Starting phenix.real_space_refine on Wed Feb 4 10:45:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h5b_51883/02_2026/9h5b_51883.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h5b_51883/02_2026/9h5b_51883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h5b_51883/02_2026/9h5b_51883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h5b_51883/02_2026/9h5b_51883.map" model { file = "/net/cci-nas-00/data/ceres_data/9h5b_51883/02_2026/9h5b_51883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h5b_51883/02_2026/9h5b_51883.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 9 5.21 5 S 6 5.16 5 C 5963 2.51 5 N 1609 2.21 5 O 2212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9801 Number of models: 1 Model: "" Number of chains: 8 Chain: "BG" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3226 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 419} Chain: "BH" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3226 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 419} Chain: "BI" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3226 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 419} Chain: "BE" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 112 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "BG" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 3, ' ZN': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BH" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "BI" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.23, per 1000 atoms: 0.23 Number of scatterers: 9801 At special positions: 0 Unit cell: (87.75, 90.45, 206.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 6 16.00 Mg 9 11.99 O 2212 8.00 N 1609 7.00 C 5963 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: 0.80 Conformation dependent library (CDL) restraints added in 453.0 milliseconds 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2432 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 22 sheets defined 6.9% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'BG' and resid 21 through 25 removed outlier: 4.111A pdb=" N GLUBG 25 " --> pdb=" O ASNBG 22 " (cutoff:3.500A) Processing helix chain 'BG' and resid 29 through 38 removed outlier: 3.519A pdb=" N ARGBG 38 " --> pdb=" O ALABG 34 " (cutoff:3.500A) Processing helix chain 'BG' and resid 62 through 66 removed outlier: 3.628A pdb=" N ASNBG 65 " --> pdb=" O ASPBG 62 " (cutoff:3.500A) Processing helix chain 'BG' and resid 246 through 251 removed outlier: 3.596A pdb=" N SERBG 251 " --> pdb=" O ALABG 248 " (cutoff:3.500A) Processing helix chain 'BG' and resid 259 through 263 Processing helix chain 'BH' and resid 29 through 38 Processing helix chain 'BH' and resid 62 through 66 Processing helix chain 'BH' and resid 216 through 220 Processing helix chain 'BH' and resid 246 through 251 removed outlier: 3.511A pdb=" N SERBH 251 " --> pdb=" O ALABH 248 " (cutoff:3.500A) Processing helix chain 'BH' and resid 259 through 263 Processing helix chain 'BI' and resid 29 through 37 Processing helix chain 'BI' and resid 62 through 66 removed outlier: 3.560A pdb=" N ASNBI 65 " --> pdb=" O ASPBI 62 " (cutoff:3.500A) Processing helix chain 'BI' and resid 216 through 220 Processing helix chain 'BI' and resid 246 through 251 removed outlier: 3.597A pdb=" N SERBI 251 " --> pdb=" O ALABI 248 " (cutoff:3.500A) Processing helix chain 'BI' and resid 259 through 263 Processing sheet with id=AA1, first strand: chain 'BG' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'BG' and resid 58 through 59 removed outlier: 6.886A pdb=" N ILEBG 70 " --> pdb=" O THRBG 111 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N THRBG 111 " --> pdb=" O ILEBG 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'BG' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'BG' and resid 135 through 138 removed outlier: 6.826A pdb=" N LEUBG 125 " --> pdb=" O LYSBG 152 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LYSBG 152 " --> pdb=" O LEUBG 125 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VALBG 127 " --> pdb=" O SERBG 150 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SERBG 150 " --> pdb=" O VALBG 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'BG' and resid 172 through 173 WARNING: can't find start of bonding for strands! previous: chain 'BG' and resid 172 through 173 current: chain 'BG' and resid 206 through 207 WARNING: can't find start of bonding for strands! previous: chain 'BG' and resid 206 through 207 current: chain 'BH' and resid 206 through 207 WARNING: can't find start of bonding for strands! previous: chain 'BH' and resid 206 through 207 current: chain 'BI' and resid 206 through 207 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'BG' and resid 272 through 275 Processing sheet with id=AA7, first strand: chain 'BG' and resid 294 through 295 WARNING: can't find start of bonding for strands! previous: chain 'BG' and resid 294 through 295 current: chain 'BG' and resid 402 through 409 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'BG' and resid 335 through 337 Processing sheet with id=AA9, first strand: chain 'BH' and resid 10 through 12 Processing sheet with id=AB1, first strand: chain 'BH' and resid 58 through 59 removed outlier: 6.989A pdb=" N ILEBH 70 " --> pdb=" O THRBH 111 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N THRBH 111 " --> pdb=" O ILEBH 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'BH' and resid 83 through 85 Processing sheet with id=AB3, first strand: chain 'BH' and resid 135 through 140 removed outlier: 3.549A pdb=" N GLYBH 140 " --> pdb=" O ASPBH 122 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEUBH 125 " --> pdb=" O LYSBH 152 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LYSBH 152 " --> pdb=" O LEUBH 125 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VALBH 127 " --> pdb=" O SERBH 150 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N SERBH 150 " --> pdb=" O VALBH 127 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'BH' and resid 272 through 275 Processing sheet with id=AB5, first strand: chain 'BH' and resid 382 through 385 removed outlier: 5.475A pdb=" N SERBH 382 " --> pdb=" O VALBH 409 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VALBH 409 " --> pdb=" O SERBH 382 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALABH 402 " --> pdb=" O VALBH 326 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALABH 404 " --> pdb=" O VALBH 324 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'BH' and resid 335 through 337 Processing sheet with id=AB7, first strand: chain 'BI' and resid 10 through 12 Processing sheet with id=AB8, first strand: chain 'BI' and resid 58 through 59 removed outlier: 6.965A pdb=" N ILEBI 70 " --> pdb=" O THRBI 111 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N THRBI 111 " --> pdb=" O ILEBI 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'BI' and resid 83 through 85 Processing sheet with id=AC1, first strand: chain 'BI' and resid 135 through 138 removed outlier: 6.770A pdb=" N LEUBI 125 " --> pdb=" O LYSBI 152 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LYSBI 152 " --> pdb=" O LEUBI 125 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VALBI 127 " --> pdb=" O SERBI 150 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N SERBI 150 " --> pdb=" O VALBI 127 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'BI' and resid 272 through 275 Processing sheet with id=AC3, first strand: chain 'BI' and resid 294 through 295 removed outlier: 3.621A pdb=" N ALABI 404 " --> pdb=" O VALBI 324 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VALBI 409 " --> pdb=" O SERBI 382 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N SERBI 382 " --> pdb=" O VALBI 409 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'BI' and resid 335 through 337 removed outlier: 3.516A pdb=" N VALBI 336 " --> pdb=" O LEUBI 369 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 417 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: 1.02 Time building geometry restraints manager: 1.02 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: 3189 1.34 - 1.46: 2480 1.46 - 1.58: 4293 1.58 - 1.70: 0 1.70 - 1.82: 9 Bond restraints: 9971 Sorted by residual: bond pdb=" C GLYBG 438 " pdb=" N PROBG 439 " ideal model delta sigma weight residual 1.334 1.356 -0.023 8.40e-03 1.42e+04 7.23e+00 bond pdb=" C ASPBG 148 " pdb=" N PROBG 149 " ideal model delta sigma weight residual 1.330 1.361 -0.031 1.19e-02 7.06e+03 6.66e+00 bond pdb=" C ALABH 332 " pdb=" N PROBH 333 " ideal model delta sigma weight residual 1.329 1.358 -0.030 1.20e-02 6.94e+03 6.09e+00 bond pdb=" C GLNBH 71 " pdb=" N PROBH 72 " ideal model delta sigma weight residual 1.330 1.359 -0.029 1.22e-02 6.72e+03 5.52e+00 bond pdb=" C GLNBI 71 " pdb=" N PROBI 72 " ideal model delta sigma weight residual 1.330 1.358 -0.028 1.22e-02 6.72e+03 5.41e+00 ... (remaining 9966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 11959 2.25 - 4.49: 1520 4.49 - 6.74: 168 6.74 - 8.99: 20 8.99 - 11.23: 1 Bond angle restraints: 13668 Sorted by residual: angle pdb=" CA SERBH 393 " pdb=" C SERBH 393 " pdb=" N GLNBH 394 " ideal model delta sigma weight residual 119.56 115.65 3.91 5.80e-01 2.97e+00 4.55e+01 angle pdb=" CA PHEBI 426 " pdb=" CB PHEBI 426 " pdb=" CG PHEBI 426 " ideal model delta sigma weight residual 113.80 120.14 -6.34 1.00e+00 1.00e+00 4.02e+01 angle pdb=" CA PHEBH 391 " pdb=" CB PHEBH 391 " pdb=" CG PHEBH 391 " ideal model delta sigma weight residual 113.80 108.15 5.65 1.00e+00 1.00e+00 3.19e+01 angle pdb=" CA PHEBI 327 " pdb=" CB PHEBI 327 " pdb=" CG PHEBI 327 " ideal model delta sigma weight residual 113.80 119.23 -5.43 1.00e+00 1.00e+00 2.95e+01 angle pdb=" CA PHEBG 327 " pdb=" CB PHEBG 327 " pdb=" CG PHEBG 327 " ideal model delta sigma weight residual 113.80 119.03 -5.23 1.00e+00 1.00e+00 2.73e+01 ... (remaining 13663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 5173 16.49 - 32.99: 573 32.99 - 49.48: 88 49.48 - 65.98: 34 65.98 - 82.47: 14 Dihedral angle restraints: 5882 sinusoidal: 2079 harmonic: 3803 Sorted by residual: dihedral pdb=" CA PHEBG 327 " pdb=" C PHEBG 327 " pdb=" N GLUBG 328 " pdb=" CA GLUBG 328 " ideal model delta harmonic sigma weight residual -180.00 -143.69 -36.31 0 5.00e+00 4.00e-02 5.27e+01 dihedral pdb=" CA ASPBI 349 " pdb=" C ASPBI 349 " pdb=" N TYRBI 350 " pdb=" CA TYRBI 350 " ideal model delta harmonic sigma weight residual -180.00 -144.08 -35.92 0 5.00e+00 4.00e-02 5.16e+01 dihedral pdb=" CA LEUBI 401 " pdb=" C LEUBI 401 " pdb=" N ALABI 402 " pdb=" CA ALABI 402 " ideal model delta harmonic sigma weight residual -180.00 -145.18 -34.82 0 5.00e+00 4.00e-02 4.85e+01 ... (remaining 5879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1038 0.110 - 0.221: 467 0.221 - 0.331: 79 0.331 - 0.441: 12 0.441 - 0.551: 10 Chirality restraints: 1606 Sorted by residual: chirality pdb=" CA ASPBG 349 " pdb=" N ASPBG 349 " pdb=" C ASPBG 349 " pdb=" CB ASPBG 349 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.60e+00 chirality pdb=" CA ASPBG 168 " pdb=" N ASPBG 168 " pdb=" C ASPBG 168 " pdb=" CB ASPBG 168 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.42e+00 chirality pdb=" CA THRBH 197 " pdb=" N THRBH 197 " pdb=" C THRBH 197 " pdb=" CB THRBH 197 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.50 2.00e-01 2.50e+01 6.25e+00 ... (remaining 1603 not shown) Planarity restraints: 1853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHEBH 391 " -0.026 2.00e-02 2.50e+03 1.89e-02 6.25e+00 pdb=" CG PHEBH 391 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHEBH 391 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHEBH 391 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHEBH 391 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHEBH 391 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHEBH 391 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLNBI 370 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C GLNBI 370 " -0.041 2.00e-02 2.50e+03 pdb=" O GLNBI 370 " 0.016 2.00e-02 2.50e+03 pdb=" N ALABI 371 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRBG 348 " 0.014 2.00e-02 2.50e+03 1.07e-02 2.29e+00 pdb=" CG TYRBG 348 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYRBG 348 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYRBG 348 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYRBG 348 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYRBG 348 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYRBG 348 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYRBG 348 " 0.002 2.00e-02 2.50e+03 ... (remaining 1850 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 55 2.51 - 3.11: 7219 3.11 - 3.71: 15812 3.71 - 4.30: 22466 4.30 - 4.90: 36482 Nonbonded interactions: 82034 Sorted by model distance: nonbonded pdb=" OE1 GLNBG 14 " pdb="MG MGBG 502 " model vdw 1.918 2.170 nonbonded pdb=" OD2 ASPBH 16 " pdb="MG MGBH 501 " model vdw 1.926 2.170 nonbonded pdb=" OE1 GLNBH 14 " pdb="MG MGBH 502 " model vdw 1.944 2.170 nonbonded pdb=" OD2 ASPBG 16 " pdb="MG MGBG 501 " model vdw 1.960 2.170 nonbonded pdb=" OD1 ASNBG 22 " pdb="MG MGBG 501 " model vdw 1.976 2.170 ... (remaining 82029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'BG' and resid 2 through 502) selection = (chain 'BH' and resid 2 through 502) selection = chain 'BI' } 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 group one per residue 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: 1.970 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.110 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 0.007 0.036 9971 Z= 0.500 Angle : 1.519 11.234 13668 Z= 1.003 Chirality : 0.121 0.551 1606 Planarity : 0.003 0.024 1853 Dihedral : 15.181 82.469 3450 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 1.72 % Allowed : 7.89 % Favored : 90.38 % Cbeta Deviations : 1.81 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.19), residues: 1334 helix: -1.05 (0.83), residues: 30 sheet: -0.22 (0.36), residues: 171 loop : -2.24 (0.16), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGBH 435 TYR 0.026 0.004 TYRBG 348 PHE 0.041 0.004 PHEBH 391 TRP 0.022 0.004 TRPBI 293 HIS 0.009 0.003 HISBI 82 Details of bonding type rmsd covalent geometry : bond 0.00746 ( 9971) covalent geometry : angle 1.51924 (13668) hydrogen bonds : bond 0.19992 ( 184) hydrogen bonds : angle 9.76813 ( 417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 401 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BG 27 TYR cc_start: 0.7777 (m-80) cc_final: 0.7440 (m-10) REVERT: BG 82 HIS cc_start: 0.8346 (m-70) cc_final: 0.7636 (m-70) REVERT: BG 98 ASP cc_start: 0.8003 (t0) cc_final: 0.7673 (t0) REVERT: BG 194 ASP cc_start: 0.8354 (t0) cc_final: 0.8027 (t0) REVERT: BG 241 GLN cc_start: 0.8376 (mm-40) cc_final: 0.8162 (mm110) REVERT: BG 311 TYR cc_start: 0.5203 (m-80) cc_final: 0.4161 (m-80) REVERT: BG 327 PHE cc_start: 0.7728 (t80) cc_final: 0.7291 (t80) REVERT: BG 379 PHE cc_start: 0.8236 (m-80) cc_final: 0.7773 (m-80) REVERT: BG 429 THR cc_start: 0.7477 (m) cc_final: 0.6674 (m) REVERT: BG 433 PHE cc_start: 0.8481 (m-80) cc_final: 0.8214 (m-10) REVERT: BH 7 ILE cc_start: 0.9242 (pt) cc_final: 0.9021 (mp) REVERT: BH 96 LEU cc_start: 0.9515 (mt) cc_final: 0.9301 (mp) REVERT: BH 194 ASP cc_start: 0.8308 (t0) cc_final: 0.7954 (t0) REVERT: BH 320 TYR cc_start: 0.7598 (m-10) cc_final: 0.7304 (m-80) REVERT: BH 369 LEU cc_start: 0.8695 (mt) cc_final: 0.8405 (mt) REVERT: BH 433 PHE cc_start: 0.8708 (m-80) cc_final: 0.8294 (m-10) REVERT: BI 24 ASP cc_start: 0.8957 (m-30) cc_final: 0.8656 (t0) REVERT: BI 32 TYR cc_start: 0.8590 (m-80) cc_final: 0.7908 (m-80) REVERT: BI 36 LEU cc_start: 0.9525 (tp) cc_final: 0.9321 (tp) REVERT: BI 50 SER cc_start: 0.9523 (p) cc_final: 0.9299 (p) REVERT: BI 165 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7942 (ptm160) REVERT: BI 194 ASP cc_start: 0.8366 (t0) cc_final: 0.8071 (t0) REVERT: BI 311 TYR cc_start: 0.4777 (m-80) cc_final: 0.4568 (m-80) REVERT: BI 338 LEU cc_start: 0.8697 (tp) cc_final: 0.8485 (tp) REVERT: BI 376 ILE cc_start: 0.8553 (tp) cc_final: 0.8175 (tp) REVERT: BI 433 PHE cc_start: 0.8634 (m-80) cc_final: 0.8306 (m-10) REVERT: BE 11 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7302 (mm-30) outliers start: 19 outliers final: 4 residues processed: 414 average time/residue: 0.0879 time to fit residues: 50.6747 Evaluate side-chains 305 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 300 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BG residue 432 VAL Chi-restraints excluded: chain BH residue 293 TRP Chi-restraints excluded: chain BI residue 95 ASN Chi-restraints excluded: chain BI residue 165 ARG Chi-restraints excluded: chain BI residue 364 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.0040 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BG 82 HIS BG 89 GLN BH 82 HIS ** BH 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 22 ASN ** BI 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.104795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.076029 restraints weight = 26855.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.079390 restraints weight = 16005.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.081752 restraints weight = 10965.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.083441 restraints weight = 8217.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.084606 restraints weight = 6563.670| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9971 Z= 0.166 Angle : 0.822 8.501 13668 Z= 0.439 Chirality : 0.051 0.197 1606 Planarity : 0.005 0.040 1853 Dihedral : 8.644 42.953 1415 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.72 % Allowed : 19.42 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.21), residues: 1334 helix: 0.82 (1.08), residues: 30 sheet: -0.56 (0.33), residues: 213 loop : -1.93 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGBG 294 TYR 0.026 0.003 TYRBI 311 PHE 0.024 0.003 PHEBI 426 TRP 0.021 0.003 TRPBG 124 HIS 0.008 0.002 HISBG 246 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9971) covalent geometry : angle 0.82221 (13668) hydrogen bonds : bond 0.04437 ( 184) hydrogen bonds : angle 7.61324 ( 417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 326 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BG 45 TYR cc_start: 0.9233 (p90) cc_final: 0.8871 (p90) REVERT: BG 119 VAL cc_start: 0.7619 (OUTLIER) cc_final: 0.7095 (m) REVERT: BG 136 TYR cc_start: 0.7496 (p90) cc_final: 0.7273 (p90) REVERT: BG 141 ASN cc_start: 0.8823 (t0) cc_final: 0.8500 (m-40) REVERT: BG 194 ASP cc_start: 0.7963 (t0) cc_final: 0.7550 (t0) REVERT: BG 241 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8049 (mp10) REVERT: BG 262 ASN cc_start: 0.8954 (m110) cc_final: 0.8546 (m110) REVERT: BG 283 MET cc_start: 0.8180 (mmm) cc_final: 0.7871 (mmm) REVERT: BG 293 TRP cc_start: 0.7723 (m100) cc_final: 0.7228 (m100) REVERT: BG 320 TYR cc_start: 0.8343 (m-10) cc_final: 0.8022 (m-10) REVERT: BG 379 PHE cc_start: 0.7580 (m-80) cc_final: 0.7020 (m-80) REVERT: BG 435 ARG cc_start: 0.7493 (tpt90) cc_final: 0.7249 (mmm-85) REVERT: BG 436 ASP cc_start: 0.8336 (m-30) cc_final: 0.7929 (t70) REVERT: BH 7 ILE cc_start: 0.9326 (pt) cc_final: 0.9079 (mp) REVERT: BH 82 HIS cc_start: 0.8891 (m170) cc_final: 0.8627 (m-70) REVERT: BH 98 ASP cc_start: 0.8829 (t0) cc_final: 0.8596 (t0) REVERT: BH 136 TYR cc_start: 0.7556 (p90) cc_final: 0.7206 (p90) REVERT: BH 165 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7883 (ptm160) REVERT: BH 186 ASP cc_start: 0.9144 (t0) cc_final: 0.8778 (t0) REVERT: BH 194 ASP cc_start: 0.7936 (t0) cc_final: 0.7656 (t0) REVERT: BH 237 LEU cc_start: 0.9166 (mp) cc_final: 0.8881 (mp) REVERT: BH 241 GLN cc_start: 0.8467 (mm110) cc_final: 0.7911 (mm110) REVERT: BH 262 ASN cc_start: 0.9146 (m110) cc_final: 0.8744 (m110) REVERT: BH 283 MET cc_start: 0.7780 (mmm) cc_final: 0.7496 (mmp) REVERT: BH 293 TRP cc_start: 0.8408 (OUTLIER) cc_final: 0.8104 (m100) REVERT: BH 294 ARG cc_start: 0.8719 (ttm-80) cc_final: 0.8510 (mmp80) REVERT: BH 319 GLU cc_start: 0.9002 (tt0) cc_final: 0.8554 (tm-30) REVERT: BH 323 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7591 (mtp85) REVERT: BH 433 PHE cc_start: 0.8793 (m-80) cc_final: 0.8118 (m-10) REVERT: BI 32 TYR cc_start: 0.9278 (m-10) cc_final: 0.8708 (m-80) REVERT: BI 53 SER cc_start: 0.8993 (m) cc_final: 0.8463 (p) REVERT: BI 119 VAL cc_start: 0.7656 (OUTLIER) cc_final: 0.7452 (m) REVERT: BI 152 LYS cc_start: 0.9367 (tttm) cc_final: 0.9043 (tppt) REVERT: BI 186 ASP cc_start: 0.9101 (t0) cc_final: 0.8841 (t0) REVERT: BI 194 ASP cc_start: 0.8025 (t0) cc_final: 0.7607 (t0) REVERT: BI 219 LYS cc_start: 0.8627 (ptpt) cc_final: 0.8078 (ptpp) REVERT: BI 262 ASN cc_start: 0.8957 (m110) cc_final: 0.8639 (m-40) REVERT: BI 283 MET cc_start: 0.7733 (mmm) cc_final: 0.7268 (mmm) REVERT: BI 292 GLN cc_start: 0.7873 (tp-100) cc_final: 0.7654 (tp-100) REVERT: BI 294 ARG cc_start: 0.7549 (mtp85) cc_final: 0.7323 (mmt-90) REVERT: BI 311 TYR cc_start: 0.2781 (m-80) cc_final: 0.2198 (m-10) REVERT: BI 319 GLU cc_start: 0.7467 (mp0) cc_final: 0.7263 (mp0) REVERT: BI 376 ILE cc_start: 0.8133 (tp) cc_final: 0.7808 (tp) REVERT: BI 419 LEU cc_start: 0.9099 (tp) cc_final: 0.8614 (pp) REVERT: BI 433 PHE cc_start: 0.8697 (m-80) cc_final: 0.8479 (m-10) REVERT: BE 9 LEU cc_start: 0.9055 (tp) cc_final: 0.8748 (tp) outliers start: 41 outliers final: 20 residues processed: 348 average time/residue: 0.0917 time to fit residues: 43.8447 Evaluate side-chains 289 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 265 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BG residue 28 ASP Chi-restraints excluded: chain BG residue 51 THR Chi-restraints excluded: chain BG residue 95 ASN Chi-restraints excluded: chain BG residue 119 VAL Chi-restraints excluded: chain BG residue 123 VAL Chi-restraints excluded: chain BG residue 181 THR Chi-restraints excluded: chain BG residue 348 TYR Chi-restraints excluded: chain BG residue 420 PHE Chi-restraints excluded: chain BG residue 421 ARG Chi-restraints excluded: chain BH residue 164 THR Chi-restraints excluded: chain BH residue 165 ARG Chi-restraints excluded: chain BH residue 185 SER Chi-restraints excluded: chain BH residue 258 ILE Chi-restraints excluded: chain BH residue 293 TRP Chi-restraints excluded: chain BH residue 348 TYR Chi-restraints excluded: chain BH residue 420 PHE Chi-restraints excluded: chain BI residue 51 THR Chi-restraints excluded: chain BI residue 119 VAL Chi-restraints excluded: chain BI residue 124 TRP Chi-restraints excluded: chain BI residue 164 THR Chi-restraints excluded: chain BI residue 181 THR Chi-restraints excluded: chain BI residue 348 TYR Chi-restraints excluded: chain BI residue 420 PHE Chi-restraints excluded: chain BI residue 431 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 86 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 69 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BG 71 GLN BG 276 GLN ** BG 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 388 GLN ** BH 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.103317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.074663 restraints weight = 26720.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.077807 restraints weight = 15979.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.080201 restraints weight = 11028.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.081837 restraints weight = 8268.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.083031 restraints weight = 6610.067| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9971 Z= 0.163 Angle : 0.766 8.289 13668 Z= 0.404 Chirality : 0.049 0.163 1606 Planarity : 0.006 0.177 1853 Dihedral : 7.723 39.740 1406 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 4.72 % Allowed : 21.87 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.21), residues: 1334 helix: 1.55 (1.06), residues: 30 sheet: -0.54 (0.33), residues: 225 loop : -1.81 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGBH 339 TYR 0.023 0.003 TYRBI 92 PHE 0.031 0.003 PHEBG 426 TRP 0.022 0.003 TRPBI 293 HIS 0.012 0.002 HISBG 82 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9971) covalent geometry : angle 0.76600 (13668) hydrogen bonds : bond 0.03978 ( 184) hydrogen bonds : angle 7.27823 ( 417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BG 45 TYR cc_start: 0.9275 (p90) cc_final: 0.8906 (p90) REVERT: BG 136 TYR cc_start: 0.7593 (p90) cc_final: 0.7323 (p90) REVERT: BG 141 ASN cc_start: 0.8813 (t0) cc_final: 0.8558 (m-40) REVERT: BG 168 ASP cc_start: 0.8530 (p0) cc_final: 0.8285 (p0) REVERT: BG 194 ASP cc_start: 0.8128 (t0) cc_final: 0.7648 (t0) REVERT: BG 241 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8105 (mp10) REVERT: BG 244 LYS cc_start: 0.8147 (ptpp) cc_final: 0.7945 (ptpp) REVERT: BG 262 ASN cc_start: 0.8982 (m110) cc_final: 0.8524 (m110) REVERT: BG 283 MET cc_start: 0.8213 (mmm) cc_final: 0.7910 (mmm) REVERT: BG 294 ARG cc_start: 0.8970 (mtp85) cc_final: 0.8747 (mmt-90) REVERT: BG 319 GLU cc_start: 0.7723 (mp0) cc_final: 0.7482 (mp0) REVERT: BG 353 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7280 (tm-30) REVERT: BG 379 PHE cc_start: 0.7529 (m-80) cc_final: 0.6957 (m-80) REVERT: BH 27 TYR cc_start: 0.7645 (m-80) cc_final: 0.7136 (m-10) REVERT: BH 45 TYR cc_start: 0.9215 (p90) cc_final: 0.8939 (p90) REVERT: BH 95 ASN cc_start: 0.9535 (m110) cc_final: 0.9176 (m-40) REVERT: BH 98 ASP cc_start: 0.8911 (t0) cc_final: 0.8606 (t0) REVERT: BH 124 TRP cc_start: 0.6592 (OUTLIER) cc_final: 0.4507 (m100) REVERT: BH 136 TYR cc_start: 0.7585 (p90) cc_final: 0.7177 (p90) REVERT: BH 152 LYS cc_start: 0.9502 (tttm) cc_final: 0.8277 (tptp) REVERT: BH 186 ASP cc_start: 0.9206 (t0) cc_final: 0.8751 (t0) REVERT: BH 194 ASP cc_start: 0.7995 (t0) cc_final: 0.7675 (t0) REVERT: BH 241 GLN cc_start: 0.8809 (mm110) cc_final: 0.8068 (mm110) REVERT: BH 262 ASN cc_start: 0.9175 (m110) cc_final: 0.8740 (m110) REVERT: BH 283 MET cc_start: 0.7808 (mmm) cc_final: 0.7354 (mmm) REVERT: BH 289 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8602 (m) REVERT: BH 293 TRP cc_start: 0.8572 (OUTLIER) cc_final: 0.8353 (m100) REVERT: BH 294 ARG cc_start: 0.8810 (ttm-80) cc_final: 0.8477 (mmp80) REVERT: BH 321 LEU cc_start: 0.8916 (tt) cc_final: 0.8541 (mp) REVERT: BH 353 GLU cc_start: 0.9122 (tp30) cc_final: 0.8829 (tm-30) REVERT: BH 433 PHE cc_start: 0.8912 (m-80) cc_final: 0.8501 (m-10) REVERT: BH 435 ARG cc_start: 0.8239 (tpt90) cc_final: 0.7682 (tpt90) REVERT: BI 24 ASP cc_start: 0.8734 (m-30) cc_final: 0.8332 (t70) REVERT: BI 32 TYR cc_start: 0.9402 (m-10) cc_final: 0.8920 (m-80) REVERT: BI 45 TYR cc_start: 0.9076 (p90) cc_final: 0.8794 (p90) REVERT: BI 53 SER cc_start: 0.9047 (m) cc_final: 0.8649 (p) REVERT: BI 119 VAL cc_start: 0.7744 (OUTLIER) cc_final: 0.7537 (m) REVERT: BI 152 LYS cc_start: 0.9399 (tttm) cc_final: 0.9023 (tppt) REVERT: BI 168 ASP cc_start: 0.8132 (t70) cc_final: 0.7831 (t70) REVERT: BI 186 ASP cc_start: 0.9230 (t0) cc_final: 0.8985 (t0) REVERT: BI 194 ASP cc_start: 0.8048 (t0) cc_final: 0.7599 (t0) REVERT: BI 198 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8795 (m) REVERT: BI 212 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7734 (mm-30) REVERT: BI 219 LYS cc_start: 0.8836 (ptpt) cc_final: 0.8305 (ptpp) REVERT: BI 283 MET cc_start: 0.7924 (mmm) cc_final: 0.7588 (mmm) REVERT: BI 292 GLN cc_start: 0.7728 (tp-100) cc_final: 0.7331 (mm-40) REVERT: BI 388 GLN cc_start: 0.8380 (mp10) cc_final: 0.7322 (mp10) REVERT: BI 419 LEU cc_start: 0.8980 (tp) cc_final: 0.8457 (pp) REVERT: BI 433 PHE cc_start: 0.8897 (m-80) cc_final: 0.8581 (m-10) REVERT: BE 9 LEU cc_start: 0.9069 (tp) cc_final: 0.8782 (tp) outliers start: 52 outliers final: 32 residues processed: 302 average time/residue: 0.0835 time to fit residues: 35.3665 Evaluate side-chains 289 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 252 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BG residue 28 ASP Chi-restraints excluded: chain BG residue 51 THR Chi-restraints excluded: chain BG residue 77 ILE Chi-restraints excluded: chain BG residue 95 ASN Chi-restraints excluded: chain BG residue 123 VAL Chi-restraints excluded: chain BG residue 163 THR Chi-restraints excluded: chain BG residue 164 THR Chi-restraints excluded: chain BG residue 181 THR Chi-restraints excluded: chain BG residue 310 THR Chi-restraints excluded: chain BG residue 348 TYR Chi-restraints excluded: chain BH residue 123 VAL Chi-restraints excluded: chain BH residue 124 TRP Chi-restraints excluded: chain BH residue 163 THR Chi-restraints excluded: chain BH residue 164 THR Chi-restraints excluded: chain BH residue 181 THR Chi-restraints excluded: chain BH residue 185 SER Chi-restraints excluded: chain BH residue 258 ILE Chi-restraints excluded: chain BH residue 289 THR Chi-restraints excluded: chain BH residue 293 TRP Chi-restraints excluded: chain BH residue 348 TYR Chi-restraints excluded: chain BH residue 363 SER Chi-restraints excluded: chain BH residue 420 PHE Chi-restraints excluded: chain BI residue 36 LEU Chi-restraints excluded: chain BI residue 51 THR Chi-restraints excluded: chain BI residue 119 VAL Chi-restraints excluded: chain BI residue 124 TRP Chi-restraints excluded: chain BI residue 163 THR Chi-restraints excluded: chain BI residue 198 THR Chi-restraints excluded: chain BI residue 251 SER Chi-restraints excluded: chain BI residue 258 ILE Chi-restraints excluded: chain BI residue 260 VAL Chi-restraints excluded: chain BI residue 268 SER Chi-restraints excluded: chain BI residue 362 THR Chi-restraints excluded: chain BI residue 373 SER Chi-restraints excluded: chain BI residue 420 PHE Chi-restraints excluded: chain BE residue 4 LEU Chi-restraints excluded: chain BE residue 14 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 111 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 104 optimal weight: 0.0070 chunk 71 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 100 optimal weight: 0.0570 chunk 15 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BG 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 82 HIS ** BH 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.102231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.073860 restraints weight = 27185.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.077072 restraints weight = 16245.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.079409 restraints weight = 11210.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.081084 restraints weight = 8399.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.082343 restraints weight = 6684.014| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9971 Z= 0.155 Angle : 0.733 8.051 13668 Z= 0.385 Chirality : 0.049 0.199 1606 Planarity : 0.006 0.130 1853 Dihedral : 7.298 38.577 1406 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 4.72 % Allowed : 23.77 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.21), residues: 1334 helix: 2.04 (1.03), residues: 30 sheet: -0.72 (0.32), residues: 231 loop : -1.76 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGBH 384 TYR 0.018 0.002 TYRBI 348 PHE 0.022 0.003 PHEBG 426 TRP 0.039 0.003 TRPBG 430 HIS 0.009 0.002 HISBI 82 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9971) covalent geometry : angle 0.73335 (13668) hydrogen bonds : bond 0.03609 ( 184) hydrogen bonds : angle 7.04861 ( 417) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BG 45 TYR cc_start: 0.9305 (p90) cc_final: 0.8907 (p90) REVERT: BG 92 TYR cc_start: 0.7457 (m-10) cc_final: 0.7129 (m-10) REVERT: BG 136 TYR cc_start: 0.7694 (p90) cc_final: 0.7378 (p90) REVERT: BG 141 ASN cc_start: 0.8839 (t0) cc_final: 0.8633 (t0) REVERT: BG 168 ASP cc_start: 0.8527 (p0) cc_final: 0.8241 (p0) REVERT: BG 194 ASP cc_start: 0.8137 (t0) cc_final: 0.7709 (t0) REVERT: BG 219 LYS cc_start: 0.8507 (ptpp) cc_final: 0.8171 (ptpp) REVERT: BG 241 GLN cc_start: 0.8364 (mm-40) cc_final: 0.7982 (mm110) REVERT: BG 244 LYS cc_start: 0.8266 (ptpp) cc_final: 0.8015 (ptpp) REVERT: BG 262 ASN cc_start: 0.8881 (m110) cc_final: 0.8442 (m110) REVERT: BG 283 MET cc_start: 0.8295 (mmm) cc_final: 0.7836 (mmm) REVERT: BG 292 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8001 (mm-40) REVERT: BG 294 ARG cc_start: 0.9110 (mtp85) cc_final: 0.8551 (mmt-90) REVERT: BG 320 TYR cc_start: 0.8446 (m-10) cc_final: 0.8241 (m-80) REVERT: BG 353 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7385 (tm-30) REVERT: BG 379 PHE cc_start: 0.7482 (m-80) cc_final: 0.6961 (m-80) REVERT: BH 27 TYR cc_start: 0.7586 (m-80) cc_final: 0.7045 (m-10) REVERT: BH 95 ASN cc_start: 0.9554 (m110) cc_final: 0.9201 (m-40) REVERT: BH 98 ASP cc_start: 0.8901 (t0) cc_final: 0.8603 (t0) REVERT: BH 102 TYR cc_start: 0.8935 (m-10) cc_final: 0.8643 (m-10) REVERT: BH 124 TRP cc_start: 0.6744 (OUTLIER) cc_final: 0.4031 (m100) REVERT: BH 136 TYR cc_start: 0.7442 (p90) cc_final: 0.6961 (p90) REVERT: BH 152 LYS cc_start: 0.9513 (tttm) cc_final: 0.8042 (tptm) REVERT: BH 186 ASP cc_start: 0.9201 (t0) cc_final: 0.8832 (t0) REVERT: BH 194 ASP cc_start: 0.8003 (t0) cc_final: 0.7652 (t0) REVERT: BH 241 GLN cc_start: 0.8756 (mm110) cc_final: 0.8100 (mm110) REVERT: BH 262 ASN cc_start: 0.9245 (m110) cc_final: 0.8779 (m110) REVERT: BH 263 LEU cc_start: 0.9242 (mt) cc_final: 0.8861 (mp) REVERT: BH 283 MET cc_start: 0.7915 (mmm) cc_final: 0.7408 (mmm) REVERT: BH 294 ARG cc_start: 0.8808 (ttm-80) cc_final: 0.8486 (mmp80) REVERT: BH 319 GLU cc_start: 0.8889 (tt0) cc_final: 0.8648 (tm-30) REVERT: BH 335 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7471 (t) REVERT: BH 353 GLU cc_start: 0.9078 (tp30) cc_final: 0.8263 (tm-30) REVERT: BH 435 ARG cc_start: 0.8116 (tpt90) cc_final: 0.7321 (tpt-90) REVERT: BH 436 ASP cc_start: 0.7423 (m-30) cc_final: 0.6987 (m-30) REVERT: BI 24 ASP cc_start: 0.8756 (m-30) cc_final: 0.8348 (t70) REVERT: BI 32 TYR cc_start: 0.9412 (m-10) cc_final: 0.9036 (m-80) REVERT: BI 45 TYR cc_start: 0.9158 (p90) cc_final: 0.8881 (p90) REVERT: BI 53 SER cc_start: 0.9061 (m) cc_final: 0.8647 (p) REVERT: BI 60 ASN cc_start: 0.8053 (t0) cc_final: 0.7283 (t0) REVERT: BI 86 SER cc_start: 0.9289 (t) cc_final: 0.8697 (p) REVERT: BI 92 TYR cc_start: 0.6750 (m-80) cc_final: 0.6393 (m-10) REVERT: BI 119 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7522 (m) REVERT: BI 152 LYS cc_start: 0.9379 (tttm) cc_final: 0.9026 (tppt) REVERT: BI 168 ASP cc_start: 0.8253 (t70) cc_final: 0.7812 (t70) REVERT: BI 186 ASP cc_start: 0.9219 (t0) cc_final: 0.8968 (t0) REVERT: BI 194 ASP cc_start: 0.8093 (t0) cc_final: 0.7478 (t0) REVERT: BI 198 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8558 (m) REVERT: BI 212 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7661 (mm-30) REVERT: BI 219 LYS cc_start: 0.8898 (ptpt) cc_final: 0.8439 (ptpp) REVERT: BI 283 MET cc_start: 0.7934 (mmm) cc_final: 0.7500 (mmm) REVERT: BI 311 TYR cc_start: 0.4888 (m-80) cc_final: 0.3285 (m-80) REVERT: BI 388 GLN cc_start: 0.7915 (mp10) cc_final: 0.7318 (mp10) REVERT: BI 419 LEU cc_start: 0.9017 (tp) cc_final: 0.8385 (pp) REVERT: BE 9 LEU cc_start: 0.9239 (tp) cc_final: 0.8921 (tp) outliers start: 52 outliers final: 35 residues processed: 293 average time/residue: 0.0837 time to fit residues: 34.4524 Evaluate side-chains 279 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BG residue 28 ASP Chi-restraints excluded: chain BG residue 51 THR Chi-restraints excluded: chain BG residue 95 ASN Chi-restraints excluded: chain BG residue 115 LEU Chi-restraints excluded: chain BG residue 123 VAL Chi-restraints excluded: chain BG residue 163 THR Chi-restraints excluded: chain BG residue 164 THR Chi-restraints excluded: chain BG residue 181 THR Chi-restraints excluded: chain BG residue 258 ILE Chi-restraints excluded: chain BG residue 292 GLN Chi-restraints excluded: chain BG residue 348 TYR Chi-restraints excluded: chain BG residue 430 TRP Chi-restraints excluded: chain BH residue 123 VAL Chi-restraints excluded: chain BH residue 124 TRP Chi-restraints excluded: chain BH residue 163 THR Chi-restraints excluded: chain BH residue 164 THR Chi-restraints excluded: chain BH residue 181 THR Chi-restraints excluded: chain BH residue 258 ILE Chi-restraints excluded: chain BH residue 293 TRP Chi-restraints excluded: chain BH residue 335 THR Chi-restraints excluded: chain BH residue 348 TYR Chi-restraints excluded: chain BH residue 363 SER Chi-restraints excluded: chain BH residue 420 PHE Chi-restraints excluded: chain BI residue 36 LEU Chi-restraints excluded: chain BI residue 51 THR Chi-restraints excluded: chain BI residue 68 VAL Chi-restraints excluded: chain BI residue 104 VAL Chi-restraints excluded: chain BI residue 115 LEU Chi-restraints excluded: chain BI residue 119 VAL Chi-restraints excluded: chain BI residue 124 TRP Chi-restraints excluded: chain BI residue 163 THR Chi-restraints excluded: chain BI residue 198 THR Chi-restraints excluded: chain BI residue 251 SER Chi-restraints excluded: chain BI residue 260 VAL Chi-restraints excluded: chain BI residue 268 SER Chi-restraints excluded: chain BI residue 348 TYR Chi-restraints excluded: chain BI residue 362 THR Chi-restraints excluded: chain BI residue 373 SER Chi-restraints excluded: chain BI residue 426 PHE Chi-restraints excluded: chain BE residue 14 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BG 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BG 89 GLN ** BG 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 132 ASN ** BH 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 425 ASN ** BI 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BI 276 GLN ** BI 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.091563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.064552 restraints weight = 27978.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.067495 restraints weight = 16869.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.069615 restraints weight = 11734.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.071137 restraints weight = 8886.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.072268 restraints weight = 7154.945| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.169 9971 Z= 0.375 Angle : 0.843 8.125 13668 Z= 0.451 Chirality : 0.050 0.184 1606 Planarity : 0.006 0.071 1853 Dihedral : 7.801 43.335 1406 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 26.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.09 % Favored : 88.83 % Rotamer: Outliers : 5.90 % Allowed : 23.77 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.21), residues: 1334 helix: 1.92 (0.99), residues: 30 sheet: -1.06 (0.32), residues: 228 loop : -1.94 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARGBH 339 TYR 0.027 0.003 TYRBH 45 PHE 0.028 0.004 PHEBI 406 TRP 0.037 0.004 TRPBG 430 HIS 0.007 0.003 HISBI 250 Details of bonding type rmsd covalent geometry : bond 0.00772 ( 9971) covalent geometry : angle 0.84303 (13668) hydrogen bonds : bond 0.05089 ( 184) hydrogen bonds : angle 7.33657 ( 417) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 249 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BG 27 TYR cc_start: 0.8557 (m-80) cc_final: 0.8193 (m-80) REVERT: BG 92 TYR cc_start: 0.7491 (m-80) cc_final: 0.6951 (m-10) REVERT: BG 124 TRP cc_start: 0.7509 (OUTLIER) cc_final: 0.6098 (m100) REVERT: BG 136 TYR cc_start: 0.8345 (p90) cc_final: 0.8020 (p90) REVERT: BG 141 ASN cc_start: 0.8872 (t0) cc_final: 0.8640 (m-40) REVERT: BG 168 ASP cc_start: 0.8525 (p0) cc_final: 0.8217 (p0) REVERT: BG 194 ASP cc_start: 0.8049 (t0) cc_final: 0.7618 (t0) REVERT: BG 219 LYS cc_start: 0.8529 (ptpp) cc_final: 0.8244 (pttm) REVERT: BG 241 GLN cc_start: 0.8291 (mm-40) cc_final: 0.8079 (mm110) REVERT: BG 244 LYS cc_start: 0.8482 (ptpp) cc_final: 0.8229 (ptpp) REVERT: BG 262 ASN cc_start: 0.8954 (m110) cc_final: 0.8558 (m110) REVERT: BG 283 MET cc_start: 0.8307 (mmm) cc_final: 0.7752 (mmm) REVERT: BG 292 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8326 (tp40) REVERT: BH 45 TYR cc_start: 0.9388 (p90) cc_final: 0.9069 (p90) REVERT: BH 82 HIS cc_start: 0.8572 (m170) cc_final: 0.8180 (m-70) REVERT: BH 89 GLN cc_start: 0.8422 (mp10) cc_final: 0.7946 (mp10) REVERT: BH 95 ASN cc_start: 0.9592 (m110) cc_final: 0.9248 (m-40) REVERT: BH 98 ASP cc_start: 0.9048 (t0) cc_final: 0.8723 (t0) REVERT: BH 136 TYR cc_start: 0.8004 (p90) cc_final: 0.7514 (p90) REVERT: BH 152 LYS cc_start: 0.9519 (tttm) cc_final: 0.8947 (tptm) REVERT: BH 186 ASP cc_start: 0.9253 (t0) cc_final: 0.9020 (t0) REVERT: BH 194 ASP cc_start: 0.8067 (t0) cc_final: 0.7772 (t0) REVERT: BH 212 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7635 (mm-30) REVERT: BH 241 GLN cc_start: 0.8689 (mm110) cc_final: 0.8267 (mm110) REVERT: BH 262 ASN cc_start: 0.9271 (m110) cc_final: 0.8757 (m-40) REVERT: BH 263 LEU cc_start: 0.9484 (mt) cc_final: 0.8982 (mp) REVERT: BH 283 MET cc_start: 0.7994 (mmm) cc_final: 0.7567 (mmm) REVERT: BH 289 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8819 (t) REVERT: BH 293 TRP cc_start: 0.9090 (OUTLIER) cc_final: 0.8185 (m-10) REVERT: BH 294 ARG cc_start: 0.8758 (ttm-80) cc_final: 0.8287 (mmp80) REVERT: BH 327 PHE cc_start: 0.7839 (t80) cc_final: 0.7076 (t80) REVERT: BH 433 PHE cc_start: 0.8976 (m-80) cc_final: 0.8680 (m-80) REVERT: BH 435 ARG cc_start: 0.8239 (tpt90) cc_final: 0.7835 (tpt90) REVERT: BI 12 PHE cc_start: 0.9445 (t80) cc_final: 0.9157 (t80) REVERT: BI 24 ASP cc_start: 0.8896 (m-30) cc_final: 0.8528 (t70) REVERT: BI 45 TYR cc_start: 0.9465 (p90) cc_final: 0.9164 (p90) REVERT: BI 53 SER cc_start: 0.9278 (m) cc_final: 0.8869 (p) REVERT: BI 77 ILE cc_start: 0.9713 (mt) cc_final: 0.9508 (tp) REVERT: BI 86 SER cc_start: 0.9322 (t) cc_final: 0.8665 (p) REVERT: BI 90 LYS cc_start: 0.9158 (tppt) cc_final: 0.8867 (tppt) REVERT: BI 92 TYR cc_start: 0.6833 (m-80) cc_final: 0.6451 (m-10) REVERT: BI 124 TRP cc_start: 0.7087 (OUTLIER) cc_final: 0.6781 (m100) REVERT: BI 152 LYS cc_start: 0.9408 (tttm) cc_final: 0.8643 (tttm) REVERT: BI 168 ASP cc_start: 0.8277 (t70) cc_final: 0.7954 (t70) REVERT: BI 186 ASP cc_start: 0.9203 (t0) cc_final: 0.8970 (t0) REVERT: BI 194 ASP cc_start: 0.8157 (t0) cc_final: 0.7502 (t0) REVERT: BI 198 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8669 (m) REVERT: BI 212 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7647 (mm-30) REVERT: BI 256 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7777 (t70) REVERT: BI 283 MET cc_start: 0.7897 (mmm) cc_final: 0.7326 (mmm) REVERT: BI 376 ILE cc_start: 0.8584 (tp) cc_final: 0.8016 (tp) REVERT: BI 388 GLN cc_start: 0.7783 (mp10) cc_final: 0.6948 (mm-40) REVERT: BI 431 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7261 (mt-10) REVERT: BE 9 LEU cc_start: 0.9302 (tp) cc_final: 0.8949 (tp) outliers start: 65 outliers final: 46 residues processed: 289 average time/residue: 0.0762 time to fit residues: 31.5110 Evaluate side-chains 282 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 229 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BG residue 28 ASP Chi-restraints excluded: chain BG residue 51 THR Chi-restraints excluded: chain BG residue 55 THR Chi-restraints excluded: chain BG residue 71 GLN Chi-restraints excluded: chain BG residue 95 ASN Chi-restraints excluded: chain BG residue 111 THR Chi-restraints excluded: chain BG residue 115 LEU Chi-restraints excluded: chain BG residue 123 VAL Chi-restraints excluded: chain BG residue 124 TRP Chi-restraints excluded: chain BG residue 127 VAL Chi-restraints excluded: chain BG residue 163 THR Chi-restraints excluded: chain BG residue 164 THR Chi-restraints excluded: chain BG residue 181 THR Chi-restraints excluded: chain BG residue 229 SER Chi-restraints excluded: chain BG residue 258 ILE Chi-restraints excluded: chain BG residue 260 VAL Chi-restraints excluded: chain BG residue 292 GLN Chi-restraints excluded: chain BG residue 430 TRP Chi-restraints excluded: chain BH residue 24 ASP Chi-restraints excluded: chain BH residue 50 SER Chi-restraints excluded: chain BH residue 104 VAL Chi-restraints excluded: chain BH residue 123 VAL Chi-restraints excluded: chain BH residue 124 TRP Chi-restraints excluded: chain BH residue 164 THR Chi-restraints excluded: chain BH residue 181 THR Chi-restraints excluded: chain BH residue 229 SER Chi-restraints excluded: chain BH residue 258 ILE Chi-restraints excluded: chain BH residue 260 VAL Chi-restraints excluded: chain BH residue 289 THR Chi-restraints excluded: chain BH residue 292 GLN Chi-restraints excluded: chain BH residue 293 TRP Chi-restraints excluded: chain BH residue 338 LEU Chi-restraints excluded: chain BH residue 363 SER Chi-restraints excluded: chain BH residue 420 PHE Chi-restraints excluded: chain BI residue 36 LEU Chi-restraints excluded: chain BI residue 51 THR Chi-restraints excluded: chain BI residue 68 VAL Chi-restraints excluded: chain BI residue 104 VAL Chi-restraints excluded: chain BI residue 124 TRP Chi-restraints excluded: chain BI residue 164 THR Chi-restraints excluded: chain BI residue 174 VAL Chi-restraints excluded: chain BI residue 187 THR Chi-restraints excluded: chain BI residue 198 THR Chi-restraints excluded: chain BI residue 218 SER Chi-restraints excluded: chain BI residue 251 SER Chi-restraints excluded: chain BI residue 256 ASP Chi-restraints excluded: chain BI residue 258 ILE Chi-restraints excluded: chain BI residue 260 VAL Chi-restraints excluded: chain BI residue 348 TYR Chi-restraints excluded: chain BI residue 362 THR Chi-restraints excluded: chain BI residue 373 SER Chi-restraints excluded: chain BI residue 426 PHE Chi-restraints excluded: chain BE residue 14 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 118 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BG 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BG 89 GLN ** BG 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BI 112 ASN ** BI 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.097378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.070011 restraints weight = 27480.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.073139 restraints weight = 16468.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075375 restraints weight = 11361.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.076975 restraints weight = 8517.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.078164 restraints weight = 6798.881| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9971 Z= 0.165 Angle : 0.734 8.002 13668 Z= 0.390 Chirality : 0.049 0.177 1606 Planarity : 0.005 0.074 1853 Dihedral : 7.192 43.006 1406 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 4.90 % Allowed : 27.40 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.21), residues: 1334 helix: 2.24 (1.01), residues: 30 sheet: -0.08 (0.35), residues: 201 loop : -1.94 (0.17), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGBI 421 TYR 0.022 0.002 TYRBG 32 PHE 0.032 0.003 PHEBG 379 TRP 0.034 0.003 TRPBG 430 HIS 0.005 0.002 HISBH 246 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9971) covalent geometry : angle 0.73403 (13668) hydrogen bonds : bond 0.03568 ( 184) hydrogen bonds : angle 6.86467 ( 417) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 238 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BG 32 TYR cc_start: 0.8916 (m-80) cc_final: 0.8690 (m-80) REVERT: BG 92 TYR cc_start: 0.7371 (m-80) cc_final: 0.6785 (m-10) REVERT: BG 119 VAL cc_start: 0.8024 (OUTLIER) cc_final: 0.7311 (p) REVERT: BG 124 TRP cc_start: 0.7029 (OUTLIER) cc_final: 0.5446 (m100) REVERT: BG 136 TYR cc_start: 0.8039 (p90) cc_final: 0.7657 (p90) REVERT: BG 141 ASN cc_start: 0.8756 (t0) cc_final: 0.8330 (t0) REVERT: BG 168 ASP cc_start: 0.8430 (p0) cc_final: 0.8166 (p0) REVERT: BG 194 ASP cc_start: 0.8174 (t0) cc_final: 0.7760 (t0) REVERT: BG 219 LYS cc_start: 0.8507 (ptpp) cc_final: 0.8146 (ptpp) REVERT: BG 244 LYS cc_start: 0.8449 (ptpp) cc_final: 0.8154 (ptpp) REVERT: BG 262 ASN cc_start: 0.8909 (m110) cc_final: 0.8551 (m110) REVERT: BG 283 MET cc_start: 0.8144 (mmm) cc_final: 0.7660 (mmm) REVERT: BG 292 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8062 (mm110) REVERT: BG 294 ARG cc_start: 0.9004 (mtp85) cc_final: 0.8381 (mmp80) REVERT: BG 341 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6473 (mm-30) REVERT: BG 379 PHE cc_start: 0.7838 (m-80) cc_final: 0.7138 (m-80) REVERT: BH 45 TYR cc_start: 0.9265 (p90) cc_final: 0.8951 (p90) REVERT: BH 89 GLN cc_start: 0.8679 (mp10) cc_final: 0.8278 (mp10) REVERT: BH 98 ASP cc_start: 0.8920 (t0) cc_final: 0.8646 (t0) REVERT: BH 124 TRP cc_start: 0.6963 (OUTLIER) cc_final: 0.4583 (m100) REVERT: BH 133 ASP cc_start: 0.8438 (m-30) cc_final: 0.7838 (m-30) REVERT: BH 136 TYR cc_start: 0.7936 (p90) cc_final: 0.7291 (p90) REVERT: BH 152 LYS cc_start: 0.9490 (tttm) cc_final: 0.8049 (tttm) REVERT: BH 186 ASP cc_start: 0.9250 (t0) cc_final: 0.9001 (t0) REVERT: BH 194 ASP cc_start: 0.8026 (t0) cc_final: 0.7763 (t0) REVERT: BH 212 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7729 (mm-30) REVERT: BH 241 GLN cc_start: 0.8703 (mm110) cc_final: 0.8341 (mp10) REVERT: BH 262 ASN cc_start: 0.9244 (m110) cc_final: 0.8836 (m110) REVERT: BH 280 THR cc_start: 0.8988 (m) cc_final: 0.8666 (t) REVERT: BH 283 MET cc_start: 0.8015 (mmm) cc_final: 0.7551 (mmm) REVERT: BH 293 TRP cc_start: 0.8622 (OUTLIER) cc_final: 0.8070 (m-10) REVERT: BH 294 ARG cc_start: 0.8807 (ttm-80) cc_final: 0.8584 (mmp80) REVERT: BH 433 PHE cc_start: 0.8832 (m-80) cc_final: 0.8628 (m-80) REVERT: BI 24 ASP cc_start: 0.8835 (m-30) cc_final: 0.8438 (t70) REVERT: BI 45 TYR cc_start: 0.9342 (p90) cc_final: 0.9077 (p90) REVERT: BI 53 SER cc_start: 0.9239 (m) cc_final: 0.8835 (p) REVERT: BI 86 SER cc_start: 0.9339 (t) cc_final: 0.8762 (p) REVERT: BI 92 TYR cc_start: 0.6613 (m-80) cc_final: 0.6297 (m-10) REVERT: BI 119 VAL cc_start: 0.7698 (OUTLIER) cc_final: 0.7451 (m) REVERT: BI 124 TRP cc_start: 0.6507 (OUTLIER) cc_final: 0.6226 (m100) REVERT: BI 152 LYS cc_start: 0.9366 (tttm) cc_final: 0.8469 (tttm) REVERT: BI 168 ASP cc_start: 0.8314 (t70) cc_final: 0.8088 (t0) REVERT: BI 186 ASP cc_start: 0.9262 (t0) cc_final: 0.8991 (t0) REVERT: BI 194 ASP cc_start: 0.8141 (t0) cc_final: 0.7546 (t0) REVERT: BI 198 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8577 (m) REVERT: BI 212 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7356 (mm-30) REVERT: BI 283 MET cc_start: 0.7974 (mmm) cc_final: 0.7602 (mmm) REVERT: BI 376 ILE cc_start: 0.8529 (tp) cc_final: 0.7850 (tp) REVERT: BI 388 GLN cc_start: 0.7759 (mp10) cc_final: 0.7108 (mm-40) REVERT: BI 431 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7187 (mt-10) REVERT: BI 435 ARG cc_start: 0.7659 (tpt-90) cc_final: 0.7438 (tpt-90) REVERT: BE 9 LEU cc_start: 0.9238 (tp) cc_final: 0.8927 (tp) outliers start: 54 outliers final: 38 residues processed: 269 average time/residue: 0.0877 time to fit residues: 32.7067 Evaluate side-chains 281 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 234 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BG residue 51 THR Chi-restraints excluded: chain BG residue 95 ASN Chi-restraints excluded: chain BG residue 115 LEU Chi-restraints excluded: chain BG residue 119 VAL Chi-restraints excluded: chain BG residue 123 VAL Chi-restraints excluded: chain BG residue 124 TRP Chi-restraints excluded: chain BG residue 127 VAL Chi-restraints excluded: chain BG residue 163 THR Chi-restraints excluded: chain BG residue 164 THR Chi-restraints excluded: chain BG residue 181 THR Chi-restraints excluded: chain BG residue 258 ILE Chi-restraints excluded: chain BG residue 292 GLN Chi-restraints excluded: chain BG residue 341 GLU Chi-restraints excluded: chain BG residue 348 TYR Chi-restraints excluded: chain BG residue 362 THR Chi-restraints excluded: chain BG residue 369 LEU Chi-restraints excluded: chain BG residue 430 TRP Chi-restraints excluded: chain BH residue 104 VAL Chi-restraints excluded: chain BH residue 123 VAL Chi-restraints excluded: chain BH residue 124 TRP Chi-restraints excluded: chain BH residue 135 VAL Chi-restraints excluded: chain BH residue 156 VAL Chi-restraints excluded: chain BH residue 164 THR Chi-restraints excluded: chain BH residue 181 THR Chi-restraints excluded: chain BH residue 185 SER Chi-restraints excluded: chain BH residue 258 ILE Chi-restraints excluded: chain BH residue 260 VAL Chi-restraints excluded: chain BH residue 292 GLN Chi-restraints excluded: chain BH residue 293 TRP Chi-restraints excluded: chain BH residue 338 LEU Chi-restraints excluded: chain BH residue 348 TYR Chi-restraints excluded: chain BH residue 420 PHE Chi-restraints excluded: chain BI residue 27 TYR Chi-restraints excluded: chain BI residue 36 LEU Chi-restraints excluded: chain BI residue 51 THR Chi-restraints excluded: chain BI residue 68 VAL Chi-restraints excluded: chain BI residue 104 VAL Chi-restraints excluded: chain BI residue 115 LEU Chi-restraints excluded: chain BI residue 119 VAL Chi-restraints excluded: chain BI residue 124 TRP Chi-restraints excluded: chain BI residue 164 THR Chi-restraints excluded: chain BI residue 198 THR Chi-restraints excluded: chain BI residue 258 ILE Chi-restraints excluded: chain BI residue 348 TYR Chi-restraints excluded: chain BI residue 362 THR Chi-restraints excluded: chain BI residue 373 SER Chi-restraints excluded: chain BI residue 426 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 122 optimal weight: 0.3980 chunk 101 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BG 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 82 HIS ** BI 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.093594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.066623 restraints weight = 27913.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.069660 restraints weight = 16825.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.071852 restraints weight = 11650.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073471 restraints weight = 8761.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.074647 restraints weight = 7007.616| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 9971 Z= 0.247 Angle : 0.751 6.882 13668 Z= 0.401 Chirality : 0.048 0.179 1606 Planarity : 0.006 0.096 1853 Dihedral : 7.255 44.420 1406 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 5.63 % Allowed : 27.22 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.21), residues: 1334 helix: 2.10 (1.01), residues: 30 sheet: -0.23 (0.35), residues: 201 loop : -1.99 (0.17), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARGBH 339 TYR 0.028 0.003 TYRBG 32 PHE 0.049 0.003 PHEBG 426 TRP 0.037 0.003 TRPBG 430 HIS 0.006 0.002 HISBG 246 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 9971) covalent geometry : angle 0.75073 (13668) hydrogen bonds : bond 0.04202 ( 184) hydrogen bonds : angle 7.01011 ( 417) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 241 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BG 79 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7463 (tm-30) REVERT: BG 92 TYR cc_start: 0.7211 (m-80) cc_final: 0.6905 (m-10) REVERT: BG 119 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.7624 (p) REVERT: BG 124 TRP cc_start: 0.7306 (OUTLIER) cc_final: 0.5797 (m100) REVERT: BG 136 TYR cc_start: 0.8314 (p90) cc_final: 0.7952 (p90) REVERT: BG 141 ASN cc_start: 0.8862 (t0) cc_final: 0.8482 (t0) REVERT: BG 168 ASP cc_start: 0.8507 (p0) cc_final: 0.8222 (p0) REVERT: BG 194 ASP cc_start: 0.8140 (t0) cc_final: 0.7714 (t0) REVERT: BG 219 LYS cc_start: 0.8506 (ptpp) cc_final: 0.8121 (pttp) REVERT: BG 241 GLN cc_start: 0.8480 (mm110) cc_final: 0.8241 (mp10) REVERT: BG 244 LYS cc_start: 0.8525 (ptpp) cc_final: 0.8204 (ptpp) REVERT: BG 283 MET cc_start: 0.8158 (mmm) cc_final: 0.7690 (mmm) REVERT: BG 292 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8129 (tp40) REVERT: BG 294 ARG cc_start: 0.9014 (mtp85) cc_final: 0.8270 (mmp80) REVERT: BG 341 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7541 (mm-30) REVERT: BG 379 PHE cc_start: 0.7932 (m-80) cc_final: 0.7318 (m-80) REVERT: BH 45 TYR cc_start: 0.9379 (p90) cc_final: 0.9009 (p90) REVERT: BH 89 GLN cc_start: 0.8702 (mp10) cc_final: 0.8240 (mp10) REVERT: BH 98 ASP cc_start: 0.8930 (t0) cc_final: 0.8643 (t0) REVERT: BH 133 ASP cc_start: 0.8491 (m-30) cc_final: 0.8036 (m-30) REVERT: BH 136 TYR cc_start: 0.8127 (p90) cc_final: 0.7461 (p90) REVERT: BH 177 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8380 (tp) REVERT: BH 186 ASP cc_start: 0.9271 (t0) cc_final: 0.9018 (t0) REVERT: BH 194 ASP cc_start: 0.8022 (t0) cc_final: 0.7734 (t0) REVERT: BH 212 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7701 (mm-30) REVERT: BH 241 GLN cc_start: 0.8752 (mm110) cc_final: 0.8409 (mp10) REVERT: BH 262 ASN cc_start: 0.9271 (m110) cc_final: 0.8862 (m110) REVERT: BH 280 THR cc_start: 0.8972 (m) cc_final: 0.8675 (t) REVERT: BH 283 MET cc_start: 0.8087 (mmm) cc_final: 0.7481 (mmm) REVERT: BH 293 TRP cc_start: 0.8843 (OUTLIER) cc_final: 0.8129 (m-10) REVERT: BH 294 ARG cc_start: 0.8816 (ttm-80) cc_final: 0.8284 (mmp80) REVERT: BH 321 LEU cc_start: 0.9211 (tt) cc_final: 0.8332 (mp) REVERT: BH 433 PHE cc_start: 0.8893 (m-80) cc_final: 0.8659 (m-80) REVERT: BI 24 ASP cc_start: 0.8903 (m-30) cc_final: 0.8485 (t70) REVERT: BI 45 TYR cc_start: 0.9386 (p90) cc_final: 0.9140 (p90) REVERT: BI 53 SER cc_start: 0.9256 (m) cc_final: 0.8831 (p) REVERT: BI 77 ILE cc_start: 0.9666 (mt) cc_final: 0.9464 (tp) REVERT: BI 92 TYR cc_start: 0.6620 (m-80) cc_final: 0.6291 (m-10) REVERT: BI 119 VAL cc_start: 0.8108 (OUTLIER) cc_final: 0.7871 (m) REVERT: BI 124 TRP cc_start: 0.6843 (OUTLIER) cc_final: 0.6552 (m100) REVERT: BI 152 LYS cc_start: 0.9380 (tttm) cc_final: 0.8564 (tttm) REVERT: BI 168 ASP cc_start: 0.8390 (t70) cc_final: 0.8172 (t0) REVERT: BI 186 ASP cc_start: 0.9194 (t0) cc_final: 0.8929 (t0) REVERT: BI 194 ASP cc_start: 0.8191 (t0) cc_final: 0.7522 (t0) REVERT: BI 198 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8629 (m) REVERT: BI 212 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7639 (mm-30) REVERT: BI 283 MET cc_start: 0.7925 (mmm) cc_final: 0.7561 (mmm) REVERT: BI 376 ILE cc_start: 0.8535 (tp) cc_final: 0.7960 (tp) REVERT: BI 431 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7241 (mt-10) REVERT: BE 9 LEU cc_start: 0.9278 (tp) cc_final: 0.8964 (tp) outliers start: 62 outliers final: 43 residues processed: 282 average time/residue: 0.0763 time to fit residues: 30.3776 Evaluate side-chains 279 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 227 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BG residue 51 THR Chi-restraints excluded: chain BG residue 95 ASN Chi-restraints excluded: chain BG residue 115 LEU Chi-restraints excluded: chain BG residue 119 VAL Chi-restraints excluded: chain BG residue 123 VAL Chi-restraints excluded: chain BG residue 124 TRP Chi-restraints excluded: chain BG residue 127 VAL Chi-restraints excluded: chain BG residue 163 THR Chi-restraints excluded: chain BG residue 164 THR Chi-restraints excluded: chain BG residue 181 THR Chi-restraints excluded: chain BG residue 258 ILE Chi-restraints excluded: chain BG residue 292 GLN Chi-restraints excluded: chain BG residue 341 GLU Chi-restraints excluded: chain BG residue 348 TYR Chi-restraints excluded: chain BG residue 362 THR Chi-restraints excluded: chain BG residue 369 LEU Chi-restraints excluded: chain BG residue 430 TRP Chi-restraints excluded: chain BH residue 24 ASP Chi-restraints excluded: chain BH residue 66 GLU Chi-restraints excluded: chain BH residue 104 VAL Chi-restraints excluded: chain BH residue 111 THR Chi-restraints excluded: chain BH residue 123 VAL Chi-restraints excluded: chain BH residue 124 TRP Chi-restraints excluded: chain BH residue 135 VAL Chi-restraints excluded: chain BH residue 164 THR Chi-restraints excluded: chain BH residue 177 LEU Chi-restraints excluded: chain BH residue 181 THR Chi-restraints excluded: chain BH residue 185 SER Chi-restraints excluded: chain BH residue 258 ILE Chi-restraints excluded: chain BH residue 260 VAL Chi-restraints excluded: chain BH residue 292 GLN Chi-restraints excluded: chain BH residue 293 TRP Chi-restraints excluded: chain BH residue 348 TYR Chi-restraints excluded: chain BH residue 419 LEU Chi-restraints excluded: chain BI residue 51 THR Chi-restraints excluded: chain BI residue 68 VAL Chi-restraints excluded: chain BI residue 104 VAL Chi-restraints excluded: chain BI residue 118 ASP Chi-restraints excluded: chain BI residue 119 VAL Chi-restraints excluded: chain BI residue 124 TRP Chi-restraints excluded: chain BI residue 164 THR Chi-restraints excluded: chain BI residue 174 VAL Chi-restraints excluded: chain BI residue 198 THR Chi-restraints excluded: chain BI residue 218 SER Chi-restraints excluded: chain BI residue 258 ILE Chi-restraints excluded: chain BI residue 260 VAL Chi-restraints excluded: chain BI residue 348 TYR Chi-restraints excluded: chain BI residue 362 THR Chi-restraints excluded: chain BI residue 373 SER Chi-restraints excluded: chain BI residue 397 THR Chi-restraints excluded: chain BI residue 426 PHE Chi-restraints excluded: chain BE residue 14 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 12 optimal weight: 0.0980 chunk 127 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BG 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 82 HIS BI 325 GLN ** BE 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.097421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.069926 restraints weight = 27760.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.073082 restraints weight = 16692.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.075325 restraints weight = 11561.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.076937 restraints weight = 8705.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.078165 restraints weight = 6973.186| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9971 Z= 0.160 Angle : 0.728 9.300 13668 Z= 0.389 Chirality : 0.049 0.229 1606 Planarity : 0.006 0.075 1853 Dihedral : 6.957 41.409 1406 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 4.99 % Allowed : 28.68 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.22), residues: 1334 helix: 2.30 (1.02), residues: 30 sheet: -0.25 (0.35), residues: 201 loop : -1.96 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGBH 339 TYR 0.018 0.002 TYRBG 45 PHE 0.027 0.003 PHEBI 406 TRP 0.032 0.003 TRPBG 430 HIS 0.004 0.001 HISBH 246 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9971) covalent geometry : angle 0.72839 (13668) hydrogen bonds : bond 0.03606 ( 184) hydrogen bonds : angle 6.88027 ( 417) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 247 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BG 45 TYR cc_start: 0.9201 (p90) cc_final: 0.8946 (p90) REVERT: BG 82 HIS cc_start: 0.8210 (m-70) cc_final: 0.7622 (m-70) REVERT: BG 92 TYR cc_start: 0.7209 (m-80) cc_final: 0.6985 (m-10) REVERT: BG 119 VAL cc_start: 0.8029 (OUTLIER) cc_final: 0.7242 (p) REVERT: BG 124 TRP cc_start: 0.7012 (OUTLIER) cc_final: 0.5409 (m100) REVERT: BG 136 TYR cc_start: 0.8149 (p90) cc_final: 0.7781 (p90) REVERT: BG 141 ASN cc_start: 0.8801 (t0) cc_final: 0.8363 (t0) REVERT: BG 168 ASP cc_start: 0.8439 (p0) cc_final: 0.8220 (p0) REVERT: BG 194 ASP cc_start: 0.8173 (t0) cc_final: 0.7729 (t0) REVERT: BG 219 LYS cc_start: 0.8490 (ptpp) cc_final: 0.8105 (pttp) REVERT: BG 244 LYS cc_start: 0.8478 (ptpp) cc_final: 0.8134 (ptpp) REVERT: BG 283 MET cc_start: 0.8089 (mmm) cc_final: 0.7553 (mmm) REVERT: BG 341 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6566 (mm-30) REVERT: BG 379 PHE cc_start: 0.7759 (m-80) cc_final: 0.7191 (m-80) REVERT: BG 435 ARG cc_start: 0.8305 (mmm160) cc_final: 0.7730 (mmm160) REVERT: BH 45 TYR cc_start: 0.9299 (p90) cc_final: 0.8934 (p90) REVERT: BH 98 ASP cc_start: 0.8879 (t0) cc_final: 0.8606 (t0) REVERT: BH 133 ASP cc_start: 0.8391 (m-30) cc_final: 0.7876 (m-30) REVERT: BH 136 TYR cc_start: 0.7974 (p90) cc_final: 0.7234 (p90) REVERT: BH 152 LYS cc_start: 0.9479 (tttm) cc_final: 0.9099 (tppt) REVERT: BH 186 ASP cc_start: 0.9257 (t0) cc_final: 0.8996 (t0) REVERT: BH 194 ASP cc_start: 0.8033 (t0) cc_final: 0.7746 (t0) REVERT: BH 212 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7672 (mm-30) REVERT: BH 241 GLN cc_start: 0.8747 (mm110) cc_final: 0.8435 (mp10) REVERT: BH 280 THR cc_start: 0.8978 (m) cc_final: 0.8634 (t) REVERT: BH 283 MET cc_start: 0.8026 (mmm) cc_final: 0.7596 (mmm) REVERT: BH 293 TRP cc_start: 0.8753 (OUTLIER) cc_final: 0.7920 (m-10) REVERT: BH 321 LEU cc_start: 0.9207 (tt) cc_final: 0.8252 (mp) REVERT: BH 431 GLU cc_start: 0.7520 (tt0) cc_final: 0.6938 (tt0) REVERT: BH 433 PHE cc_start: 0.8807 (m-80) cc_final: 0.8032 (m-10) REVERT: BI 24 ASP cc_start: 0.8809 (m-30) cc_final: 0.8384 (t70) REVERT: BI 45 TYR cc_start: 0.9327 (p90) cc_final: 0.9094 (p90) REVERT: BI 53 SER cc_start: 0.9224 (m) cc_final: 0.8797 (p) REVERT: BI 92 TYR cc_start: 0.6692 (m-80) cc_final: 0.6385 (m-10) REVERT: BI 119 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7547 (m) REVERT: BI 124 TRP cc_start: 0.6553 (OUTLIER) cc_final: 0.6258 (m100) REVERT: BI 152 LYS cc_start: 0.9335 (tttm) cc_final: 0.8445 (tttm) REVERT: BI 186 ASP cc_start: 0.9270 (t0) cc_final: 0.8996 (t0) REVERT: BI 194 ASP cc_start: 0.8145 (t0) cc_final: 0.7532 (t0) REVERT: BI 198 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8544 (m) REVERT: BI 212 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7595 (mm-30) REVERT: BI 283 MET cc_start: 0.7985 (mmm) cc_final: 0.7584 (mmm) REVERT: BI 324 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8707 (t) REVERT: BI 388 GLN cc_start: 0.7009 (mm-40) cc_final: 0.6513 (mt0) REVERT: BI 419 LEU cc_start: 0.9163 (tp) cc_final: 0.8451 (pp) REVERT: BI 431 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7195 (mt-10) REVERT: BE 9 LEU cc_start: 0.9314 (tp) cc_final: 0.9029 (tp) outliers start: 55 outliers final: 40 residues processed: 280 average time/residue: 0.0932 time to fit residues: 36.3844 Evaluate side-chains 274 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BG residue 28 ASP Chi-restraints excluded: chain BG residue 51 THR Chi-restraints excluded: chain BG residue 95 ASN Chi-restraints excluded: chain BG residue 115 LEU Chi-restraints excluded: chain BG residue 119 VAL Chi-restraints excluded: chain BG residue 123 VAL Chi-restraints excluded: chain BG residue 124 TRP Chi-restraints excluded: chain BG residue 127 VAL Chi-restraints excluded: chain BG residue 163 THR Chi-restraints excluded: chain BG residue 164 THR Chi-restraints excluded: chain BG residue 181 THR Chi-restraints excluded: chain BG residue 258 ILE Chi-restraints excluded: chain BG residue 327 PHE Chi-restraints excluded: chain BG residue 341 GLU Chi-restraints excluded: chain BG residue 348 TYR Chi-restraints excluded: chain BG residue 362 THR Chi-restraints excluded: chain BG residue 369 LEU Chi-restraints excluded: chain BG residue 430 TRP Chi-restraints excluded: chain BH residue 96 LEU Chi-restraints excluded: chain BH residue 104 VAL Chi-restraints excluded: chain BH residue 123 VAL Chi-restraints excluded: chain BH residue 124 TRP Chi-restraints excluded: chain BH residue 135 VAL Chi-restraints excluded: chain BH residue 156 VAL Chi-restraints excluded: chain BH residue 164 THR Chi-restraints excluded: chain BH residue 181 THR Chi-restraints excluded: chain BH residue 185 SER Chi-restraints excluded: chain BH residue 258 ILE Chi-restraints excluded: chain BH residue 260 VAL Chi-restraints excluded: chain BH residue 293 TRP Chi-restraints excluded: chain BH residue 347 SER Chi-restraints excluded: chain BH residue 348 TYR Chi-restraints excluded: chain BH residue 419 LEU Chi-restraints excluded: chain BI residue 21 SER Chi-restraints excluded: chain BI residue 36 LEU Chi-restraints excluded: chain BI residue 51 THR Chi-restraints excluded: chain BI residue 119 VAL Chi-restraints excluded: chain BI residue 124 TRP Chi-restraints excluded: chain BI residue 198 THR Chi-restraints excluded: chain BI residue 258 ILE Chi-restraints excluded: chain BI residue 260 VAL Chi-restraints excluded: chain BI residue 324 VAL Chi-restraints excluded: chain BI residue 325 GLN Chi-restraints excluded: chain BI residue 348 TYR Chi-restraints excluded: chain BI residue 362 THR Chi-restraints excluded: chain BI residue 373 SER Chi-restraints excluded: chain BI residue 397 THR Chi-restraints excluded: chain BI residue 426 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 100 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BG 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BG 292 GLN ** BG 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 82 HIS BI 89 GLN BI 298 ASN ** BI 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.095423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.068432 restraints weight = 28015.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.071529 restraints weight = 16848.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.073720 restraints weight = 11652.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.075321 restraints weight = 8756.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.076523 restraints weight = 7013.133| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 9971 Z= 0.211 Angle : 0.762 8.434 13668 Z= 0.405 Chirality : 0.049 0.227 1606 Planarity : 0.006 0.073 1853 Dihedral : 6.995 41.132 1406 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 4.81 % Allowed : 29.58 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.22), residues: 1334 helix: 1.79 (1.00), residues: 30 sheet: -0.33 (0.35), residues: 201 loop : -2.01 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGBH 339 TYR 0.024 0.002 TYRBG 32 PHE 0.055 0.003 PHEBG 426 TRP 0.038 0.003 TRPBG 430 HIS 0.007 0.002 HISBG 82 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 9971) covalent geometry : angle 0.76170 (13668) hydrogen bonds : bond 0.03947 ( 184) hydrogen bonds : angle 6.83898 ( 417) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BG 71 GLN cc_start: 0.8985 (mm110) cc_final: 0.8757 (mm-40) REVERT: BG 92 TYR cc_start: 0.7249 (m-80) cc_final: 0.7026 (m-10) REVERT: BG 119 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7455 (p) REVERT: BG 124 TRP cc_start: 0.7214 (OUTLIER) cc_final: 0.5652 (m100) REVERT: BG 136 TYR cc_start: 0.8279 (p90) cc_final: 0.7915 (p90) REVERT: BG 141 ASN cc_start: 0.8861 (t0) cc_final: 0.8468 (t0) REVERT: BG 194 ASP cc_start: 0.8149 (t0) cc_final: 0.7693 (t0) REVERT: BG 219 LYS cc_start: 0.8527 (ptpp) cc_final: 0.8131 (pttp) REVERT: BG 244 LYS cc_start: 0.8479 (ptpp) cc_final: 0.8144 (ptpp) REVERT: BG 262 ASN cc_start: 0.9044 (m110) cc_final: 0.8741 (m110) REVERT: BG 283 MET cc_start: 0.8106 (mmm) cc_final: 0.7594 (mmm) REVERT: BG 294 ARG cc_start: 0.9057 (mtp85) cc_final: 0.8644 (mmp80) REVERT: BG 341 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6509 (mm-30) REVERT: BG 379 PHE cc_start: 0.7835 (m-80) cc_final: 0.7222 (m-80) REVERT: BH 45 TYR cc_start: 0.9357 (p90) cc_final: 0.8997 (p90) REVERT: BH 98 ASP cc_start: 0.8917 (t0) cc_final: 0.8633 (t0) REVERT: BH 133 ASP cc_start: 0.8439 (m-30) cc_final: 0.8099 (m-30) REVERT: BH 136 TYR cc_start: 0.8082 (p90) cc_final: 0.7321 (p90) REVERT: BH 186 ASP cc_start: 0.9275 (t0) cc_final: 0.9024 (t0) REVERT: BH 194 ASP cc_start: 0.8026 (t0) cc_final: 0.7718 (t0) REVERT: BH 212 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7635 (mm-30) REVERT: BH 241 GLN cc_start: 0.8698 (mm110) cc_final: 0.8343 (mp10) REVERT: BH 283 MET cc_start: 0.8097 (mmm) cc_final: 0.7499 (mmm) REVERT: BH 293 TRP cc_start: 0.9017 (OUTLIER) cc_final: 0.8069 (m-10) REVERT: BH 321 LEU cc_start: 0.9127 (tt) cc_final: 0.8299 (mp) REVERT: BH 324 VAL cc_start: 0.9369 (p) cc_final: 0.9132 (t) REVERT: BH 406 PHE cc_start: 0.8830 (p90) cc_final: 0.8617 (p90) REVERT: BH 431 GLU cc_start: 0.7830 (tt0) cc_final: 0.7277 (tt0) REVERT: BH 433 PHE cc_start: 0.8870 (m-80) cc_final: 0.8453 (m-10) REVERT: BI 24 ASP cc_start: 0.8846 (m-30) cc_final: 0.8415 (t70) REVERT: BI 45 TYR cc_start: 0.9363 (p90) cc_final: 0.9129 (p90) REVERT: BI 53 SER cc_start: 0.9064 (m) cc_final: 0.8643 (p) REVERT: BI 92 TYR cc_start: 0.6720 (m-80) cc_final: 0.6218 (m-10) REVERT: BI 119 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7811 (m) REVERT: BI 124 TRP cc_start: 0.6734 (OUTLIER) cc_final: 0.6467 (m100) REVERT: BI 152 LYS cc_start: 0.9325 (tttm) cc_final: 0.8509 (tttm) REVERT: BI 186 ASP cc_start: 0.9278 (t0) cc_final: 0.9016 (t0) REVERT: BI 194 ASP cc_start: 0.8146 (t0) cc_final: 0.7517 (t0) REVERT: BI 198 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8590 (m) REVERT: BI 212 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7643 (mm-30) REVERT: BI 244 LYS cc_start: 0.8384 (mtpp) cc_final: 0.8124 (mttp) REVERT: BI 283 MET cc_start: 0.8019 (mmm) cc_final: 0.7499 (mmm) REVERT: BI 317 PHE cc_start: 0.9377 (m-10) cc_final: 0.9026 (m-10) REVERT: BI 324 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8620 (t) REVERT: BI 431 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7233 (mt-10) REVERT: BE 9 LEU cc_start: 0.9287 (tp) cc_final: 0.8975 (tp) outliers start: 53 outliers final: 40 residues processed: 265 average time/residue: 0.1069 time to fit residues: 39.0736 Evaluate side-chains 272 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BG residue 28 ASP Chi-restraints excluded: chain BG residue 51 THR Chi-restraints excluded: chain BG residue 95 ASN Chi-restraints excluded: chain BG residue 105 ILE Chi-restraints excluded: chain BG residue 115 LEU Chi-restraints excluded: chain BG residue 119 VAL Chi-restraints excluded: chain BG residue 123 VAL Chi-restraints excluded: chain BG residue 124 TRP Chi-restraints excluded: chain BG residue 127 VAL Chi-restraints excluded: chain BG residue 163 THR Chi-restraints excluded: chain BG residue 164 THR Chi-restraints excluded: chain BG residue 181 THR Chi-restraints excluded: chain BG residue 258 ILE Chi-restraints excluded: chain BG residue 341 GLU Chi-restraints excluded: chain BG residue 348 TYR Chi-restraints excluded: chain BG residue 362 THR Chi-restraints excluded: chain BG residue 369 LEU Chi-restraints excluded: chain BG residue 430 TRP Chi-restraints excluded: chain BH residue 104 VAL Chi-restraints excluded: chain BH residue 123 VAL Chi-restraints excluded: chain BH residue 124 TRP Chi-restraints excluded: chain BH residue 135 VAL Chi-restraints excluded: chain BH residue 163 THR Chi-restraints excluded: chain BH residue 181 THR Chi-restraints excluded: chain BH residue 185 SER Chi-restraints excluded: chain BH residue 258 ILE Chi-restraints excluded: chain BH residue 260 VAL Chi-restraints excluded: chain BH residue 293 TRP Chi-restraints excluded: chain BH residue 347 SER Chi-restraints excluded: chain BH residue 348 TYR Chi-restraints excluded: chain BH residue 419 LEU Chi-restraints excluded: chain BI residue 21 SER Chi-restraints excluded: chain BI residue 36 LEU Chi-restraints excluded: chain BI residue 51 THR Chi-restraints excluded: chain BI residue 89 GLN Chi-restraints excluded: chain BI residue 118 ASP Chi-restraints excluded: chain BI residue 119 VAL Chi-restraints excluded: chain BI residue 124 TRP Chi-restraints excluded: chain BI residue 198 THR Chi-restraints excluded: chain BI residue 258 ILE Chi-restraints excluded: chain BI residue 260 VAL Chi-restraints excluded: chain BI residue 324 VAL Chi-restraints excluded: chain BI residue 345 GLN Chi-restraints excluded: chain BI residue 348 TYR Chi-restraints excluded: chain BI residue 362 THR Chi-restraints excluded: chain BI residue 373 SER Chi-restraints excluded: chain BI residue 397 THR Chi-restraints excluded: chain BI residue 426 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 105 optimal weight: 0.0170 chunk 119 optimal weight: 0.7980 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BG 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BH 89 GLN ** BH 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 82 HIS BI 89 GLN ** BI 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.094976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.068482 restraints weight = 27640.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.071531 restraints weight = 16731.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.073648 restraints weight = 11582.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.075274 restraints weight = 8727.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.076463 restraints weight = 6949.215| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.6345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 9971 Z= 0.214 Angle : 0.776 9.593 13668 Z= 0.413 Chirality : 0.050 0.235 1606 Planarity : 0.006 0.080 1853 Dihedral : 7.015 42.247 1406 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 5.08 % Allowed : 29.22 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.21), residues: 1334 helix: 1.34 (1.05), residues: 30 sheet: -0.39 (0.35), residues: 201 loop : -2.03 (0.17), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGBH 339 TYR 0.028 0.003 TYRBG 32 PHE 0.041 0.003 PHEBI 385 TRP 0.040 0.003 TRPBG 430 HIS 0.008 0.002 HISBG 82 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 9971) covalent geometry : angle 0.77562 (13668) hydrogen bonds : bond 0.04027 ( 184) hydrogen bonds : angle 6.82213 ( 417) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2668 Ramachandran restraints generated. 1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 233 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BG 92 TYR cc_start: 0.7219 (m-80) cc_final: 0.6936 (m-10) REVERT: BG 119 VAL cc_start: 0.8216 (OUTLIER) cc_final: 0.7442 (p) REVERT: BG 124 TRP cc_start: 0.7094 (OUTLIER) cc_final: 0.5591 (m100) REVERT: BG 141 ASN cc_start: 0.8918 (t0) cc_final: 0.8561 (t0) REVERT: BG 194 ASP cc_start: 0.8164 (t0) cc_final: 0.7701 (t0) REVERT: BG 219 LYS cc_start: 0.8505 (ptpp) cc_final: 0.8179 (pttp) REVERT: BG 244 LYS cc_start: 0.8485 (ptpp) cc_final: 0.8152 (ptpp) REVERT: BG 262 ASN cc_start: 0.9019 (m110) cc_final: 0.8734 (m110) REVERT: BG 283 MET cc_start: 0.8096 (mmm) cc_final: 0.7591 (mmm) REVERT: BG 294 ARG cc_start: 0.9004 (mtp85) cc_final: 0.8601 (mmp80) REVERT: BG 341 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.6529 (mm-30) REVERT: BG 379 PHE cc_start: 0.7851 (m-80) cc_final: 0.7291 (m-80) REVERT: BH 45 TYR cc_start: 0.9364 (p90) cc_final: 0.9011 (p90) REVERT: BH 53 SER cc_start: 0.9185 (m) cc_final: 0.8715 (p) REVERT: BH 92 TYR cc_start: 0.7389 (m-80) cc_final: 0.6546 (m-80) REVERT: BH 98 ASP cc_start: 0.8901 (t0) cc_final: 0.8625 (t0) REVERT: BH 133 ASP cc_start: 0.8421 (m-30) cc_final: 0.8101 (m-30) REVERT: BH 136 TYR cc_start: 0.8079 (p90) cc_final: 0.7291 (p90) REVERT: BH 186 ASP cc_start: 0.9282 (t0) cc_final: 0.9032 (t0) REVERT: BH 194 ASP cc_start: 0.8042 (t0) cc_final: 0.7738 (t0) REVERT: BH 212 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7509 (mm-30) REVERT: BH 241 GLN cc_start: 0.8643 (mm110) cc_final: 0.8368 (mp10) REVERT: BH 283 MET cc_start: 0.8078 (mmm) cc_final: 0.7467 (mmm) REVERT: BH 293 TRP cc_start: 0.9045 (OUTLIER) cc_final: 0.7973 (m-10) REVERT: BH 321 LEU cc_start: 0.9187 (tt) cc_final: 0.8446 (mp) REVERT: BH 324 VAL cc_start: 0.9367 (p) cc_final: 0.9154 (t) REVERT: BH 419 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8865 (pp) REVERT: BH 431 GLU cc_start: 0.7583 (tt0) cc_final: 0.7003 (tt0) REVERT: BH 433 PHE cc_start: 0.8894 (m-80) cc_final: 0.8394 (m-10) REVERT: BI 24 ASP cc_start: 0.8836 (m-30) cc_final: 0.8330 (t0) REVERT: BI 45 TYR cc_start: 0.9367 (p90) cc_final: 0.9139 (p90) REVERT: BI 53 SER cc_start: 0.9128 (m) cc_final: 0.8687 (p) REVERT: BI 92 TYR cc_start: 0.6430 (m-80) cc_final: 0.5975 (m-10) REVERT: BI 119 VAL cc_start: 0.8024 (OUTLIER) cc_final: 0.7781 (m) REVERT: BI 124 TRP cc_start: 0.6731 (OUTLIER) cc_final: 0.6459 (m100) REVERT: BI 152 LYS cc_start: 0.9322 (tttm) cc_final: 0.8459 (tttm) REVERT: BI 186 ASP cc_start: 0.9283 (t0) cc_final: 0.9016 (t0) REVERT: BI 194 ASP cc_start: 0.8174 (t0) cc_final: 0.7548 (t0) REVERT: BI 198 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8593 (m) REVERT: BI 244 LYS cc_start: 0.8408 (mtpp) cc_final: 0.8131 (mttp) REVERT: BI 283 MET cc_start: 0.8027 (mmm) cc_final: 0.7495 (mmm) REVERT: BI 317 PHE cc_start: 0.9385 (m-10) cc_final: 0.9036 (m-10) REVERT: BI 324 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8684 (t) REVERT: BI 431 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7280 (mt-10) outliers start: 56 outliers final: 40 residues processed: 266 average time/residue: 0.1038 time to fit residues: 38.2998 Evaluate side-chains 282 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BG residue 28 ASP Chi-restraints excluded: chain BG residue 51 THR Chi-restraints excluded: chain BG residue 95 ASN Chi-restraints excluded: chain BG residue 115 LEU Chi-restraints excluded: chain BG residue 119 VAL Chi-restraints excluded: chain BG residue 123 VAL Chi-restraints excluded: chain BG residue 124 TRP Chi-restraints excluded: chain BG residue 127 VAL Chi-restraints excluded: chain BG residue 163 THR Chi-restraints excluded: chain BG residue 164 THR Chi-restraints excluded: chain BG residue 181 THR Chi-restraints excluded: chain BG residue 258 ILE Chi-restraints excluded: chain BG residue 341 GLU Chi-restraints excluded: chain BG residue 348 TYR Chi-restraints excluded: chain BG residue 362 THR Chi-restraints excluded: chain BG residue 430 TRP Chi-restraints excluded: chain BG residue 433 PHE Chi-restraints excluded: chain BH residue 104 VAL Chi-restraints excluded: chain BH residue 123 VAL Chi-restraints excluded: chain BH residue 124 TRP Chi-restraints excluded: chain BH residue 135 VAL Chi-restraints excluded: chain BH residue 163 THR Chi-restraints excluded: chain BH residue 181 THR Chi-restraints excluded: chain BH residue 185 SER Chi-restraints excluded: chain BH residue 258 ILE Chi-restraints excluded: chain BH residue 260 VAL Chi-restraints excluded: chain BH residue 293 TRP Chi-restraints excluded: chain BH residue 347 SER Chi-restraints excluded: chain BH residue 348 TYR Chi-restraints excluded: chain BH residue 419 LEU Chi-restraints excluded: chain BI residue 21 SER Chi-restraints excluded: chain BI residue 36 LEU Chi-restraints excluded: chain BI residue 51 THR Chi-restraints excluded: chain BI residue 89 GLN Chi-restraints excluded: chain BI residue 104 VAL Chi-restraints excluded: chain BI residue 118 ASP Chi-restraints excluded: chain BI residue 119 VAL Chi-restraints excluded: chain BI residue 124 TRP Chi-restraints excluded: chain BI residue 174 VAL Chi-restraints excluded: chain BI residue 198 THR Chi-restraints excluded: chain BI residue 258 ILE Chi-restraints excluded: chain BI residue 260 VAL Chi-restraints excluded: chain BI residue 324 VAL Chi-restraints excluded: chain BI residue 345 GLN Chi-restraints excluded: chain BI residue 348 TYR Chi-restraints excluded: chain BI residue 362 THR Chi-restraints excluded: chain BI residue 373 SER Chi-restraints excluded: chain BI residue 397 THR Chi-restraints excluded: chain BI residue 426 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 35 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 108 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 125 optimal weight: 0.0170 chunk 3 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BG 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 82 HIS ** BH 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 82 HIS ** BI 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.099255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.072088 restraints weight = 27335.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075195 restraints weight = 16465.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.077439 restraints weight = 11357.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.079075 restraints weight = 8542.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.080300 restraints weight = 6810.851| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9971 Z= 0.147 Angle : 0.778 9.339 13668 Z= 0.409 Chirality : 0.050 0.352 1606 Planarity : 0.006 0.072 1853 Dihedral : 6.815 40.515 1406 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 4.36 % Allowed : 30.31 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.21), residues: 1334 helix: 0.94 (1.06), residues: 30 sheet: -0.32 (0.34), residues: 204 loop : -1.99 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGBH 339 TYR 0.032 0.002 TYRBG 32 PHE 0.033 0.003 PHEBG 426 TRP 0.039 0.002 TRPBG 430 HIS 0.005 0.001 HISBG 82 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9971) covalent geometry : angle 0.77775 (13668) hydrogen bonds : bond 0.03711 ( 184) hydrogen bonds : angle 6.78275 ( 417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1899.05 seconds wall clock time: 33 minutes 33.79 seconds (2013.79 seconds total)