Starting phenix.real_space_refine on Wed Jun 3 15:36:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uxb_64579/06_2026/9uxb_64579_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uxb_64579/06_2026/9uxb_64579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uxb_64579/06_2026/9uxb_64579_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uxb_64579/06_2026/9uxb_64579_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uxb_64579/06_2026/9uxb_64579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uxb_64579/06_2026/9uxb_64579.map" } resolution = 2.92 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= 0.025 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 P 6 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 4229 2.51 5 N 1144 2.21 5 O 1284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6709 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 446 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} Chain: "B" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2785 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 18, 'TRANS': 338} Chain breaks: 1 Chain: "C" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3186 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 22, 'TRANS': 387} Chain breaks: 1 Chain: "D" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 228 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.84, per 1000 atoms: 0.27 Number of scatterers: 6709 At special positions: 0 Unit cell: (75.19, 89.79, 105.85, 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) S 44 16.00 P 6 15.00 Mg 2 11.99 O 1284 8.00 N 1144 7.00 C 4229 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: 0.51 Conformation dependent library (CDL) restraints added in 317.6 milliseconds 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 13 sheets defined 47.7% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 464 through 514 removed outlier: 3.550A pdb=" N ARG A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 81 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.804A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.072A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.676A pdb=" N GLY B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.604A pdb=" N ARG B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.756A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 4.318A pdb=" N LYS B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 4.132A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.585A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 70 through 76 removed outlier: 4.090A pdb=" N ALA C 74 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG C 76 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 110 Processing helix chain 'C' and resid 129 through 143 Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 198 through 213 Processing helix chain 'C' and resid 219 through 221 No H-bonds generated for 'chain 'C' and resid 219 through 221' Processing helix chain 'C' and resid 247 through 266 Processing helix chain 'C' and resid 275 through 281 removed outlier: 3.678A pdb=" N GLN C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.807A pdb=" N PHE C 309 " --> pdb=" O PRO C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 Processing helix chain 'C' and resid 337 through 339 No H-bonds generated for 'chain 'C' and resid 337 through 339' Processing helix chain 'C' and resid 340 through 346 Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.536A pdb=" N ILE C 357 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 372 removed outlier: 3.886A pdb=" N ARG C 363 " --> pdb=" O SER C 359 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 370 " --> pdb=" O ARG C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 391 Processing helix chain 'C' and resid 391 through 402 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 422 through 428 removed outlier: 3.701A pdb=" N ARG C 426 " --> pdb=" O GLN C 422 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.684A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.500A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N MET B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 238 through 242 removed outlier: 3.752A pdb=" N GLN B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 35 through 38 removed outlier: 3.640A pdb=" N PHE C 37 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 123 " --> pdb=" O PHE C 16 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 44 removed outlier: 3.740A pdb=" N VAL C 44 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR C 67 " --> pdb=" O VAL C 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 88 through 89 Processing sheet with id=AA9, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB1, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB2, first strand: chain 'C' and resid 223 through 226 removed outlier: 6.933A pdb=" N LYS C 238 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 285 through 288 Processing sheet with id=AB4, first strand: chain 'D' and resid 31 through 37 324 hydrogen bonds defined for protein. 867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.81 Time building geometry restraints manager: 0.71 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: 1949 1.34 - 1.45: 1072 1.45 - 1.57: 3753 1.57 - 1.69: 10 1.69 - 1.81: 73 Bond restraints: 6857 Sorted by residual: bond pdb=" N ILE D 45 " pdb=" CA ILE D 45 " ideal model delta sigma weight residual 1.458 1.490 -0.033 1.14e-02 7.69e+03 8.13e+00 bond pdb=" N ILE C 70 " pdb=" CA ILE C 70 " ideal model delta sigma weight residual 1.455 1.493 -0.037 1.32e-02 5.74e+03 8.04e+00 bond pdb=" N VAL B 35 " pdb=" CA VAL B 35 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.29e-02 6.01e+03 6.41e+00 bond pdb=" N LEU C 323 " pdb=" CA LEU C 323 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.35e+00 bond pdb=" N ASP C 71 " pdb=" CA ASP C 71 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.33e+00 ... (remaining 6852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 9157 2.68 - 5.35: 117 5.35 - 8.03: 19 8.03 - 10.71: 2 10.71 - 13.38: 1 Bond angle restraints: 9296 Sorted by residual: angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 131.36 8.51 1.00e+00 1.00e+00 7.24e+01 angle pdb=" C3' ATP B 501 " pdb=" C4' ATP B 501 " pdb=" C5' ATP B 501 " ideal model delta sigma weight residual 115.19 128.57 -13.38 1.76e+00 3.23e-01 5.78e+01 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 129.34 7.49 1.00e+00 1.00e+00 5.61e+01 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 133.41 6.46 1.00e+00 1.00e+00 4.18e+01 angle pdb=" C5' ATP B 501 " pdb=" C4' ATP B 501 " pdb=" O4' ATP B 501 " ideal model delta sigma weight residual 109.53 117.36 -7.83 1.44e+00 4.84e-01 2.97e+01 ... (remaining 9291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 3599 17.66 - 35.33: 378 35.33 - 52.99: 127 52.99 - 70.65: 37 70.65 - 88.32: 12 Dihedral angle restraints: 4153 sinusoidal: 1713 harmonic: 2440 Sorted by residual: dihedral pdb=" CG ARG C 248 " pdb=" CD ARG C 248 " pdb=" NE ARG C 248 " pdb=" CZ ARG C 248 " ideal model delta sinusoidal sigma weight residual 90.00 41.03 48.97 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CG ARG A 513 " pdb=" CD ARG A 513 " pdb=" NE ARG A 513 " pdb=" CZ ARG A 513 " ideal model delta sinusoidal sigma weight residual 90.00 41.62 48.38 2 1.50e+01 4.44e-03 1.19e+01 dihedral pdb=" CA ASP C 171 " pdb=" CB ASP C 171 " pdb=" CG ASP C 171 " pdb=" OD1 ASP C 171 " ideal model delta sinusoidal sigma weight residual -30.00 -88.91 58.91 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 4150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.309: 1021 0.309 - 0.617: 0 0.617 - 0.926: 0 0.926 - 1.234: 0 1.234 - 1.543: 1 Chirality restraints: 1022 Sorted by residual: chirality pdb=" C4' ATP B 501 " pdb=" C3' ATP B 501 " pdb=" C5' ATP B 501 " pdb=" O4' ATP B 501 " both_signs ideal model delta sigma weight residual False -2.49 -0.95 -1.54 2.00e-01 2.50e+01 5.95e+01 chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ILE C 70 " pdb=" N ILE C 70 " pdb=" C ILE C 70 " pdb=" CB ILE C 70 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.22e-01 ... (remaining 1019 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 26 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO B 27 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 27 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 27 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 377 " 0.158 9.50e-02 1.11e+02 7.13e-02 3.88e+00 pdb=" NE ARG C 377 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 377 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG C 377 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 377 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 195 " -0.008 2.00e-02 2.50e+03 1.74e-02 3.01e+00 pdb=" CD GLU B 195 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU B 195 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 195 " -0.011 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1348 2.78 - 3.31: 6114 3.31 - 3.84: 11323 3.84 - 4.37: 13439 4.37 - 4.90: 22978 Nonbonded interactions: 55202 Sorted by model distance: nonbonded pdb=" O ASP B 157 " pdb=" OD1 ASP B 157 " model vdw 2.253 3.040 nonbonded pdb="MG MG B 500 " pdb=" O2G ATP B 501 " model vdw 2.257 2.170 nonbonded pdb=" O MET B 190 " pdb=" OG1 THR B 194 " model vdw 2.282 3.040 nonbonded pdb=" O GLY C 191 " pdb=" OG SER C 332 " model vdw 2.295 3.040 nonbonded pdb=" OG1 THR B 160 " pdb=" O LEU B 180 " model vdw 2.311 3.040 ... (remaining 55197 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.300 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: 0.020 Set scattering table: 0.030 Process input model: 7.750 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 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 : 0.004 0.047 6857 Z= 0.218 Angle : 0.798 13.382 9296 Z= 0.492 Chirality : 0.067 1.543 1022 Planarity : 0.006 0.071 1184 Dihedral : 17.403 88.317 2585 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.28 % Allowed : 23.07 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.28), residues: 833 helix: -0.45 (0.27), residues: 362 sheet: -0.08 (0.44), residues: 128 loop : -0.03 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 377 TYR 0.012 0.001 TYR A 475 PHE 0.018 0.001 PHE A 486 TRP 0.010 0.001 TRP B 79 HIS 0.003 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.22 ( 6857) covalent geometry : angle 0.79819 / 0.49 ( 9296) hydrogen bonds : bond 0.18166 / 12.46 ( 320) hydrogen bonds : angle 7.28749 / 5.33 ( 867) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.283 Fit side-chains REVERT: A 488 GLU cc_start: 0.7296 (tp30) cc_final: 0.6406 (pt0) REVERT: A 502 LYS cc_start: 0.5975 (mptm) cc_final: 0.5590 (mmtm) REVERT: B 95 ARG cc_start: 0.6834 (mtp85) cc_final: 0.6634 (mmt-90) REVERT: B 214 GLU cc_start: 0.6343 (mt-10) cc_final: 0.6089 (mt-10) REVERT: B 276 GLU cc_start: 0.6266 (mt-10) cc_final: 0.5925 (mm-30) REVERT: B 354 GLN cc_start: 0.7925 (mt0) cc_final: 0.7642 (pt0) REVERT: C 27 TYR cc_start: 0.7130 (m-80) cc_final: 0.6777 (m-80) REVERT: C 43 MET cc_start: 0.6156 (ttm) cc_final: 0.5198 (ttp) REVERT: C 44 VAL cc_start: 0.6033 (m) cc_final: 0.5563 (t) REVERT: C 80 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6562 (mp0) REVERT: C 95 ASP cc_start: 0.7490 (t0) cc_final: 0.7232 (t0) REVERT: C 145 ASN cc_start: 0.8031 (t0) cc_final: 0.7746 (t0) REVERT: C 212 GLU cc_start: 0.6621 (pp20) cc_final: 0.6043 (mm-30) REVERT: C 238 LYS cc_start: 0.6993 (mmpt) cc_final: 0.5648 (mttm) outliers start: 2 outliers final: 3 residues processed: 131 average time/residue: 0.5931 time to fit residues: 81.3787 Evaluate side-chains 94 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain D residue 49 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.3980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0270 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS B 12 ASN B 296 ASN C 100 GLN C 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.193391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.167805 restraints weight = 7023.859| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.36 r_work: 0.3651 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6857 Z= 0.137 Angle : 0.544 6.928 9296 Z= 0.289 Chirality : 0.044 0.140 1022 Planarity : 0.005 0.039 1184 Dihedral : 8.309 85.754 985 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.14 % Allowed : 20.86 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.29), residues: 833 helix: 0.42 (0.28), residues: 349 sheet: -0.13 (0.41), residues: 139 loop : 0.35 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 372 TYR 0.015 0.002 TYR A 475 PHE 0.017 0.002 PHE A 486 TRP 0.012 0.001 TRP C 394 HIS 0.005 0.002 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 6857) covalent geometry : angle 0.54365 / 0.29 ( 9296) hydrogen bonds : bond 0.03716 / 2.63 ( 320) hydrogen bonds : angle 5.05090 / 3.72 ( 867) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 488 GLU cc_start: 0.8362 (tp30) cc_final: 0.8045 (pt0) REVERT: A 502 LYS cc_start: 0.7598 (mptm) cc_final: 0.7266 (mmtm) REVERT: B 119 MET cc_start: 0.8504 (mtp) cc_final: 0.8296 (mtm) REVERT: B 128 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7947 (t0) REVERT: B 190 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.6300 (mtt) REVERT: B 353 GLN cc_start: 0.8301 (mm110) cc_final: 0.7980 (mm110) REVERT: B 354 GLN cc_start: 0.8292 (mt0) cc_final: 0.7848 (pt0) REVERT: C 10 GLU cc_start: 0.4965 (OUTLIER) cc_final: 0.3713 (pp20) REVERT: C 27 TYR cc_start: 0.8299 (m-80) cc_final: 0.7991 (m-80) REVERT: C 43 MET cc_start: 0.7163 (ttm) cc_final: 0.6839 (ttp) REVERT: C 44 VAL cc_start: 0.7023 (OUTLIER) cc_final: 0.6647 (t) REVERT: C 177 THR cc_start: 0.9189 (t) cc_final: 0.8778 (m) REVERT: C 288 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7952 (tt0) outliers start: 30 outliers final: 14 residues processed: 116 average time/residue: 0.5698 time to fit residues: 69.2215 Evaluate side-chains 106 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 49 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS A 498 GLN B 296 ASN C 110 HIS C 354 ASN C 422 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.177549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.151125 restraints weight = 6907.981| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.46 r_work: 0.3460 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 6857 Z= 0.254 Angle : 0.662 8.374 9296 Z= 0.348 Chirality : 0.051 0.244 1022 Planarity : 0.005 0.038 1184 Dihedral : 9.122 89.103 982 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.80 % Allowed : 19.06 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.29), residues: 833 helix: 0.12 (0.27), residues: 354 sheet: -0.04 (0.42), residues: 128 loop : 0.26 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 389 TYR 0.021 0.002 TYR A 475 PHE 0.025 0.002 PHE C 37 TRP 0.016 0.002 TRP C 394 HIS 0.007 0.002 HIS C 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.25 ( 6857) covalent geometry : angle 0.66236 / 0.35 ( 9296) hydrogen bonds : bond 0.04760 / 3.34 ( 320) hydrogen bonds : angle 5.26386 / 3.86 ( 867) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 92 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 502 LYS cc_start: 0.7967 (mptm) cc_final: 0.7684 (mmtm) REVERT: A 506 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8626 (m) REVERT: B 82 MET cc_start: 0.7023 (tpp) cc_final: 0.6767 (tpp) REVERT: B 190 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6701 (mtt) REVERT: B 353 GLN cc_start: 0.8531 (mm110) cc_final: 0.8295 (mm110) REVERT: C 27 TYR cc_start: 0.8753 (m-80) cc_final: 0.8426 (m-80) REVERT: C 43 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7258 (tmm) REVERT: C 140 MET cc_start: 0.8576 (tpt) cc_final: 0.8341 (tpt) REVERT: C 177 THR cc_start: 0.9461 (t) cc_final: 0.9037 (m) REVERT: C 288 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: C 296 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6833 (t70) outliers start: 42 outliers final: 17 residues processed: 119 average time/residue: 0.4766 time to fit residues: 59.9451 Evaluate side-chains 105 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 56 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 82 optimal weight: 0.0040 chunk 25 optimal weight: 1.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN B 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.178249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.151531 restraints weight = 6837.060| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.33 r_work: 0.3459 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6857 Z= 0.160 Angle : 0.538 7.239 9296 Z= 0.286 Chirality : 0.046 0.137 1022 Planarity : 0.004 0.035 1184 Dihedral : 8.367 77.670 982 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.39 % Allowed : 19.06 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.29), residues: 833 helix: 0.40 (0.28), residues: 355 sheet: 0.09 (0.42), residues: 122 loop : 0.33 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 248 TYR 0.015 0.002 TYR A 475 PHE 0.023 0.002 PHE A 486 TRP 0.013 0.002 TRP C 394 HIS 0.006 0.001 HIS C 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 6857) covalent geometry : angle 0.53826 / 0.29 ( 9296) hydrogen bonds : bond 0.03775 / 2.68 ( 320) hydrogen bonds : angle 4.95963 / 3.63 ( 867) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 83 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 LYS cc_start: 0.7985 (mptm) cc_final: 0.7686 (mmtm) REVERT: B 149 THR cc_start: 0.8183 (t) cc_final: 0.7745 (m) REVERT: B 190 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6635 (mtt) REVERT: B 315 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8312 (tttt) REVERT: B 360 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: C 10 GLU cc_start: 0.5662 (OUTLIER) cc_final: 0.4473 (pp20) REVERT: C 27 TYR cc_start: 0.8712 (m-80) cc_final: 0.8371 (m-80) REVERT: C 43 MET cc_start: 0.7765 (ttm) cc_final: 0.7267 (tmm) REVERT: C 140 MET cc_start: 0.8569 (tpt) cc_final: 0.8363 (tpt) REVERT: C 177 THR cc_start: 0.9424 (t) cc_final: 0.9084 (m) outliers start: 39 outliers final: 19 residues processed: 112 average time/residue: 0.5440 time to fit residues: 64.0886 Evaluate side-chains 100 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 49 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 70 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS B 92 ASN B 296 ASN B 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.180318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.153754 restraints weight = 6875.320| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.34 r_work: 0.3491 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6857 Z= 0.120 Angle : 0.494 6.801 9296 Z= 0.264 Chirality : 0.044 0.133 1022 Planarity : 0.004 0.034 1184 Dihedral : 7.996 80.131 982 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.52 % Allowed : 19.06 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.29), residues: 833 helix: 0.76 (0.29), residues: 349 sheet: 0.06 (0.41), residues: 134 loop : 0.46 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 372 TYR 0.013 0.001 TYR A 475 PHE 0.024 0.001 PHE A 486 TRP 0.010 0.001 TRP C 394 HIS 0.004 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 6857) covalent geometry : angle 0.49385 / 0.26 ( 9296) hydrogen bonds : bond 0.03357 / 2.40 ( 320) hydrogen bonds : angle 4.76514 / 3.48 ( 867) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 83 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8457 (m) REVERT: A 502 LYS cc_start: 0.7834 (mptm) cc_final: 0.7520 (mmtm) REVERT: B 149 THR cc_start: 0.8125 (t) cc_final: 0.7696 (m) REVERT: B 190 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6431 (mtt) REVERT: B 315 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8300 (tttt) REVERT: B 325 MET cc_start: 0.8144 (ttm) cc_final: 0.7796 (ttm) REVERT: B 353 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8228 (mm110) REVERT: B 360 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7892 (tt0) REVERT: C 27 TYR cc_start: 0.8686 (m-80) cc_final: 0.8331 (m-80) REVERT: C 43 MET cc_start: 0.7610 (ttm) cc_final: 0.7149 (tmm) REVERT: C 73 ASN cc_start: 0.7577 (m-40) cc_final: 0.7325 (m110) REVERT: C 89 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7838 (pttm) REVERT: C 177 THR cc_start: 0.9350 (t) cc_final: 0.9142 (m) REVERT: C 247 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.8046 (m) outliers start: 40 outliers final: 21 residues processed: 112 average time/residue: 0.5214 time to fit residues: 61.5970 Evaluate side-chains 107 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 49 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.0770 chunk 30 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 34 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 60 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS B 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.182112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.155624 restraints weight = 6847.665| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.35 r_work: 0.3515 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6857 Z= 0.104 Angle : 0.475 6.543 9296 Z= 0.254 Chirality : 0.043 0.128 1022 Planarity : 0.004 0.033 1184 Dihedral : 7.633 87.336 982 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.56 % Allowed : 20.03 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.30), residues: 833 helix: 0.97 (0.29), residues: 349 sheet: 0.09 (0.42), residues: 132 loop : 0.57 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 248 TYR 0.012 0.001 TYR A 475 PHE 0.021 0.001 PHE A 486 TRP 0.008 0.001 TRP D 35 HIS 0.003 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 ( 6857) covalent geometry : angle 0.47454 / 0.25 ( 9296) hydrogen bonds : bond 0.03129 / 2.24 ( 320) hydrogen bonds : angle 4.61317 / 3.37 ( 867) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8508 (m) REVERT: A 502 LYS cc_start: 0.7818 (mptm) cc_final: 0.7512 (mmtm) REVERT: B 149 THR cc_start: 0.8055 (t) cc_final: 0.7627 (m) REVERT: B 190 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6486 (mtt) REVERT: B 315 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8265 (tttt) REVERT: B 325 MET cc_start: 0.8084 (ttm) cc_final: 0.7774 (ttm) REVERT: B 353 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8236 (mm110) REVERT: B 360 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: C 10 GLU cc_start: 0.5480 (OUTLIER) cc_final: 0.4410 (pp20) REVERT: C 27 TYR cc_start: 0.8679 (m-80) cc_final: 0.8339 (m-80) REVERT: C 43 MET cc_start: 0.7602 (ttm) cc_final: 0.7198 (tmm) REVERT: C 73 ASN cc_start: 0.7552 (m-40) cc_final: 0.7287 (m110) REVERT: C 89 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7866 (pttm) outliers start: 33 outliers final: 18 residues processed: 109 average time/residue: 0.5532 time to fit residues: 63.5281 Evaluate side-chains 103 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 49 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 20 optimal weight: 0.0030 chunk 21 optimal weight: 0.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS B 92 ASN B 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.181870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.156061 restraints weight = 6768.366| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.28 r_work: 0.3512 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6857 Z= 0.111 Angle : 0.480 6.789 9296 Z= 0.256 Chirality : 0.043 0.129 1022 Planarity : 0.004 0.033 1184 Dihedral : 7.465 87.941 982 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.56 % Allowed : 19.48 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.30), residues: 833 helix: 1.05 (0.29), residues: 350 sheet: 0.15 (0.42), residues: 132 loop : 0.74 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 248 TYR 0.011 0.001 TYR C 144 PHE 0.024 0.001 PHE A 486 TRP 0.009 0.001 TRP C 394 HIS 0.004 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 6857) covalent geometry : angle 0.48047 / 0.26 ( 9296) hydrogen bonds : bond 0.03162 / 2.24 ( 320) hydrogen bonds : angle 4.59783 / 3.36 ( 867) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 84 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8554 (m) REVERT: A 502 LYS cc_start: 0.7842 (mptm) cc_final: 0.7542 (mmtm) REVERT: B 149 THR cc_start: 0.8125 (t) cc_final: 0.7691 (m) REVERT: B 190 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6500 (mtt) REVERT: B 315 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8280 (tttt) REVERT: B 325 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7789 (ttm) REVERT: B 353 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8240 (mm110) REVERT: B 360 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: C 10 GLU cc_start: 0.5515 (OUTLIER) cc_final: 0.4455 (pp20) REVERT: C 27 TYR cc_start: 0.8684 (m-80) cc_final: 0.8344 (m-80) REVERT: C 43 MET cc_start: 0.7610 (ttm) cc_final: 0.7242 (tmm) REVERT: C 73 ASN cc_start: 0.7555 (m-40) cc_final: 0.7281 (m110) REVERT: C 89 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7907 (pttm) outliers start: 33 outliers final: 15 residues processed: 107 average time/residue: 0.5836 time to fit residues: 65.6700 Evaluate side-chains 102 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 361 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 60 optimal weight: 0.0170 chunk 67 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS B 92 ASN B 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.180015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.153500 restraints weight = 6872.240| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.35 r_work: 0.3477 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6857 Z= 0.129 Angle : 0.502 7.263 9296 Z= 0.267 Chirality : 0.044 0.131 1022 Planarity : 0.004 0.032 1184 Dihedral : 7.614 89.271 981 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.97 % Allowed : 19.20 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.30), residues: 833 helix: 0.94 (0.29), residues: 356 sheet: 0.22 (0.45), residues: 120 loop : 0.72 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 372 TYR 0.012 0.001 TYR C 144 PHE 0.021 0.001 PHE A 486 TRP 0.010 0.001 TRP C 394 HIS 0.004 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 6857) covalent geometry : angle 0.50198 / 0.27 ( 9296) hydrogen bonds : bond 0.03376 / 2.40 ( 320) hydrogen bonds : angle 4.65014 / 3.39 ( 867) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 LYS cc_start: 0.7717 (mptm) cc_final: 0.7375 (mmtm) REVERT: B 119 MET cc_start: 0.8623 (mtp) cc_final: 0.8340 (mtm) REVERT: B 149 THR cc_start: 0.8075 (t) cc_final: 0.7740 (m) REVERT: B 190 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.6308 (mtt) REVERT: B 315 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8177 (tttt) REVERT: B 325 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7732 (ttm) REVERT: B 360 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7851 (tt0) REVERT: C 10 GLU cc_start: 0.5308 (OUTLIER) cc_final: 0.4310 (pp20) REVERT: C 27 TYR cc_start: 0.8570 (m-80) cc_final: 0.8251 (m-80) REVERT: C 73 ASN cc_start: 0.7446 (m-40) cc_final: 0.7167 (m110) REVERT: C 89 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7919 (pttm) outliers start: 36 outliers final: 17 residues processed: 108 average time/residue: 0.5447 time to fit residues: 62.0518 Evaluate side-chains 101 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 28 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 30 optimal weight: 3.9990 chunk 76 optimal weight: 0.0060 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS B 296 ASN B 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.178519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.153021 restraints weight = 6882.230| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.37 r_work: 0.3498 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6857 Z= 0.125 Angle : 0.505 7.179 9296 Z= 0.267 Chirality : 0.044 0.136 1022 Planarity : 0.004 0.032 1184 Dihedral : 7.637 89.592 981 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.28 % Allowed : 20.03 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.30), residues: 833 helix: 0.95 (0.29), residues: 356 sheet: 0.19 (0.45), residues: 120 loop : 0.75 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 372 TYR 0.012 0.001 TYR A 475 PHE 0.024 0.001 PHE A 486 TRP 0.010 0.001 TRP C 394 HIS 0.004 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 6857) covalent geometry : angle 0.50488 / 0.27 ( 9296) hydrogen bonds : bond 0.03332 / 2.36 ( 320) hydrogen bonds : angle 4.63527 / 3.38 ( 867) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 LYS cc_start: 0.7879 (mptm) cc_final: 0.7546 (mmtm) REVERT: B 119 MET cc_start: 0.8692 (mtp) cc_final: 0.8419 (mtm) REVERT: B 149 THR cc_start: 0.8176 (t) cc_final: 0.7724 (m) REVERT: B 190 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6457 (mtt) REVERT: B 215 LYS cc_start: 0.8222 (ttmm) cc_final: 0.7903 (mttt) REVERT: B 315 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8262 (tttt) REVERT: B 325 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7792 (ttm) REVERT: B 360 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: C 27 TYR cc_start: 0.8682 (m-80) cc_final: 0.8343 (m-80) REVERT: C 73 ASN cc_start: 0.7527 (m-40) cc_final: 0.7246 (m110) REVERT: C 89 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8006 (pttm) REVERT: C 231 GLU cc_start: 0.6554 (mp0) cc_final: 0.6297 (mt-10) outliers start: 31 outliers final: 19 residues processed: 106 average time/residue: 0.5896 time to fit residues: 65.6793 Evaluate side-chains 109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 28 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 0.0000 chunk 60 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS B 92 ASN B 296 ASN B 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.179844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.154284 restraints weight = 6843.902| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.39 r_work: 0.3492 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6857 Z= 0.124 Angle : 0.504 7.191 9296 Z= 0.267 Chirality : 0.044 0.131 1022 Planarity : 0.004 0.032 1184 Dihedral : 7.615 89.936 981 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.28 % Allowed : 19.75 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.30), residues: 833 helix: 0.98 (0.29), residues: 356 sheet: 0.17 (0.46), residues: 120 loop : 0.77 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 372 TYR 0.011 0.001 TYR C 144 PHE 0.021 0.001 PHE A 486 TRP 0.010 0.001 TRP C 394 HIS 0.003 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 6857) covalent geometry : angle 0.50354 / 0.27 ( 9296) hydrogen bonds : bond 0.03334 / 2.37 ( 320) hydrogen bonds : angle 4.64108 / 3.39 ( 867) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 LYS cc_start: 0.7893 (mptm) cc_final: 0.7557 (mmtm) REVERT: B 119 MET cc_start: 0.8692 (mtp) cc_final: 0.8417 (mtm) REVERT: B 149 THR cc_start: 0.8166 (t) cc_final: 0.7713 (m) REVERT: B 190 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6464 (mtt) REVERT: B 215 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7921 (mttt) REVERT: B 315 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8270 (tttt) REVERT: B 325 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7821 (ttm) REVERT: B 360 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: C 27 TYR cc_start: 0.8686 (m-80) cc_final: 0.8344 (m-80) REVERT: C 89 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8030 (pttm) REVERT: C 231 GLU cc_start: 0.6554 (mp0) cc_final: 0.6310 (mt-10) outliers start: 31 outliers final: 17 residues processed: 105 average time/residue: 0.5567 time to fit residues: 61.5102 Evaluate side-chains 105 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 28 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 15 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 chunk 54 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS B 296 ASN B 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.180859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.154439 restraints weight = 6809.407| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.35 r_work: 0.3515 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6857 Z= 0.111 Angle : 0.490 6.998 9296 Z= 0.260 Chirality : 0.043 0.129 1022 Planarity : 0.004 0.032 1184 Dihedral : 7.401 88.065 981 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.14 % Allowed : 20.03 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.30), residues: 833 helix: 1.12 (0.29), residues: 350 sheet: 0.12 (0.45), residues: 126 loop : 0.84 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 372 TYR 0.011 0.001 TYR C 144 PHE 0.024 0.001 PHE A 486 TRP 0.008 0.001 TRP C 394 HIS 0.005 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 6857) covalent geometry : angle 0.49006 / 0.26 ( 9296) hydrogen bonds : bond 0.03165 / 2.24 ( 320) hydrogen bonds : angle 4.57359 / 3.34 ( 867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2450.03 seconds wall clock time: 42 minutes 50.92 seconds (2570.92 seconds total)