Starting phenix.real_space_refine on Mon Jan 13 18:16:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwl_60532/01_2025/8zwl_60532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwl_60532/01_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_60532/01_2025/8zwl_60532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwl_60532/01_2025/8zwl_60532.map" model { file = "/net/cci-nas-00/data/ceres_data/8zwl_60532/01_2025/8zwl_60532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwl_60532/01_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-5571/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: 2.46, per 1000 atoms: 0.71 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: 0.86 Conformation dependent library (CDL) restraints added in 431.9 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: 0.69 Time building geometry restraints manager: 0.96 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: 0.02 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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.420 Find NCS groups from input model: 0.060 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- 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 : 0.414 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: 0.2872 time to fit residues: 13.3366 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 : 0.372 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.119186 restraints weight = 4553.532| |-----------------------------------------------------------------------------| 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: 0.8240 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 : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 379 ARG cc_start: 0.7064 (mtt180) cc_final: 0.6310 (tpt90) REVERT: D 311 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7930 (mtmt) REVERT: D 379 ARG cc_start: 0.6784 (mtt180) cc_final: 0.6056 (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: 0.6124 (tpt90) REVERT: F 344 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8064 (mt) REVERT: F 378 PHE cc_start: 0.8441 (t80) cc_final: 0.7979 (t80) REVERT: A 379 ARG cc_start: 0.7039 (mtt180) cc_final: 0.6351 (tpt90) REVERT: B 342 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7711 (mp0) REVERT: B 348 ASP cc_start: 0.7895 (t0) cc_final: 0.7560 (m-30) REVERT: B 379 ARG cc_start: 0.6924 (mtt180) cc_final: 0.6245 (tpt90) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.2082 time to fit residues: 8.9970 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 : 0.375 ------------------------------------------------------------------------------- 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: 9.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.138439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.121192 restraints weight = 4673.776| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.52 r_work: 0.3905 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3522 Z= 0.278 Angle : 0.613 5.022 4710 Z= 0.319 Chirality : 0.050 0.118 528 Planarity : 0.003 0.018 600 Dihedral : 5.261 14.906 468 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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: -3.54 (0.26), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.20), 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 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 35 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 22 time to evaluate : 0.482 Fit side-chains REVERT: C 379 ARG cc_start: 0.7085 (mtt180) cc_final: 0.6303 (tpt90) REVERT: D 379 ARG cc_start: 0.6847 (mtt180) cc_final: 0.6073 (tpt90) REVERT: E 379 ARG cc_start: 0.7017 (mtt180) cc_final: 0.6140 (tpt90) REVERT: F 378 PHE cc_start: 0.8428 (t80) cc_final: 0.8117 (t80) REVERT: A 379 ARG cc_start: 0.7082 (mtt180) cc_final: 0.6361 (tpt90) REVERT: B 342 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7818 (mp0) REVERT: B 357 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8550 (tt) REVERT: B 379 ARG cc_start: 0.6991 (mtt180) cc_final: 0.6399 (tpt90) outliers start: 13 outliers final: 9 residues processed: 33 average time/residue: 0.2083 time to fit residues: 8.4116 Evaluate side-chains 29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 356 SER 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: 6.9990 chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.140505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.123232 restraints weight = 4673.020| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.51 r_work: 0.3926 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2318 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= 0.213 Angle : 0.551 4.392 4710 Z= 0.285 Chirality : 0.049 0.121 528 Planarity : 0.002 0.019 600 Dihedral : 4.968 13.991 468 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.53 % Allowed : 6.82 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.27), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (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 D 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 34 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.391 Fit side-chains REVERT: C 379 ARG cc_start: 0.7090 (mtt180) cc_final: 0.6306 (tpt90) REVERT: D 379 ARG cc_start: 0.6802 (mtt180) cc_final: 0.6043 (tpt90) REVERT: E 342 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7688 (mp0) REVERT: E 379 ARG cc_start: 0.7112 (mtt180) cc_final: 0.6161 (tpt90) REVERT: F 378 PHE cc_start: 0.8386 (t80) cc_final: 0.8068 (t80) REVERT: A 379 ARG cc_start: 0.7184 (mtt180) cc_final: 0.6351 (tpt90) REVERT: B 342 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7812 (mp0) REVERT: B 379 ARG cc_start: 0.6986 (mtt180) cc_final: 0.6406 (tpt90) outliers start: 10 outliers final: 8 residues processed: 31 average time/residue: 0.2269 time to fit residues: 8.4674 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 : 0.374 ------------------------------------------------------------------------------- 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: 3.9990 chunk 41 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.143369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.125665 restraints weight = 4601.165| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 2.55 r_work: 0.3953 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3844 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2595 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= 0.170 Angle : 0.509 3.928 4710 Z= 0.262 Chirality : 0.048 0.123 528 Planarity : 0.002 0.018 600 Dihedral : 4.669 12.603 468 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 2.53 % Allowed : 8.59 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.005 0.001 PHE D 378 TYR 0.013 0.003 TYR C 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 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 Fit side-chains REVERT: C 379 ARG cc_start: 0.7038 (mtt180) cc_final: 0.6282 (tpt90) REVERT: D 379 ARG cc_start: 0.6884 (mtt180) cc_final: 0.6082 (tpt90) REVERT: E 379 ARG cc_start: 0.7164 (mtt180) cc_final: 0.6220 (tpt90) REVERT: F 378 PHE cc_start: 0.8430 (t80) cc_final: 0.8019 (t80) REVERT: A 379 ARG cc_start: 0.7119 (mtt180) cc_final: 0.6336 (tpt90) REVERT: B 342 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7799 (mp0) REVERT: B 357 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8536 (tt) REVERT: B 379 ARG cc_start: 0.6984 (mtt180) cc_final: 0.6321 (tpt90) outliers start: 10 outliers final: 7 residues processed: 28 average time/residue: 0.2496 time to fit residues: 8.4352 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 : 0.407 ------------------------------------------------------------------------------- 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 356 SER 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: 7.9990 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.134209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.117551 restraints weight = 4735.740| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.51 r_work: 0.3836 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3522 Z= 0.419 Angle : 0.652 4.333 4710 Z= 0.347 Chirality : 0.050 0.122 528 Planarity : 0.003 0.020 600 Dihedral : 5.460 17.745 468 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.78 % Allowed : 11.62 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.011 0.003 PHE D 378 TYR 0.021 0.005 TYR F 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.369 Fit side-chains REVERT: C 379 ARG cc_start: 0.7010 (mtt180) cc_final: 0.6286 (tpt90) REVERT: D 379 ARG cc_start: 0.6801 (mtt180) cc_final: 0.6049 (tpt90) REVERT: E 342 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7686 (mp0) REVERT: E 379 ARG cc_start: 0.7176 (mtt180) cc_final: 0.6181 (tpt90) REVERT: A 338 GLU cc_start: 0.8052 (tt0) cc_final: 0.7385 (mt-10) REVERT: A 379 ARG cc_start: 0.7225 (mtt180) cc_final: 0.6362 (tpt90) REVERT: B 342 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7829 (mp0) REVERT: B 357 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8588 (tt) REVERT: B 379 ARG cc_start: 0.6983 (mtt180) cc_final: 0.6372 (tpt90) outliers start: 11 outliers final: 8 residues processed: 39 average time/residue: 0.1710 time to fit residues: 8.4195 Evaluate side-chains 39 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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: 0.0670 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.143851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.126295 restraints weight = 4462.488| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.54 r_work: 0.3973 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2918 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= 0.125 Angle : 0.503 5.268 4710 Z= 0.256 Chirality : 0.048 0.122 528 Planarity : 0.002 0.019 600 Dihedral : 4.697 12.380 468 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.77 % Allowed : 13.13 % 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: -3.04 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.003 0.001 PHE F 346 TYR 0.012 0.003 TYR C 310 ARG 0.001 0.000 ARG F 379 *********************** 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 25 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.411 Fit side-chains REVERT: C 379 ARG cc_start: 0.7090 (mtt180) cc_final: 0.6318 (tpt90) REVERT: D 379 ARG cc_start: 0.6877 (mtt180) cc_final: 0.6122 (tpt90) REVERT: E 379 ARG cc_start: 0.7200 (mtt180) cc_final: 0.6232 (tpt90) REVERT: A 379 ARG cc_start: 0.7112 (mtt180) cc_final: 0.6331 (tpt90) REVERT: B 379 ARG cc_start: 0.7015 (mtt180) cc_final: 0.6390 (tpt90) outliers start: 7 outliers final: 6 residues processed: 22 average time/residue: 0.2928 time to fit residues: 7.8353 Evaluate side-chains 24 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 F residue 356 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 8.9990 chunk 13 optimal weight: 0.0370 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.138325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.121316 restraints weight = 4568.923| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.54 r_work: 0.3898 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2887 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= 0.255 Angle : 0.548 3.918 4710 Z= 0.286 Chirality : 0.049 0.119 528 Planarity : 0.003 0.021 600 Dihedral : 4.884 14.139 468 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.27 % Allowed : 12.88 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.007 0.002 PHE D 378 TYR 0.016 0.004 TYR F 310 ARG 0.005 0.001 ARG F 379 *********************** 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 33 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.378 Fit side-chains REVERT: C 379 ARG cc_start: 0.7098 (mtt180) cc_final: 0.6322 (tpt90) REVERT: D 379 ARG cc_start: 0.6997 (mtt180) cc_final: 0.6107 (tpt90) REVERT: E 342 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7706 (mp0) REVERT: E 379 ARG cc_start: 0.7220 (mtt180) cc_final: 0.6279 (tpt90) REVERT: A 379 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6359 (tpt90) REVERT: B 342 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7845 (mp0) REVERT: B 379 ARG cc_start: 0.7040 (mtt180) cc_final: 0.6420 (tpt90) outliers start: 9 outliers final: 8 residues processed: 31 average time/residue: 0.1962 time to fit residues: 7.5647 Evaluate side-chains 32 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 0.0010 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.2168 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.145067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.127435 restraints weight = 4378.487| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.53 r_work: 0.3992 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3522 Z= 0.134 Angle : 0.492 3.786 4710 Z= 0.250 Chirality : 0.048 0.122 528 Planarity : 0.002 0.019 600 Dihedral : 4.507 11.980 468 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.02 % Allowed : 13.38 % 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: -2.90 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.004 0.001 PHE A 378 TYR 0.013 0.003 TYR F 310 ARG 0.004 0.000 ARG F 379 *********************** 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 25 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.440 Fit side-chains REVERT: C 379 ARG cc_start: 0.7161 (mtt180) cc_final: 0.6376 (tpt90) REVERT: D 379 ARG cc_start: 0.6945 (mtt180) cc_final: 0.6160 (tpt90) REVERT: E 311 LYS cc_start: 0.8454 (mtmt) cc_final: 0.8014 (mtmm) REVERT: E 379 ARG cc_start: 0.7175 (mtt180) cc_final: 0.6295 (tpt90) REVERT: A 379 ARG cc_start: 0.7080 (mtt180) cc_final: 0.6335 (tpt90) REVERT: B 379 ARG cc_start: 0.7008 (mtt180) cc_final: 0.6402 (tpt90) outliers start: 8 outliers final: 4 residues processed: 24 average time/residue: 0.2456 time to fit residues: 7.2062 Evaluate side-chains 20 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain B residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 0.4980 chunk 13 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.138625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.121499 restraints weight = 4549.586| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.53 r_work: 0.3901 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3522 Z= 0.279 Angle : 0.564 4.494 4710 Z= 0.293 Chirality : 0.049 0.120 528 Planarity : 0.003 0.022 600 Dihedral : 4.872 14.274 468 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.52 % Allowed : 13.64 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.008 0.002 PHE D 378 TYR 0.017 0.004 TYR F 310 ARG 0.004 0.000 ARG F 379 ********************** 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 29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.405 Fit side-chains REVERT: C 379 ARG cc_start: 0.7298 (mtt180) cc_final: 0.6385 (tpt90) REVERT: D 379 ARG cc_start: 0.6973 (mtt180) cc_final: 0.6092 (tpt90) REVERT: E 342 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7674 (mp0) REVERT: E 379 ARG cc_start: 0.7186 (mtt180) cc_final: 0.6294 (tpt90) REVERT: A 338 GLU cc_start: 0.7970 (tt0) cc_final: 0.7357 (mt-10) REVERT: A 379 ARG cc_start: 0.7079 (mtt180) cc_final: 0.6327 (tpt90) REVERT: B 342 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7816 (mp0) REVERT: B 379 ARG cc_start: 0.7039 (mtt180) cc_final: 0.6424 (tpt90) outliers start: 6 outliers final: 6 residues processed: 29 average time/residue: 0.2131 time to fit residues: 7.6794 Evaluate side-chains 29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.139451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.122372 restraints weight = 4503.490| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.52 r_work: 0.3912 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3075 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= 0.247 Angle : 0.555 4.975 4710 Z= 0.287 Chirality : 0.049 0.120 528 Planarity : 0.003 0.021 600 Dihedral : 4.867 12.635 468 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.52 % Allowed : 14.14 % Favored : 84.34 % 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: -2.95 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (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 0.004 0.000 ARG F 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1934.20 seconds wall clock time: 35 minutes 16.55 seconds (2116.55 seconds total)