4453.967| |-----------------------------------------------------------------------------| 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: 0.3821 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3034 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= 0.187 Angle : 0.536 5.771 4710 Z= 0.275 Chirality : 0.049 0.124 528 Planarity : 0.002 0.019 600 Dihedral : 4.822 12.132 468 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.27 % Allowed : 13.13 % 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: -3.03 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.005 0.001 PHE A 378 TYR 0.015 0.003 TYR F 310 ARG 0.001 0.000 ARG D 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 29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.369 Fit side-chains REVERT: C 379 ARG cc_start: 0.7271 (mtt180) cc_final: 0.6392 (tpt90) REVERT: D 379 ARG cc_start: 0.7013 (mtt180) cc_final: 0.6132 (tpt90) REVERT: E 379 ARG cc_start: 0.7230 (mtt180) cc_final: 0.6300 (tpt90) REVERT: A 379 ARG cc_start: 0.7128 (mtt180) cc_final: 0.6369 (tpt90) REVERT: B 342 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7822 (mp0) REVERT: B 357 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8530 (tt) REVERT: B 379 ARG cc_start: 0.7053 (mtt180) cc_final: 0.6425 (tpt90) outliers start: 9 outliers final: 7 residues processed: 29 average time/residue: 0.1989 time to fit residues: 7.1739 Evaluate side-chains 27 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 38 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 40 optimal weight: 0.0010 overall best weight: 2.3992 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.139817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.122637 restraints weight = 4547.824| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.53 r_work: 0.3912 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3800 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3522 Z= 0.236 Angle : 0.546 4.893 4710 Z= 0.282 Chirality : 0.049 0.120 528 Planarity : 0.003 0.021 600 Dihedral : 4.847 12.949 468 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % 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: -3.02 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (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 0.016 0.004 TYR F 310 ARG 0.001 0.000 ARG C 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 28 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.462 Fit side-chains REVERT: C 379 ARG cc_start: 0.7281 (mtt180) cc_final: 0.6398 (tpt90) REVERT: D 379 ARG cc_start: 0.6984 (mtt180) cc_final: 0.6110 (tpt90) REVERT: E 342 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7700 (mp0) REVERT: E 379 ARG cc_start: 0.7210 (mtt180) cc_final: 0.6297 (tpt90) REVERT: A 379 ARG cc_start: 0.7102 (mtt180) cc_final: 0.6332 (tpt90) REVERT: B 342 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7833 (mp0) REVERT: B 357 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8545 (tt) REVERT: B 379 ARG cc_start: 0.7054 (mtt180) cc_final: 0.6437 (tpt90) outliers start: 8 outliers final: 7 residues processed: 28 average time/residue: 0.2244 time to fit residues: 7.9063 Evaluate side-chains 28 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 41 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 35 optimal weight: 0.0000 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 overall best weight: 2.5590 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.139262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.122164 restraints weight = 4538.434| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.53 r_work: 0.3909 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3094 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= 0.249 Angle : 0.556 4.937 4710 Z= 0.289 Chirality : 0.049 0.119 528 Planarity : 0.003 0.021 600 Dihedral : 4.915 12.777 468 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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: -3.02 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (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 0.016 0.004 TYR F 310 ARG 0.001 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1968.16 seconds wall clock time: 34 minutes 53.39 seconds (2093.39 seconds total)