Starting phenix.real_space_refine on Sat Aug 23 00:56:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8trm_41583/08_2025/8trm_41583.cif Found real_map, /net/cci-nas-00/data/ceres_data/8trm_41583/08_2025/8trm_41583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8trm_41583/08_2025/8trm_41583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8trm_41583/08_2025/8trm_41583.map" model { file = "/net/cci-nas-00/data/ceres_data/8trm_41583/08_2025/8trm_41583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8trm_41583/08_2025/8trm_41583.cif" } resolution = 2.5 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= 0.359 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 3 5.21 5 S 57 5.16 5 C 5544 2.51 5 N 1470 2.21 5 O 1734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8814 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Restraints were copied for chains: B, C Time building chain proxies: 1.40, per 1000 atoms: 0.16 Number of scatterers: 8814 At special positions: 0 Unit cell: (77.464, 99.356, 138.93, 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 57 16.00 P 6 15.00 Mg 3 11.99 O 1734 8.00 N 1470 7.00 C 5544 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: 0.59 Conformation dependent library (CDL) restraints added in 382.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 18 sheets defined 50.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 113 through 127 removed outlier: 4.018A pdb=" N ARG A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 146 Processing helix chain 'A' and resid 173 through 176 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 203 through 218 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.575A pdb=" N THR A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.540A pdb=" N GLN A 354 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN A 355 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 367 Processing helix chain 'A' and resid 369 through 375 removed outlier: 4.113A pdb=" N ARG A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 113 through 127 removed outlier: 4.019A pdb=" N ARG B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'B' and resid 173 through 176 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 203 through 218 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.575A pdb=" N THR B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 338 through 349 Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.540A pdb=" N GLN B 354 " --> pdb=" O SER B 351 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B 355 " --> pdb=" O THR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 367 Processing helix chain 'B' and resid 369 through 375 removed outlier: 4.113A pdb=" N ARG B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 79 through 93 Processing helix chain 'C' and resid 113 through 127 removed outlier: 4.018A pdb=" N ARG C 117 " --> pdb=" O PRO C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 146 Processing helix chain 'C' and resid 173 through 176 Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 203 through 218 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 290 through 297 Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.574A pdb=" N THR C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 338 through 349 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.540A pdb=" N GLN C 354 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN C 355 " --> pdb=" O THR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 367 Processing helix chain 'C' and resid 369 through 375 removed outlier: 4.113A pdb=" N ARG C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33 removed outlier: 6.669A pdb=" N LEU A 9 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR A 107 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N VAL A 11 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 171 removed outlier: 6.832A pdb=" N VAL A 298 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.669A pdb=" N LEU B 9 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR B 107 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N VAL B 11 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 171 Processing sheet with id=AB2, first strand: chain 'B' and resid 170 through 171 removed outlier: 6.832A pdb=" N VAL B 298 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 239 through 242 Processing sheet with id=AB4, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.669A pdb=" N LEU C 9 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR C 107 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL C 11 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 72 through 73 Processing sheet with id=AB7, first strand: chain 'C' and resid 170 through 171 Processing sheet with id=AB8, first strand: chain 'C' and resid 170 through 171 removed outlier: 6.832A pdb=" N VAL C 298 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 239 through 242 447 hydrogen bonds defined for protein. 1143 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: 1.01 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2870 1.34 - 1.46: 1656 1.46 - 1.57: 4339 1.57 - 1.69: 9 1.69 - 1.81: 99 Bond restraints: 8973 Sorted by residual: bond pdb=" N ASP B 212 " pdb=" CA ASP B 212 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.76e+00 bond pdb=" N ASP C 212 " pdb=" CA ASP C 212 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.55e+00 bond pdb=" N ASP A 212 " pdb=" CA ASP A 212 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.50e+00 bond pdb=" C4 ADP C 402 " pdb=" C5 ADP C 402 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" C4 ADP A 402 " pdb=" C5 ADP A 402 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.43e+00 ... (remaining 8968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 11802 1.41 - 2.82: 247 2.82 - 4.24: 86 4.24 - 5.65: 13 5.65 - 7.06: 14 Bond angle restraints: 12162 Sorted by residual: angle pdb=" N ILE C 290 " pdb=" CA ILE C 290 " pdb=" C ILE C 290 " ideal model delta sigma weight residual 113.42 109.06 4.36 1.17e+00 7.31e-01 1.39e+01 angle pdb=" N ILE B 290 " pdb=" CA ILE B 290 " pdb=" C ILE B 290 " ideal model delta sigma weight residual 113.42 109.06 4.36 1.17e+00 7.31e-01 1.39e+01 angle pdb=" N ILE A 290 " pdb=" CA ILE A 290 " pdb=" C ILE A 290 " ideal model delta sigma weight residual 113.42 109.07 4.35 1.17e+00 7.31e-01 1.38e+01 angle pdb=" CA ILE A 290 " pdb=" C ILE A 290 " pdb=" N ARG A 291 " ideal model delta sigma weight residual 118.90 115.55 3.35 9.40e-01 1.13e+00 1.27e+01 angle pdb=" CA ILE B 290 " pdb=" C ILE B 290 " pdb=" N ARG B 291 " ideal model delta sigma weight residual 118.90 115.58 3.32 9.40e-01 1.13e+00 1.25e+01 ... (remaining 12157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.62: 5010 28.62 - 57.24: 351 57.24 - 85.86: 36 85.86 - 114.48: 3 114.48 - 143.10: 6 Dihedral angle restraints: 5406 sinusoidal: 2205 harmonic: 3201 Sorted by residual: dihedral pdb=" O1B ADP C 402 " pdb=" O3A ADP C 402 " pdb=" PB ADP C 402 " pdb=" PA ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 83.10 -143.10 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" O1B ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PB ADP B 402 " pdb=" PA ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 83.07 -143.08 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" O1B ADP A 402 " pdb=" O3A ADP A 402 " pdb=" PB ADP A 402 " pdb=" PA ADP A 402 " ideal model delta sinusoidal sigma weight residual -60.00 83.05 -143.05 1 2.00e+01 2.50e-03 4.32e+01 ... (remaining 5403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 654 0.027 - 0.053: 378 0.053 - 0.080: 156 0.080 - 0.106: 122 0.106 - 0.133: 34 Chirality restraints: 1344 Sorted by residual: chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE B 358 " pdb=" N ILE B 358 " pdb=" C ILE B 358 " pdb=" CB ILE B 358 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE C 358 " pdb=" N ILE C 358 " pdb=" C ILE C 358 " pdb=" CB ILE C 358 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1341 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 164 " 0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO A 165 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 164 " -0.020 5.00e-02 4.00e+02 3.11e-02 1.54e+00 pdb=" N PRO B 165 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 164 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO C 165 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 165 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 165 " -0.017 5.00e-02 4.00e+02 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 42 2.51 - 3.11: 5956 3.11 - 3.70: 13252 3.70 - 4.30: 20131 4.30 - 4.90: 32954 Nonbonded interactions: 72335 Sorted by model distance: nonbonded pdb="MG MG A 401 " pdb=" O HOH A 507 " model vdw 1.909 2.170 nonbonded pdb="MG MG B 401 " pdb=" O HOH B 507 " model vdw 1.909 2.170 nonbonded pdb="MG MG C 401 " pdb=" O HOH C 507 " model vdw 1.909 2.170 nonbonded pdb="MG MG A 401 " pdb=" O HOH A 503 " model vdw 1.921 2.170 nonbonded pdb="MG MG C 401 " pdb=" O HOH C 503 " model vdw 1.921 2.170 ... (remaining 72330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.000 Find NCS groups from input model: 0.040 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:5.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 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 : 0.003 0.029 8973 Z= 0.140 Angle : 0.606 7.058 12162 Z= 0.310 Chirality : 0.047 0.133 1344 Planarity : 0.004 0.031 1557 Dihedral : 18.288 143.104 3360 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.68 % Allowed : 15.67 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.26), residues: 1107 helix: 0.82 (0.25), residues: 459 sheet: 0.95 (0.37), residues: 186 loop : 1.55 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 257 TYR 0.009 0.001 TYR A 295 PHE 0.007 0.001 PHE C 256 TRP 0.012 0.002 TRP C 80 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8973) covalent geometry : angle 0.60590 (12162) hydrogen bonds : bond 0.16277 ( 441) hydrogen bonds : angle 5.70776 ( 1143) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.338 Fit side-chains REVERT: A 177 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8825 (mtm) REVERT: B 96 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7906 (mtm-85) REVERT: B 168 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8460 (mm-30) REVERT: B 180 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7709 (t0) REVERT: B 226 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7429 (mt-10) REVERT: B 229 LYS cc_start: 0.7756 (mtpm) cc_final: 0.7488 (mttm) REVERT: B 287 ASP cc_start: 0.8178 (m-30) cc_final: 0.7974 (m-30) REVERT: B 293 ASP cc_start: 0.8327 (m-30) cc_final: 0.8011 (m-30) REVERT: B 312 GLU cc_start: 0.8495 (mp0) cc_final: 0.8280 (mp0) REVERT: B 329 LYS cc_start: 0.8842 (tmtm) cc_final: 0.8624 (tptp) REVERT: B 354 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8287 (mm-40) REVERT: B 362 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7952 (mt-10) REVERT: C 51 LYS cc_start: 0.7915 (mtmt) cc_final: 0.7681 (mtpt) REVERT: C 84 GLU cc_start: 0.8460 (tt0) cc_final: 0.8251 (tt0) REVERT: C 96 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7640 (mtt-85) REVERT: C 100 GLU cc_start: 0.8090 (pm20) cc_final: 0.7888 (pm20) REVERT: C 122 GLN cc_start: 0.8699 (tt0) cc_final: 0.8487 (tt0) REVERT: C 148 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7969 (mmt90) REVERT: C 168 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8392 (mt-10) REVERT: C 223 ASP cc_start: 0.8301 (t0) cc_final: 0.7973 (t0) REVERT: C 325 THR cc_start: 0.8732 (m) cc_final: 0.8382 (p) REVERT: C 355 GLN cc_start: 0.8178 (mm110) cc_final: 0.7872 (mp-120) outliers start: 16 outliers final: 4 residues processed: 208 average time/residue: 0.6475 time to fit residues: 141.2807 Evaluate side-chains 187 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 181 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 180 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.096939 restraints weight = 10344.953| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.29 r_work: 0.2854 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8973 Z= 0.123 Angle : 0.584 7.380 12162 Z= 0.288 Chirality : 0.046 0.151 1344 Planarity : 0.004 0.042 1557 Dihedral : 11.508 145.058 1249 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.36 % Allowed : 14.83 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.26), residues: 1107 helix: 1.11 (0.25), residues: 462 sheet: 0.93 (0.37), residues: 186 loop : 1.70 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 291 TYR 0.011 0.001 TYR C 295 PHE 0.009 0.001 PHE C 256 TRP 0.011 0.002 TRP A 80 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8973) covalent geometry : angle 0.58372 (12162) hydrogen bonds : bond 0.04479 ( 441) hydrogen bonds : angle 4.71551 ( 1143) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.348 Fit side-chains REVERT: A 96 ARG cc_start: 0.8314 (mtp85) cc_final: 0.7998 (mtm-85) REVERT: A 317 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8806 (mm-30) REVERT: A 329 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8364 (tttm) REVERT: A 360 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7754 (tptm) REVERT: B 29 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.7984 (ptp-170) REVERT: B 58 GLU cc_start: 0.8356 (tt0) cc_final: 0.8128 (tt0) REVERT: B 73 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: B 96 ARG cc_start: 0.8339 (mtp85) cc_final: 0.8079 (mtm-85) REVERT: B 168 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8370 (mm-30) REVERT: B 229 LYS cc_start: 0.8010 (mtpm) cc_final: 0.7741 (mttm) REVERT: B 293 ASP cc_start: 0.8314 (m-30) cc_final: 0.8035 (m-30) REVERT: B 312 GLU cc_start: 0.8567 (mp0) cc_final: 0.8345 (mp0) REVERT: B 354 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8393 (mm-40) REVERT: B 362 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7939 (mt-10) REVERT: C 84 GLU cc_start: 0.8524 (tt0) cc_final: 0.8290 (tt0) REVERT: C 122 GLN cc_start: 0.8853 (tt0) cc_final: 0.8647 (tt0) REVERT: C 168 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8414 (mt-10) REVERT: C 223 ASP cc_start: 0.8313 (t0) cc_final: 0.7911 (t0) REVERT: C 325 THR cc_start: 0.8597 (m) cc_final: 0.8313 (p) REVERT: C 355 GLN cc_start: 0.8271 (mm110) cc_final: 0.7974 (mp-120) outliers start: 32 outliers final: 13 residues processed: 206 average time/residue: 0.6252 time to fit residues: 135.2777 Evaluate side-chains 203 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 352 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 0.0370 chunk 69 optimal weight: 0.0020 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.7868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.097189 restraints weight = 10344.507| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.29 r_work: 0.2880 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8973 Z= 0.124 Angle : 0.579 7.218 12162 Z= 0.285 Chirality : 0.046 0.161 1344 Planarity : 0.004 0.033 1557 Dihedral : 11.275 153.523 1239 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.26 % Allowed : 15.46 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.26), residues: 1107 helix: 1.18 (0.25), residues: 462 sheet: 0.97 (0.36), residues: 201 loop : 1.81 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 96 TYR 0.010 0.001 TYR C 295 PHE 0.009 0.001 PHE B 256 TRP 0.011 0.002 TRP A 80 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8973) covalent geometry : angle 0.57869 (12162) hydrogen bonds : bond 0.04317 ( 441) hydrogen bonds : angle 4.59045 ( 1143) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.250 Fit side-chains REVERT: A 73 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: A 96 ARG cc_start: 0.8303 (mtp85) cc_final: 0.8009 (mtm-85) REVERT: A 329 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8358 (tttm) REVERT: A 360 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7741 (tptm) REVERT: B 58 GLU cc_start: 0.8335 (tt0) cc_final: 0.8128 (tt0) REVERT: B 73 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: B 177 MET cc_start: 0.9219 (mmm) cc_final: 0.8695 (mtp) REVERT: B 229 LYS cc_start: 0.8026 (mtpm) cc_final: 0.7743 (mttp) REVERT: B 293 ASP cc_start: 0.8304 (m-30) cc_final: 0.7990 (m-30) REVERT: B 354 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8439 (mm-40) REVERT: B 362 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7874 (mt-10) REVERT: C 73 GLU cc_start: 0.8081 (mp0) cc_final: 0.7828 (mp0) REVERT: C 84 GLU cc_start: 0.8515 (tt0) cc_final: 0.8277 (tt0) REVERT: C 168 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8492 (mt-10) REVERT: C 212 ASP cc_start: 0.8793 (t70) cc_final: 0.8551 (t70) REVERT: C 223 ASP cc_start: 0.8371 (t0) cc_final: 0.7924 (t0) REVERT: C 325 THR cc_start: 0.8563 (m) cc_final: 0.8309 (p) REVERT: C 355 GLN cc_start: 0.8288 (mm110) cc_final: 0.7997 (mp-120) outliers start: 31 outliers final: 18 residues processed: 206 average time/residue: 0.6447 time to fit residues: 139.4505 Evaluate side-chains 207 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.108883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.095253 restraints weight = 10365.939| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.29 r_work: 0.2816 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8973 Z= 0.164 Angle : 0.613 7.708 12162 Z= 0.304 Chirality : 0.048 0.168 1344 Planarity : 0.005 0.038 1557 Dihedral : 11.467 157.784 1239 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.89 % Allowed : 15.14 % Favored : 80.97 % 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 aren not related in a simple way. whole: 1.80 (0.26), residues: 1107 helix: 1.11 (0.25), residues: 462 sheet: 0.90 (0.36), residues: 201 loop : 1.75 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.010 0.001 TYR C 295 PHE 0.010 0.001 PHE C 256 TRP 0.013 0.003 TRP A 341 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8973) covalent geometry : angle 0.61327 (12162) hydrogen bonds : bond 0.04958 ( 441) hydrogen bonds : angle 4.65620 ( 1143) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.351 Fit side-chains REVERT: A 65 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.8793 (pp) REVERT: A 73 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: A 96 ARG cc_start: 0.8322 (mtp85) cc_final: 0.7999 (mtm-85) REVERT: A 329 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8346 (tttm) REVERT: B 58 GLU cc_start: 0.8353 (tt0) cc_final: 0.8153 (tt0) REVERT: B 73 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: B 229 LYS cc_start: 0.8044 (mtpm) cc_final: 0.7720 (mttt) REVERT: B 354 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8470 (mm-40) REVERT: B 362 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7930 (mt-10) REVERT: C 84 GLU cc_start: 0.8544 (tt0) cc_final: 0.8302 (tt0) REVERT: C 168 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8520 (mt-10) REVERT: C 212 ASP cc_start: 0.8758 (t70) cc_final: 0.8485 (t70) REVERT: C 223 ASP cc_start: 0.8403 (t0) cc_final: 0.7954 (t0) REVERT: C 325 THR cc_start: 0.8609 (m) cc_final: 0.8390 (p) REVERT: C 355 GLN cc_start: 0.8311 (mm110) cc_final: 0.7979 (mp-120) REVERT: C 373 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7688 (ptm-80) outliers start: 37 outliers final: 19 residues processed: 201 average time/residue: 0.6316 time to fit residues: 133.4104 Evaluate side-chains 206 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 373 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.111710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.098234 restraints weight = 10389.595| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.29 r_work: 0.2911 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8973 Z= 0.108 Angle : 0.565 7.032 12162 Z= 0.275 Chirality : 0.045 0.160 1344 Planarity : 0.004 0.033 1557 Dihedral : 11.256 161.040 1239 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.47 % Allowed : 15.67 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.26), residues: 1107 helix: 1.30 (0.25), residues: 462 sheet: 0.93 (0.36), residues: 201 loop : 1.80 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.009 0.001 TYR B 295 PHE 0.008 0.001 PHE B 256 TRP 0.012 0.002 TRP C 80 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8973) covalent geometry : angle 0.56534 (12162) hydrogen bonds : bond 0.03796 ( 441) hydrogen bonds : angle 4.51286 ( 1143) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.288 Fit side-chains REVERT: A 73 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: A 96 ARG cc_start: 0.8306 (mtp85) cc_final: 0.8003 (mtm-85) REVERT: A 216 LYS cc_start: 0.8676 (mptp) cc_final: 0.8372 (tppt) REVERT: A 329 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8355 (tttm) REVERT: A 360 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7788 (tptm) REVERT: B 58 GLU cc_start: 0.8288 (tt0) cc_final: 0.8080 (tt0) REVERT: B 229 LYS cc_start: 0.8030 (mtpm) cc_final: 0.7734 (mttt) REVERT: B 293 ASP cc_start: 0.8305 (m-30) cc_final: 0.7981 (m-30) REVERT: B 335 GLU cc_start: 0.8430 (pm20) cc_final: 0.8166 (pm20) REVERT: B 354 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8382 (mm-40) REVERT: B 362 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7912 (mt-10) REVERT: C 41 ASN cc_start: 0.8149 (m110) cc_final: 0.7889 (m110) REVERT: C 84 GLU cc_start: 0.8542 (tt0) cc_final: 0.8298 (tt0) REVERT: C 168 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8488 (mt-10) REVERT: C 212 ASP cc_start: 0.8765 (t70) cc_final: 0.8508 (t70) REVERT: C 223 ASP cc_start: 0.8346 (t0) cc_final: 0.7969 (t0) REVERT: C 325 THR cc_start: 0.8583 (m) cc_final: 0.8354 (p) REVERT: C 355 GLN cc_start: 0.8305 (mm110) cc_final: 0.7984 (mp-120) outliers start: 33 outliers final: 15 residues processed: 206 average time/residue: 0.6601 time to fit residues: 142.7452 Evaluate side-chains 207 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.108346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.094609 restraints weight = 10243.462| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.29 r_work: 0.2803 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8973 Z= 0.183 Angle : 0.633 7.718 12162 Z= 0.313 Chirality : 0.048 0.170 1344 Planarity : 0.005 0.042 1557 Dihedral : 11.528 160.969 1239 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.15 % Allowed : 15.77 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.26), residues: 1107 helix: 1.13 (0.25), residues: 462 sheet: 0.90 (0.36), residues: 201 loop : 1.73 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 96 TYR 0.009 0.001 TYR C 295 PHE 0.011 0.001 PHE C 256 TRP 0.014 0.003 TRP A 341 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8973) covalent geometry : angle 0.63285 (12162) hydrogen bonds : bond 0.05142 ( 441) hydrogen bonds : angle 4.66497 ( 1143) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.247 Fit side-chains REVERT: A 65 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.8817 (pp) REVERT: A 73 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: A 96 ARG cc_start: 0.8327 (mtp85) cc_final: 0.7997 (mtm-85) REVERT: A 216 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8513 (tppt) REVERT: A 328 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9037 (mm) REVERT: A 329 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8356 (tttm) REVERT: A 360 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7748 (tptm) REVERT: B 58 GLU cc_start: 0.8342 (tt0) cc_final: 0.8129 (tt0) REVERT: B 73 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: B 229 LYS cc_start: 0.8075 (mtpm) cc_final: 0.7796 (mttm) REVERT: B 335 GLU cc_start: 0.8483 (pm20) cc_final: 0.8277 (pm20) REVERT: B 354 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8468 (mm-40) REVERT: B 362 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7929 (mt-10) REVERT: C 84 GLU cc_start: 0.8572 (tt0) cc_final: 0.8335 (tt0) REVERT: C 168 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8523 (mt-10) REVERT: C 212 ASP cc_start: 0.8768 (t70) cc_final: 0.8498 (t70) REVERT: C 223 ASP cc_start: 0.8413 (t0) cc_final: 0.7979 (t0) REVERT: C 229 LYS cc_start: 0.8292 (mtpp) cc_final: 0.7918 (mtmt) REVERT: C 325 THR cc_start: 0.8640 (m) cc_final: 0.8433 (p) REVERT: C 355 GLN cc_start: 0.8328 (mm110) cc_final: 0.7997 (mp-120) outliers start: 30 outliers final: 19 residues processed: 201 average time/residue: 0.6171 time to fit residues: 130.3944 Evaluate side-chains 205 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 97 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 103 optimal weight: 0.0050 chunk 109 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 2 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.096599 restraints weight = 10337.936| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.28 r_work: 0.2853 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8973 Z= 0.137 Angle : 0.597 7.407 12162 Z= 0.293 Chirality : 0.046 0.166 1344 Planarity : 0.004 0.038 1557 Dihedral : 11.417 162.528 1239 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.26 % Allowed : 15.98 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.26), residues: 1107 helix: 1.19 (0.25), residues: 462 sheet: 0.92 (0.37), residues: 201 loop : 1.76 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.009 0.001 TYR B 295 PHE 0.009 0.001 PHE B 256 TRP 0.013 0.002 TRP C 80 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8973) covalent geometry : angle 0.59718 (12162) hydrogen bonds : bond 0.04383 ( 441) hydrogen bonds : angle 4.58217 ( 1143) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.373 Fit side-chains REVERT: A 65 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.8790 (pp) REVERT: A 73 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: A 96 ARG cc_start: 0.8325 (mtp85) cc_final: 0.8010 (mtm-85) REVERT: A 216 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8504 (tppt) REVERT: A 329 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8377 (tttm) REVERT: A 360 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7772 (tptm) REVERT: B 58 GLU cc_start: 0.8303 (tt0) cc_final: 0.8093 (tt0) REVERT: B 73 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: B 229 LYS cc_start: 0.8052 (mtpm) cc_final: 0.7753 (mttt) REVERT: B 362 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7927 (mt-10) REVERT: C 84 GLU cc_start: 0.8594 (tt0) cc_final: 0.8354 (tt0) REVERT: C 168 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8516 (mt-10) REVERT: C 212 ASP cc_start: 0.8790 (t70) cc_final: 0.8514 (t70) REVERT: C 223 ASP cc_start: 0.8384 (t0) cc_final: 0.7989 (t0) REVERT: C 329 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8690 (tmtm) REVERT: C 355 GLN cc_start: 0.8322 (mm110) cc_final: 0.8012 (mp-120) outliers start: 31 outliers final: 19 residues processed: 197 average time/residue: 0.6094 time to fit residues: 126.4058 Evaluate side-chains 207 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 4 optimal weight: 0.0060 chunk 110 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.112003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.098571 restraints weight = 10342.556| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.29 r_work: 0.2878 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8973 Z= 0.107 Angle : 0.571 7.655 12162 Z= 0.276 Chirality : 0.045 0.159 1344 Planarity : 0.004 0.042 1557 Dihedral : 11.233 165.857 1239 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.15 % Allowed : 16.40 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.26), residues: 1107 helix: 1.36 (0.25), residues: 462 sheet: 0.95 (0.37), residues: 201 loop : 1.80 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 96 TYR 0.008 0.001 TYR B 295 PHE 0.008 0.001 PHE B 256 TRP 0.012 0.002 TRP C 80 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8973) covalent geometry : angle 0.57081 (12162) hydrogen bonds : bond 0.03688 ( 441) hydrogen bonds : angle 4.48207 ( 1143) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.248 Fit side-chains REVERT: A 65 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.8764 (pp) REVERT: A 73 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: A 96 ARG cc_start: 0.8288 (mtp85) cc_final: 0.7972 (mtm-85) REVERT: A 212 ASP cc_start: 0.8835 (t70) cc_final: 0.8619 (t70) REVERT: A 216 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8410 (tppt) REVERT: A 329 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8376 (tttm) REVERT: A 360 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7719 (tptm) REVERT: B 58 GLU cc_start: 0.8279 (tt0) cc_final: 0.8046 (tt0) REVERT: B 73 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: B 229 LYS cc_start: 0.8007 (mtpm) cc_final: 0.7719 (mttt) REVERT: B 293 ASP cc_start: 0.8307 (m-30) cc_final: 0.7975 (m-30) REVERT: B 335 GLU cc_start: 0.8471 (pm20) cc_final: 0.8253 (pm20) REVERT: B 362 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7931 (mt-10) REVERT: C 84 GLU cc_start: 0.8565 (tt0) cc_final: 0.8275 (mt-10) REVERT: C 168 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8448 (mt-10) REVERT: C 212 ASP cc_start: 0.8766 (t70) cc_final: 0.8488 (t70) REVERT: C 223 ASP cc_start: 0.8323 (t0) cc_final: 0.7932 (t0) REVERT: C 229 LYS cc_start: 0.8228 (mtpp) cc_final: 0.7861 (mtmt) REVERT: C 329 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8662 (tmtm) REVERT: C 355 GLN cc_start: 0.8303 (mm110) cc_final: 0.7991 (mp-120) outliers start: 30 outliers final: 16 residues processed: 201 average time/residue: 0.6466 time to fit residues: 136.4780 Evaluate side-chains 209 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 68 optimal weight: 0.0270 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.112588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.099147 restraints weight = 10384.308| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.29 r_work: 0.2910 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8973 Z= 0.105 Angle : 0.567 7.868 12162 Z= 0.273 Chirality : 0.045 0.159 1344 Planarity : 0.004 0.041 1557 Dihedral : 11.032 169.546 1239 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.42 % Allowed : 17.35 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.26), residues: 1107 helix: 1.40 (0.25), residues: 462 sheet: 0.97 (0.37), residues: 201 loop : 1.82 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.008 0.001 TYR B 295 PHE 0.008 0.001 PHE B 256 TRP 0.011 0.002 TRP C 80 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8973) covalent geometry : angle 0.56669 (12162) hydrogen bonds : bond 0.03614 ( 441) hydrogen bonds : angle 4.44083 ( 1143) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.213 Fit side-chains REVERT: A 65 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.8731 (pp) REVERT: A 73 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: A 96 ARG cc_start: 0.8287 (mtp85) cc_final: 0.7991 (mtm-85) REVERT: A 216 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8498 (tppt) REVERT: A 329 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8379 (tttm) REVERT: A 360 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7775 (tptm) REVERT: B 58 GLU cc_start: 0.8281 (tt0) cc_final: 0.8054 (tt0) REVERT: B 73 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: B 229 LYS cc_start: 0.8006 (mtpm) cc_final: 0.7709 (mttt) REVERT: B 293 ASP cc_start: 0.8318 (m-30) cc_final: 0.7984 (m-30) REVERT: B 335 GLU cc_start: 0.8487 (pm20) cc_final: 0.8278 (pm20) REVERT: B 362 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7931 (mt-10) REVERT: C 41 ASN cc_start: 0.8155 (m110) cc_final: 0.7913 (m110) REVERT: C 84 GLU cc_start: 0.8569 (tt0) cc_final: 0.8281 (mt-10) REVERT: C 168 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8434 (mt-10) REVERT: C 212 ASP cc_start: 0.8758 (t70) cc_final: 0.8499 (t70) REVERT: C 223 ASP cc_start: 0.8341 (t0) cc_final: 0.7953 (t0) REVERT: C 229 LYS cc_start: 0.8266 (mtpp) cc_final: 0.7906 (mtmt) REVERT: C 329 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8648 (tmtm) REVERT: C 355 GLN cc_start: 0.8288 (mm110) cc_final: 0.7967 (mp-120) outliers start: 23 outliers final: 15 residues processed: 200 average time/residue: 0.6706 time to fit residues: 140.6261 Evaluate side-chains 206 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.110979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.097458 restraints weight = 10357.786| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.29 r_work: 0.2847 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8973 Z= 0.129 Angle : 0.597 8.130 12162 Z= 0.289 Chirality : 0.046 0.161 1344 Planarity : 0.004 0.041 1557 Dihedral : 11.128 169.842 1239 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.31 % Allowed : 17.77 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.26), residues: 1107 helix: 1.31 (0.25), residues: 462 sheet: 1.06 (0.37), residues: 198 loop : 1.78 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.008 0.001 TYR B 295 PHE 0.009 0.001 PHE B 256 TRP 0.011 0.002 TRP A 80 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8973) covalent geometry : angle 0.59654 (12162) hydrogen bonds : bond 0.04126 ( 441) hydrogen bonds : angle 4.50343 ( 1143) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.356 Fit side-chains REVERT: A 65 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.8770 (pp) REVERT: A 73 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: A 96 ARG cc_start: 0.8312 (mtp85) cc_final: 0.7996 (mtm-85) REVERT: A 216 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8421 (tppt) REVERT: A 329 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8395 (tttm) REVERT: A 360 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7737 (tptm) REVERT: B 58 GLU cc_start: 0.8288 (tt0) cc_final: 0.8053 (tt0) REVERT: B 73 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: B 229 LYS cc_start: 0.8017 (mtpm) cc_final: 0.7749 (mttm) REVERT: B 293 ASP cc_start: 0.8281 (m-30) cc_final: 0.7969 (m-30) REVERT: B 335 GLU cc_start: 0.8504 (pm20) cc_final: 0.8287 (pm20) REVERT: B 362 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7878 (mt-10) REVERT: C 84 GLU cc_start: 0.8596 (tt0) cc_final: 0.8382 (tt0) REVERT: C 168 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8453 (mt-10) REVERT: C 212 ASP cc_start: 0.8776 (t70) cc_final: 0.8511 (t70) REVERT: C 223 ASP cc_start: 0.8347 (t0) cc_final: 0.7952 (t0) REVERT: C 229 LYS cc_start: 0.8258 (mtpp) cc_final: 0.7886 (mtmt) REVERT: C 329 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8697 (tmtm) outliers start: 22 outliers final: 15 residues processed: 188 average time/residue: 0.6702 time to fit residues: 132.3369 Evaluate side-chains 202 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 40 optimal weight: 0.0010 chunk 55 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.109067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.095512 restraints weight = 10241.908| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.28 r_work: 0.2825 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8973 Z= 0.174 Angle : 0.638 8.697 12162 Z= 0.314 Chirality : 0.048 0.163 1344 Planarity : 0.005 0.042 1557 Dihedral : 11.427 165.245 1239 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.73 % Allowed : 17.25 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.26), residues: 1107 helix: 1.15 (0.25), residues: 462 sheet: 1.02 (0.37), residues: 198 loop : 1.69 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 96 TYR 0.009 0.001 TYR B 295 PHE 0.010 0.001 PHE C 256 TRP 0.014 0.003 TRP A 341 HIS 0.004 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 8973) covalent geometry : angle 0.63840 (12162) hydrogen bonds : bond 0.04949 ( 441) hydrogen bonds : angle 4.62768 ( 1143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3256.47 seconds wall clock time: 56 minutes 3.11 seconds (3363.11 seconds total)