Starting phenix.real_space_refine on Wed Sep 17 03:39:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h5g_51884/09_2025/9h5g_51884.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h5g_51884/09_2025/9h5g_51884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9h5g_51884/09_2025/9h5g_51884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h5g_51884/09_2025/9h5g_51884.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h5g_51884/09_2025/9h5g_51884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h5g_51884/09_2025/9h5g_51884.map" } resolution = 2.48 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2076 2.51 5 N 600 2.21 5 O 618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3300 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "C" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "D" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "E" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "F" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Time building chain proxies: 1.25, per 1000 atoms: 0.38 Number of scatterers: 3300 At special positions: 0 Unit cell: (89.28, 139.128, 33.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 618 8.00 N 600 7.00 C 2076 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: 0.27 Conformation dependent library (CDL) restraints added in 137.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 310 removed outlier: 6.547A pdb=" N VAL A 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.714A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322 removed outlier: 6.555A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330 removed outlier: 7.030A pdb=" N GLY D 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN A 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.662A pdb=" N GLN A 336 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N VAL D 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU A 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346 removed outlier: 6.454A pdb=" N LYS A 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N PHE D 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP A 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 356 removed outlier: 6.802A pdb=" N SER D 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N ILE B 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.685A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.722A pdb=" N LYS B 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 375 removed outlier: 6.598A pdb=" N HIS B 374 " --> pdb=" O LYS D 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 308 through 310 Processing sheet with id=AB3, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AB4, first strand: chain 'C' and resid 317 through 322 Processing sheet with id=AB5, first strand: chain 'C' and resid 325 through 330 removed outlier: 5.951A pdb=" N GLY C 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N HIS E 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLY E 326 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N HIS F 329 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE E 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 336 through 339 Processing sheet with id=AB7, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AB8, first strand: chain 'C' and resid 354 through 356 removed outlier: 8.404A pdb=" N ILE C 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ILE E 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.658A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN E 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N HIS F 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR E 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 369 through 371 removed outlier: 6.654A pdb=" N LYS C 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS E 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 374 through 375 removed outlier: 6.560A pdb=" N HIS C 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N HIS E 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 49 hydrogen bonds defined for protein. 147 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: 0.40 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 857 1.33 - 1.45: 476 1.45 - 1.57: 2015 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3354 Sorted by residual: bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.56e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.41e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.31e+00 bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.12e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.55e+00 ... (remaining 3349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 2223 1.29 - 2.59: 1415 2.59 - 3.88: 613 3.88 - 5.18: 180 5.18 - 6.47: 57 Bond angle restraints: 4488 Sorted by residual: angle pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " pdb=" CG PHE B 346 " ideal model delta sigma weight residual 113.80 120.20 -6.40 1.00e+00 1.00e+00 4.10e+01 angle pdb=" CA PHE C 346 " pdb=" CB PHE C 346 " pdb=" CG PHE C 346 " ideal model delta sigma weight residual 113.80 119.78 -5.98 1.00e+00 1.00e+00 3.57e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 119.68 -5.88 1.00e+00 1.00e+00 3.46e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 119.57 -5.77 1.00e+00 1.00e+00 3.33e+01 angle pdb=" CA PHE F 346 " pdb=" CB PHE F 346 " pdb=" CG PHE F 346 " ideal model delta sigma weight residual 113.80 119.09 -5.29 1.00e+00 1.00e+00 2.80e+01 ... (remaining 4483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.00: 1694 10.00 - 20.01: 275 20.01 - 30.01: 39 30.01 - 40.01: 18 40.01 - 50.01: 14 Dihedral angle restraints: 2040 sinusoidal: 852 harmonic: 1188 Sorted by residual: dihedral pdb=" CA VAL D 318 " pdb=" C VAL D 318 " pdb=" N THR D 319 " pdb=" CA THR D 319 " ideal model delta harmonic sigma weight residual -180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA VAL A 318 " pdb=" C VAL A 318 " pdb=" N THR A 319 " pdb=" CA THR A 319 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLN B 351 " pdb=" C GLN B 351 " pdb=" N SER B 352 " pdb=" CA SER B 352 " ideal model delta harmonic sigma weight residual 180.00 -161.07 -18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 2037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 191 0.050 - 0.101: 201 0.101 - 0.151: 69 0.151 - 0.201: 28 0.201 - 0.251: 15 Chirality restraints: 504 Sorted by residual: chirality pdb=" CA ARG C 349 " pdb=" N ARG C 349 " pdb=" C ARG C 349 " pdb=" CB ARG C 349 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA LYS F 347 " pdb=" N LYS F 347 " pdb=" C LYS F 347 " pdb=" CB LYS F 347 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA LYS C 317 " pdb=" N LYS C 317 " pdb=" C LYS C 317 " pdb=" CB LYS C 317 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 501 not shown) Planarity restraints: 570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.089 2.00e-02 2.50e+03 4.62e-02 4.26e+01 pdb=" CG TYR F 310 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.081 2.00e-02 2.50e+03 4.37e-02 3.82e+01 pdb=" CG TYR E 310 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.074 2.00e-02 2.50e+03 3.82e-02 2.92e+01 pdb=" CG TYR A 310 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.050 2.00e-02 2.50e+03 ... (remaining 567 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 1622 3.02 - 3.49: 2671 3.49 - 3.96: 5213 3.96 - 4.43: 5199 4.43 - 4.90: 10228 Nonbonded interactions: 24933 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.550 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.551 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.563 3.040 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.574 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.576 3.040 ... (remaining 24928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.830 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.730 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.012 0.036 3354 Z= 0.760 Angle : 1.988 6.474 4488 Z= 1.309 Chirality : 0.088 0.251 504 Planarity : 0.011 0.046 570 Dihedral : 10.879 50.013 1284 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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 (0.35), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG F 349 TYR 0.089 0.030 TYR F 310 PHE 0.031 0.011 PHE A 378 HIS 0.014 0.005 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.01201 ( 3354) covalent geometry : angle 1.98779 ( 4488) hydrogen bonds : bond 0.14668 ( 49) hydrogen bonds : angle 6.74998 ( 147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.149 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.8148 time to fit residues: 86.3960 Evaluate side-chains 89 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN C 351 GLN C 368 ASN F 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.166782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.135664 restraints weight = 3397.267| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.90 r_work: 0.3757 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3354 Z= 0.170 Angle : 0.796 10.052 4488 Z= 0.398 Chirality : 0.051 0.158 504 Planarity : 0.003 0.019 570 Dihedral : 6.429 17.700 438 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.03 % Allowed : 13.23 % Favored : 81.75 % 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: -2.40 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 349 TYR 0.013 0.003 TYR B 310 PHE 0.008 0.002 PHE A 346 HIS 0.005 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 3354) covalent geometry : angle 0.79623 ( 4488) hydrogen bonds : bond 0.02723 ( 49) hydrogen bonds : angle 4.86569 ( 147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.142 Fit side-chains REVERT: A 340 LYS cc_start: 0.8370 (mmtp) cc_final: 0.7954 (mmtm) REVERT: A 343 LYS cc_start: 0.8339 (mttt) cc_final: 0.8037 (mttm) REVERT: A 351 GLN cc_start: 0.7803 (tt0) cc_final: 0.7491 (mt0) REVERT: B 342 GLU cc_start: 0.7967 (mm-30) cc_final: 0.6743 (mp0) REVERT: C 325 LEU cc_start: 0.7998 (tp) cc_final: 0.7795 (tt) REVERT: C 340 LYS cc_start: 0.8256 (mmtm) cc_final: 0.7921 (mmtt) REVERT: D 340 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7917 (mmtm) REVERT: E 343 LYS cc_start: 0.8281 (mttt) cc_final: 0.7999 (mttm) outliers start: 19 outliers final: 7 residues processed: 97 average time/residue: 0.8212 time to fit residues: 81.1142 Evaluate side-chains 90 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 331 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 0.4980 chunk 30 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.165893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.134486 restraints weight = 3318.619| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.89 r_work: 0.3722 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3354 Z= 0.181 Angle : 0.782 9.280 4488 Z= 0.387 Chirality : 0.051 0.154 504 Planarity : 0.004 0.025 570 Dihedral : 6.342 17.993 438 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.82 % Allowed : 14.29 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.65 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.012 0.003 TYR E 310 PHE 0.007 0.002 PHE E 346 HIS 0.005 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 3354) covalent geometry : angle 0.78160 ( 4488) hydrogen bonds : bond 0.02629 ( 49) hydrogen bonds : angle 4.50316 ( 147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.147 Fit side-chains REVERT: A 340 LYS cc_start: 0.8401 (mmtp) cc_final: 0.8033 (mmtm) REVERT: A 343 LYS cc_start: 0.8273 (mttt) cc_final: 0.7964 (mttm) REVERT: A 351 GLN cc_start: 0.7765 (tt0) cc_final: 0.7498 (mt0) REVERT: A 370 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8832 (tptp) REVERT: B 342 GLU cc_start: 0.7976 (mm-30) cc_final: 0.6740 (mp0) REVERT: B 351 GLN cc_start: 0.8078 (tt0) cc_final: 0.7681 (mt0) REVERT: C 325 LEU cc_start: 0.8035 (tp) cc_final: 0.7830 (tt) REVERT: C 340 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7837 (mmtt) REVERT: E 343 LYS cc_start: 0.8263 (mttt) cc_final: 0.7968 (mttm) REVERT: E 351 GLN cc_start: 0.7750 (tt0) cc_final: 0.7543 (mt0) outliers start: 22 outliers final: 12 residues processed: 93 average time/residue: 0.8128 time to fit residues: 77.0261 Evaluate side-chains 93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 331 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.162119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.131637 restraints weight = 3315.287| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.85 r_work: 0.3702 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3354 Z= 0.214 Angle : 0.808 9.574 4488 Z= 0.397 Chirality : 0.051 0.161 504 Planarity : 0.004 0.030 570 Dihedral : 6.403 18.393 438 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.56 % Allowed : 15.08 % Favored : 79.37 % 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: -2.82 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.013 0.003 TYR C 310 PHE 0.008 0.002 PHE C 378 HIS 0.004 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 3354) covalent geometry : angle 0.80827 ( 4488) hydrogen bonds : bond 0.02848 ( 49) hydrogen bonds : angle 4.47687 ( 147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.161 Fit side-chains REVERT: A 340 LYS cc_start: 0.8446 (mmtp) cc_final: 0.8089 (mmtm) REVERT: A 343 LYS cc_start: 0.8195 (mttt) cc_final: 0.7503 (tptm) REVERT: A 351 GLN cc_start: 0.7895 (tt0) cc_final: 0.7628 (mt0) REVERT: A 370 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8844 (tptp) REVERT: B 340 LYS cc_start: 0.8610 (mmtp) cc_final: 0.8242 (mmtm) REVERT: B 342 GLU cc_start: 0.7949 (mm-30) cc_final: 0.6737 (mp0) REVERT: B 351 GLN cc_start: 0.8231 (tt0) cc_final: 0.7862 (mt0) REVERT: C 325 LEU cc_start: 0.8123 (tp) cc_final: 0.7909 (tt) REVERT: C 340 LYS cc_start: 0.8268 (mmtm) cc_final: 0.7926 (mmtt) REVERT: C 351 GLN cc_start: 0.8072 (tt0) cc_final: 0.7803 (mt0) REVERT: D 343 LYS cc_start: 0.8097 (mttt) cc_final: 0.7726 (mttm) REVERT: D 351 GLN cc_start: 0.7707 (tt0) cc_final: 0.7399 (mt0) REVERT: E 343 LYS cc_start: 0.8265 (mttt) cc_final: 0.7982 (mttm) REVERT: E 351 GLN cc_start: 0.7857 (tt0) cc_final: 0.7650 (mt0) REVERT: F 351 GLN cc_start: 0.7853 (tt0) cc_final: 0.7535 (mt0) outliers start: 21 outliers final: 13 residues processed: 91 average time/residue: 0.8089 time to fit residues: 75.0009 Evaluate side-chains 95 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 331 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4246 r_free = 0.4246 target = 0.165028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.134012 restraints weight = 3300.542| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.87 r_work: 0.3729 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3354 Z= 0.164 Angle : 0.736 10.110 4488 Z= 0.357 Chirality : 0.050 0.157 504 Planarity : 0.004 0.030 570 Dihedral : 6.064 16.981 438 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.56 % Allowed : 15.08 % Favored : 79.37 % 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: -2.75 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.011 0.003 TYR F 310 PHE 0.006 0.002 PHE C 378 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3354) covalent geometry : angle 0.73579 ( 4488) hydrogen bonds : bond 0.02361 ( 49) hydrogen bonds : angle 4.39634 ( 147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.239 Fit side-chains REVERT: A 340 LYS cc_start: 0.8434 (mmtp) cc_final: 0.8072 (mmtm) REVERT: A 343 LYS cc_start: 0.8290 (mttt) cc_final: 0.7601 (tptm) REVERT: A 351 GLN cc_start: 0.7836 (tt0) cc_final: 0.7592 (mt0) REVERT: B 340 LYS cc_start: 0.8567 (mmtp) cc_final: 0.8185 (mmtm) REVERT: B 342 GLU cc_start: 0.7968 (mm-30) cc_final: 0.6740 (mp0) REVERT: B 351 GLN cc_start: 0.8200 (tt0) cc_final: 0.7853 (mt0) REVERT: C 340 LYS cc_start: 0.8250 (mmtm) cc_final: 0.7874 (mmtt) REVERT: C 351 GLN cc_start: 0.8018 (tt0) cc_final: 0.7801 (mt0) REVERT: D 343 LYS cc_start: 0.8113 (mttt) cc_final: 0.7767 (mttm) REVERT: D 351 GLN cc_start: 0.7647 (tt0) cc_final: 0.7416 (mt0) REVERT: E 343 LYS cc_start: 0.8261 (mttt) cc_final: 0.7987 (mttm) REVERT: F 351 GLN cc_start: 0.7785 (tt0) cc_final: 0.7527 (mt0) outliers start: 21 outliers final: 14 residues processed: 94 average time/residue: 0.7893 time to fit residues: 75.7765 Evaluate side-chains 97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 331 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.160036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.129499 restraints weight = 3325.474| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.86 r_work: 0.3667 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 3354 Z= 0.347 Angle : 0.934 11.611 4488 Z= 0.466 Chirality : 0.055 0.180 504 Planarity : 0.005 0.036 570 Dihedral : 6.663 18.880 438 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 6.88 % Allowed : 15.08 % Favored : 78.04 % 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: -3.02 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 349 TYR 0.017 0.005 TYR C 310 PHE 0.013 0.003 PHE C 378 HIS 0.004 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00821 ( 3354) covalent geometry : angle 0.93387 ( 4488) hydrogen bonds : bond 0.03831 ( 49) hydrogen bonds : angle 4.68712 ( 147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.162 Fit side-chains REVERT: A 340 LYS cc_start: 0.8486 (mmtp) cc_final: 0.8117 (mmtm) REVERT: A 343 LYS cc_start: 0.8109 (mttt) cc_final: 0.7418 (tptm) REVERT: A 351 GLN cc_start: 0.7975 (tt0) cc_final: 0.7723 (mt0) REVERT: A 370 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8837 (tptp) REVERT: A 376 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7740 (tt) REVERT: B 351 GLN cc_start: 0.8348 (tt0) cc_final: 0.8049 (mt0) REVERT: C 340 LYS cc_start: 0.8331 (mmtm) cc_final: 0.7988 (mmtt) REVERT: C 351 GLN cc_start: 0.8147 (tt0) cc_final: 0.7904 (mt0) REVERT: D 343 LYS cc_start: 0.8063 (mttt) cc_final: 0.7691 (mttm) REVERT: D 351 GLN cc_start: 0.7770 (tt0) cc_final: 0.7479 (mt0) REVERT: E 343 LYS cc_start: 0.8266 (mttt) cc_final: 0.7949 (mttm) REVERT: F 343 LYS cc_start: 0.8099 (mttt) cc_final: 0.7711 (mttm) REVERT: F 351 GLN cc_start: 0.7889 (tt0) cc_final: 0.7589 (mt0) outliers start: 26 outliers final: 17 residues processed: 98 average time/residue: 0.8365 time to fit residues: 83.5128 Evaluate side-chains 93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 331 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.165064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.134221 restraints weight = 3330.632| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.88 r_work: 0.3734 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3354 Z= 0.143 Angle : 0.732 11.911 4488 Z= 0.348 Chirality : 0.051 0.171 504 Planarity : 0.004 0.032 570 Dihedral : 5.895 16.324 438 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 6.61 % Allowed : 16.67 % Favored : 76.72 % 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: -2.79 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 349 TYR 0.009 0.002 TYR F 310 PHE 0.011 0.001 PHE D 378 HIS 0.002 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3354) covalent geometry : angle 0.73165 ( 4488) hydrogen bonds : bond 0.02108 ( 49) hydrogen bonds : angle 4.35455 ( 147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.143 Fit side-chains REVERT: A 340 LYS cc_start: 0.8438 (mmtp) cc_final: 0.8088 (mmtm) REVERT: A 343 LYS cc_start: 0.8285 (mttt) cc_final: 0.7622 (tptm) REVERT: A 351 GLN cc_start: 0.7865 (tt0) cc_final: 0.7647 (mt0) REVERT: A 370 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8804 (tptp) REVERT: B 342 GLU cc_start: 0.7950 (mm-30) cc_final: 0.6743 (mp0) REVERT: B 351 GLN cc_start: 0.8201 (tt0) cc_final: 0.7876 (mt0) REVERT: C 340 LYS cc_start: 0.8254 (mmtm) cc_final: 0.7889 (mmtt) REVERT: D 343 LYS cc_start: 0.8103 (mttt) cc_final: 0.7873 (mttp) REVERT: E 325 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7929 (mt) REVERT: E 343 LYS cc_start: 0.8277 (mttt) cc_final: 0.7997 (mttm) REVERT: E 349 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6707 (mtt180) REVERT: F 343 LYS cc_start: 0.8112 (mttt) cc_final: 0.7726 (mttm) REVERT: F 351 GLN cc_start: 0.7732 (tt0) cc_final: 0.7507 (mt0) outliers start: 25 outliers final: 13 residues processed: 97 average time/residue: 0.8035 time to fit residues: 79.4602 Evaluate side-chains 92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain F residue 331 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 0.0000 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 overall best weight: 4.1992 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.162663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.131672 restraints weight = 3377.950| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.88 r_work: 0.3704 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3354 Z= 0.206 Angle : 0.811 12.841 4488 Z= 0.388 Chirality : 0.052 0.191 504 Planarity : 0.004 0.033 570 Dihedral : 6.111 17.359 438 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 6.08 % Allowed : 17.72 % Favored : 76.19 % 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: -2.87 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.012 0.003 TYR F 310 PHE 0.011 0.002 PHE D 378 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 3354) covalent geometry : angle 0.81103 ( 4488) hydrogen bonds : bond 0.02748 ( 49) hydrogen bonds : angle 4.43576 ( 147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.173 Fit side-chains REVERT: A 338 GLU cc_start: 0.8635 (tt0) cc_final: 0.8430 (tm-30) REVERT: A 340 LYS cc_start: 0.8434 (mmtp) cc_final: 0.8005 (mmtm) REVERT: A 343 LYS cc_start: 0.8188 (mttt) cc_final: 0.7436 (tptm) REVERT: A 351 GLN cc_start: 0.7894 (tt0) cc_final: 0.7691 (mt0) REVERT: A 370 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8811 (tptp) REVERT: B 342 GLU cc_start: 0.7979 (mm-30) cc_final: 0.6734 (mp0) REVERT: B 351 GLN cc_start: 0.8238 (tt0) cc_final: 0.7935 (mt0) REVERT: C 340 LYS cc_start: 0.8290 (mmtm) cc_final: 0.7933 (mmtt) REVERT: E 343 LYS cc_start: 0.8253 (mttt) cc_final: 0.7970 (mttm) REVERT: E 349 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6748 (mtp180) REVERT: F 351 GLN cc_start: 0.7776 (tt0) cc_final: 0.7530 (mt0) outliers start: 23 outliers final: 16 residues processed: 89 average time/residue: 0.7576 time to fit residues: 68.8066 Evaluate side-chains 93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain F residue 331 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.167237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.136474 restraints weight = 3323.019| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.86 r_work: 0.3761 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3354 Z= 0.112 Angle : 0.700 13.178 4488 Z= 0.324 Chirality : 0.050 0.196 504 Planarity : 0.004 0.031 570 Dihedral : 5.456 15.233 438 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 6.08 % Allowed : 17.46 % Favored : 76.46 % 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: -2.65 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.006 0.002 TYR C 310 PHE 0.008 0.001 PHE D 378 HIS 0.002 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 3354) covalent geometry : angle 0.69983 ( 4488) hydrogen bonds : bond 0.01745 ( 49) hydrogen bonds : angle 4.15406 ( 147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.097 Fit side-chains REVERT: A 340 LYS cc_start: 0.8414 (mmtp) cc_final: 0.8059 (mmtm) REVERT: A 343 LYS cc_start: 0.8277 (mttt) cc_final: 0.7595 (tptm) REVERT: A 370 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8790 (tptp) REVERT: B 340 LYS cc_start: 0.8566 (mmtm) cc_final: 0.8256 (mmtm) REVERT: B 342 GLU cc_start: 0.7913 (mm-30) cc_final: 0.6701 (mp0) REVERT: B 351 GLN cc_start: 0.8108 (tt0) cc_final: 0.7893 (mt0) REVERT: C 340 LYS cc_start: 0.8222 (mmtm) cc_final: 0.7854 (mmtm) REVERT: D 343 LYS cc_start: 0.8108 (mttt) cc_final: 0.7768 (mttm) REVERT: E 343 LYS cc_start: 0.8263 (mttt) cc_final: 0.7991 (mttm) REVERT: E 349 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6657 (mtp180) outliers start: 23 outliers final: 11 residues processed: 93 average time/residue: 0.7858 time to fit residues: 74.4730 Evaluate side-chains 90 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.162699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.131713 restraints weight = 3352.055| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.88 r_work: 0.3703 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3354 Z= 0.229 Angle : 0.822 14.292 4488 Z= 0.396 Chirality : 0.052 0.227 504 Planarity : 0.004 0.033 570 Dihedral : 6.035 17.113 438 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.97 % Allowed : 20.63 % Favored : 75.40 % 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: -2.81 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.012 0.003 TYR B 310 PHE 0.011 0.002 PHE D 378 HIS 0.003 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00538 ( 3354) covalent geometry : angle 0.82226 ( 4488) hydrogen bonds : bond 0.02840 ( 49) hydrogen bonds : angle 4.36069 ( 147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.151 Fit side-chains REVERT: A 340 LYS cc_start: 0.8468 (mmtp) cc_final: 0.8101 (mmtm) REVERT: A 343 LYS cc_start: 0.8201 (mttt) cc_final: 0.7451 (tptm) REVERT: A 370 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8819 (tptp) REVERT: B 342 GLU cc_start: 0.7976 (mm-30) cc_final: 0.6754 (mp0) REVERT: B 351 GLN cc_start: 0.8218 (tt0) cc_final: 0.7991 (mt0) REVERT: C 340 LYS cc_start: 0.8293 (mmtm) cc_final: 0.7932 (mmtt) REVERT: E 349 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6751 (mtt180) outliers start: 15 outliers final: 9 residues processed: 82 average time/residue: 0.7875 time to fit residues: 65.8852 Evaluate side-chains 87 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 0.0670 chunk 7 optimal weight: 10.0000 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.163584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.132537 restraints weight = 3369.384| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.88 r_work: 0.3696 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3354 Z= 0.198 Angle : 0.791 13.495 4488 Z= 0.380 Chirality : 0.051 0.207 504 Planarity : 0.004 0.031 570 Dihedral : 6.014 16.775 438 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.76 % Allowed : 19.31 % Favored : 75.93 % 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: -2.78 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.011 0.003 TYR B 310 PHE 0.011 0.002 PHE D 378 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 3354) covalent geometry : angle 0.79085 ( 4488) hydrogen bonds : bond 0.02642 ( 49) hydrogen bonds : angle 4.38023 ( 147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2159.08 seconds wall clock time: 37 minutes 39.27 seconds (2259.27 seconds total)