Starting phenix.real_space_refine on Tue Mar 3 14:46:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w8o_21576/03_2026/6w8o_21576.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w8o_21576/03_2026/6w8o_21576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6w8o_21576/03_2026/6w8o_21576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w8o_21576/03_2026/6w8o_21576.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w8o_21576/03_2026/6w8o_21576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w8o_21576/03_2026/6w8o_21576.map" } resolution = 3.4 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= 0.009 sd= 0.071 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 40 5.16 5 C 4184 2.51 5 N 1018 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6332 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3166 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain breaks: 4 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 6, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3166 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain breaks: 4 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 6, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 46 Time building chain proxies: 1.47, per 1000 atoms: 0.23 Number of scatterers: 6332 At special positions: 0 Unit cell: (78.375, 84.15, 77.55, 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 40 16.00 O 1090 8.00 N 1018 7.00 C 4184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 196 " distance=2.03 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: 0.62 Conformation dependent library (CDL) restraints added in 234.4 milliseconds 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 0 sheets defined 83.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.573A pdb=" N SER A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 67 through 101 Processing helix chain 'A' and resid 106 through 122 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 136 through 164 removed outlier: 4.052A pdb=" N ILE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 180 through 204 removed outlier: 3.993A pdb=" N GLY A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Proline residue: A 193 - end of helix removed outlier: 3.614A pdb=" N CYS A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 223 removed outlier: 3.516A pdb=" N THR A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 257 through 284 removed outlier: 3.755A pdb=" N ILE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS A 281 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 removed outlier: 3.690A pdb=" N VAL A 291 " --> pdb=" O PRO A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.943A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 332 Processing helix chain 'A' and resid 338 through 363 removed outlier: 3.665A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 374 through 395 removed outlier: 4.145A pdb=" N ILE A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 436 removed outlier: 5.154A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 444 through 469 Proline residue: A 456 - end of helix removed outlier: 4.120A pdb=" N LEU A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU A 461 " --> pdb=" O CYS A 457 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.583A pdb=" N SER B 38 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 67 through 101 Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 136 through 164 removed outlier: 4.046A pdb=" N ILE B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 150 " --> pdb=" O CYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 180 through 205 removed outlier: 4.063A pdb=" N GLY B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Proline residue: B 193 - end of helix removed outlier: 3.637A pdb=" N CYS B 196 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 223 Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 257 through 284 removed outlier: 3.798A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 298 through 304 removed outlier: 3.955A pdb=" N ALA B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 332 removed outlier: 3.824A pdb=" N ALA B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 363 removed outlier: 3.649A pdb=" N LEU B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 373 through 395 removed outlier: 4.261A pdb=" N ARG B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 435 removed outlier: 5.226A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 444 through 458 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 463 through 469 447 hydrogen bonds defined for protein. 1311 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: 0.79 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.54: 6408 1.54 - 1.90: 72 1.90 - 2.25: 0 2.25 - 2.60: 0 2.60 - 2.96: 2 Bond restraints: 6482 Sorted by residual: bond pdb=" C ARG B 294 " pdb=" N SER B 296 " ideal model delta sigma weight residual 1.332 2.956 -1.623 1.40e-02 5.10e+03 1.34e+04 bond pdb=" C ARG A 294 " pdb=" N SER A 296 " ideal model delta sigma weight residual 1.332 2.914 -1.582 1.40e-02 5.10e+03 1.28e+04 bond pdb=" C ILE B 277 " pdb=" O ILE B 277 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.32e-02 5.74e+03 1.32e+01 bond pdb=" C ILE A 46 " pdb=" O ILE A 46 " ideal model delta sigma weight residual 1.237 1.196 0.041 1.17e-02 7.31e+03 1.24e+01 bond pdb=" C LEU B 278 " pdb=" O LEU B 278 " ideal model delta sigma weight residual 1.237 1.197 0.039 1.19e-02 7.06e+03 1.10e+01 ... (remaining 6477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.15: 8839 10.15 - 20.30: 7 20.30 - 30.44: 0 30.44 - 40.59: 0 40.59 - 50.74: 2 Bond angle restraints: 8848 Sorted by residual: angle pdb=" O ARG A 294 " pdb=" C ARG A 294 " pdb=" N SER A 296 " ideal model delta sigma weight residual 122.59 71.85 50.74 1.33e+00 5.65e-01 1.46e+03 angle pdb=" O ARG B 294 " pdb=" C ARG B 294 " pdb=" N SER B 296 " ideal model delta sigma weight residual 122.59 76.84 45.75 1.33e+00 5.65e-01 1.18e+03 angle pdb=" CA ARG A 294 " pdb=" C ARG A 294 " pdb=" N SER A 296 " ideal model delta sigma weight residual 116.84 135.75 -18.91 1.71e+00 3.42e-01 1.22e+02 angle pdb=" C ARG A 294 " pdb=" N SER A 296 " pdb=" CA SER A 296 " ideal model delta sigma weight residual 121.54 139.31 -17.77 1.91e+00 2.74e-01 8.66e+01 angle pdb=" N ASP A 279 " pdb=" CA ASP A 279 " pdb=" C ASP A 279 " ideal model delta sigma weight residual 113.88 103.08 10.80 1.23e+00 6.61e-01 7.71e+01 ... (remaining 8843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.16: 3417 22.16 - 44.31: 293 44.31 - 66.47: 67 66.47 - 88.62: 5 88.62 - 110.78: 4 Dihedral angle restraints: 3786 sinusoidal: 1356 harmonic: 2430 Sorted by residual: dihedral pdb=" CA ARG B 294 " pdb=" C ARG B 294 " pdb=" N SER B 296 " pdb=" CA SER B 296 " ideal model delta harmonic sigma weight residual -180.00 -69.22 -110.78 0 5.00e+00 4.00e-02 4.91e+02 dihedral pdb=" CA ARG A 294 " pdb=" C ARG A 294 " pdb=" N SER A 296 " pdb=" CA SER A 296 " ideal model delta harmonic sigma weight residual -180.00 -69.36 -110.64 0 5.00e+00 4.00e-02 4.90e+02 dihedral pdb=" CB CYS A 144 " pdb=" SG CYS A 144 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 156.86 -63.86 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 3783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1064 0.112 - 0.224: 28 0.224 - 0.336: 2 0.336 - 0.448: 0 0.448 - 0.559: 2 Chirality restraints: 1096 Sorted by residual: chirality pdb=" CB ILE A 277 " pdb=" CA ILE A 277 " pdb=" CG1 ILE A 277 " pdb=" CG2 ILE A 277 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" CA ILE A 277 " pdb=" N ILE A 277 " pdb=" C ILE A 277 " pdb=" CB ILE A 277 " both_signs ideal model delta sigma weight residual False 2.43 1.92 0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" CA TYR A 222 " pdb=" N TYR A 222 " pdb=" C TYR A 222 " pdb=" CB TYR A 222 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1093 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 294 " 0.179 2.00e-02 2.50e+03 2.24e-01 5.00e+02 pdb=" C ARG B 294 " -0.380 2.00e-02 2.50e+03 pdb=" O ARG B 294 " 0.144 2.00e-02 2.50e+03 pdb=" N SER B 296 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 294 " 0.179 2.00e-02 2.50e+03 2.17e-01 4.72e+02 pdb=" C ARG A 294 " -0.369 2.00e-02 2.50e+03 pdb=" O ARG A 294 " 0.130 2.00e-02 2.50e+03 pdb=" N SER A 296 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 276 " 0.039 2.00e-02 2.50e+03 7.70e-02 5.93e+01 pdb=" C LEU A 276 " -0.133 2.00e-02 2.50e+03 pdb=" O LEU A 276 " 0.051 2.00e-02 2.50e+03 pdb=" N ILE A 277 " 0.044 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.91: 3 1.91 - 2.66: 153 2.66 - 3.40: 10405 3.40 - 4.15: 14728 4.15 - 4.90: 26316 Nonbonded interactions: 51605 Sorted by model distance: nonbonded pdb=" CG2 ILE A 277 " pdb=" CE1 TYR A 313 " model vdw 1.161 3.760 nonbonded pdb=" CG2 ILE A 277 " pdb=" CZ TYR A 313 " model vdw 1.582 3.680 nonbonded pdb=" CG2 ILE A 277 " pdb=" CD1 TYR A 313 " model vdw 1.655 3.760 nonbonded pdb=" O LEU A 213 " pdb=" OG1 THR A 216 " model vdw 2.223 3.040 nonbonded pdb=" O LEU B 213 " pdb=" OG1 THR B 216 " model vdw 2.226 3.040 ... (remaining 51600 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' } 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=0.00 max=1.00 mean=0.98 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: 1.040 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.220 Find NCS groups from input model: 0.090 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 0.029 1.623 6484 Z= 2.030 Angle : 1.198 50.741 8852 Z= 0.795 Chirality : 0.050 0.559 1096 Planarity : 0.011 0.224 1080 Dihedral : 17.622 110.781 2192 Min Nonbonded Distance : 1.161 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 11.79 % Allowed : 21.49 % Favored : 66.72 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.26), residues: 808 helix: -1.66 (0.18), residues: 626 sheet: None (None), residues: 0 loop : -3.25 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 377 TYR 0.016 0.002 TYR B 313 PHE 0.009 0.001 PHE B 99 TRP 0.007 0.001 TRP B 324 HIS 0.006 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.02857 ( 6482) covalent geometry : angle 1.19783 ( 8848) SS BOND : bond 0.00475 ( 2) SS BOND : angle 0.74542 ( 4) hydrogen bonds : bond 0.19401 ( 447) hydrogen bonds : angle 7.30135 ( 1311) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 236 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASN cc_start: 0.9432 (t0) cc_final: 0.9090 (t0) REVERT: A 154 GLN cc_start: 0.9722 (mt0) cc_final: 0.9459 (mt0) REVERT: A 191 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8872 (pm20) REVERT: A 214 MET cc_start: 0.8627 (mtm) cc_final: 0.8355 (mtm) REVERT: A 254 GLU cc_start: 0.8860 (mm-30) cc_final: 0.7861 (mm-30) REVERT: A 284 ASN cc_start: 0.7351 (m110) cc_final: 0.6864 (m110) REVERT: A 322 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8977 (mm) REVERT: A 393 MET cc_start: 0.9138 (mtm) cc_final: 0.8888 (ttm) REVERT: B 59 GLU cc_start: 0.8809 (mp0) cc_final: 0.8558 (tm-30) REVERT: B 191 GLN cc_start: 0.9280 (pp30) cc_final: 0.8907 (pp30) REVERT: B 254 GLU cc_start: 0.8832 (mm-30) cc_final: 0.7870 (mm-30) REVERT: B 284 ASN cc_start: 0.7733 (m110) cc_final: 0.7322 (m110) REVERT: B 322 LEU cc_start: 0.9416 (mm) cc_final: 0.9032 (mm) REVERT: B 393 MET cc_start: 0.9078 (mtm) cc_final: 0.8864 (ttm) outliers start: 79 outliers final: 52 residues processed: 284 average time/residue: 0.0696 time to fit residues: 26.9475 Evaluate side-chains 243 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 211 TYR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 460 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0270 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS A 449 HIS B 154 GLN B 166 HIS B 345 ASN B 390 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.103734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.082509 restraints weight = 15713.368| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 4.52 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6484 Z= 0.179 Angle : 0.820 15.079 8852 Z= 0.392 Chirality : 0.044 0.199 1096 Planarity : 0.005 0.045 1080 Dihedral : 11.249 87.275 971 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.79 % Favored : 93.84 % Rotamer: Outliers : 10.30 % Allowed : 27.76 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.29), residues: 812 helix: -0.18 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -2.17 (0.50), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 35 TYR 0.020 0.002 TYR B 160 PHE 0.012 0.001 PHE B 122 TRP 0.011 0.001 TRP A 410 HIS 0.009 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 6482) covalent geometry : angle 0.82032 ( 8848) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.96547 ( 4) hydrogen bonds : bond 0.06051 ( 447) hydrogen bonds : angle 5.19376 ( 1311) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 262 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASN cc_start: 0.9508 (t0) cc_final: 0.8679 (t0) REVERT: A 117 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.8214 (mpp) REVERT: A 160 TYR cc_start: 0.9309 (t80) cc_final: 0.9019 (t80) REVERT: A 171 GLN cc_start: 0.9161 (mm110) cc_final: 0.8740 (mm110) REVERT: A 191 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8827 (pp30) REVERT: A 206 PHE cc_start: 0.6268 (OUTLIER) cc_final: 0.5855 (m-10) REVERT: A 254 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8622 (tm-30) REVERT: A 284 ASN cc_start: 0.7833 (m110) cc_final: 0.7429 (m110) REVERT: A 322 LEU cc_start: 0.9389 (mm) cc_final: 0.9032 (mm) REVERT: A 374 GLU cc_start: 0.8777 (tp30) cc_final: 0.8471 (tp30) REVERT: A 460 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7865 (mm) REVERT: B 106 ASP cc_start: 0.8869 (t0) cc_final: 0.8648 (t70) REVERT: B 113 ASN cc_start: 0.9238 (t0) cc_final: 0.8421 (t0) REVERT: B 160 TYR cc_start: 0.9275 (t80) cc_final: 0.9039 (t80) REVERT: B 191 GLN cc_start: 0.9094 (pp30) cc_final: 0.8845 (pp30) REVERT: B 254 GLU cc_start: 0.8839 (mm-30) cc_final: 0.7796 (mm-30) REVERT: B 262 GLU cc_start: 0.8563 (tt0) cc_final: 0.8148 (tp30) REVERT: B 284 ASN cc_start: 0.7573 (m110) cc_final: 0.7150 (m110) REVERT: B 322 LEU cc_start: 0.9441 (mm) cc_final: 0.9078 (mm) REVERT: B 374 GLU cc_start: 0.8724 (tt0) cc_final: 0.7965 (tp30) REVERT: B 393 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8965 (ttm) REVERT: B 415 GLU cc_start: 0.9036 (pm20) cc_final: 0.8814 (pm20) outliers start: 69 outliers final: 44 residues processed: 286 average time/residue: 0.0540 time to fit residues: 22.1195 Evaluate side-chains 274 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 225 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS A 345 ASN B 166 HIS ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.103215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.081972 restraints weight = 15669.647| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 4.46 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6484 Z= 0.193 Angle : 0.806 13.862 8852 Z= 0.390 Chirality : 0.044 0.210 1096 Planarity : 0.004 0.042 1080 Dihedral : 9.687 59.928 937 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 12.09 % Allowed : 27.91 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.30), residues: 812 helix: 0.30 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.69 (0.55), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 335 TYR 0.025 0.003 TYR A 211 PHE 0.011 0.001 PHE A 127 TRP 0.007 0.001 TRP A 324 HIS 0.015 0.002 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 6482) covalent geometry : angle 0.80560 ( 8848) SS BOND : bond 0.00157 ( 2) SS BOND : angle 1.06809 ( 4) hydrogen bonds : bond 0.05837 ( 447) hydrogen bonds : angle 5.07066 ( 1311) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 244 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASN cc_start: 0.9483 (t0) cc_final: 0.8616 (t0) REVERT: A 117 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.8155 (mpp) REVERT: A 130 MET cc_start: 0.9393 (tmm) cc_final: 0.8767 (tmm) REVERT: A 160 TYR cc_start: 0.9366 (t80) cc_final: 0.9096 (t80) REVERT: A 171 GLN cc_start: 0.9058 (mm110) cc_final: 0.8691 (mm110) REVERT: A 181 TYR cc_start: 0.8630 (m-80) cc_final: 0.8277 (m-80) REVERT: A 191 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8781 (pp30) REVERT: A 254 GLU cc_start: 0.8929 (mm-30) cc_final: 0.7785 (mm-30) REVERT: A 262 GLU cc_start: 0.8530 (tt0) cc_final: 0.7747 (tp30) REVERT: A 284 ASN cc_start: 0.7664 (m110) cc_final: 0.7303 (m110) REVERT: A 322 LEU cc_start: 0.9373 (mm) cc_final: 0.9037 (mm) REVERT: A 374 GLU cc_start: 0.8770 (tp30) cc_final: 0.8460 (tp30) REVERT: A 415 GLU cc_start: 0.9026 (pm20) cc_final: 0.8753 (pm20) REVERT: A 460 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7886 (mm) REVERT: B 59 GLU cc_start: 0.8896 (mp0) cc_final: 0.8618 (tm-30) REVERT: B 113 ASN cc_start: 0.8814 (t0) cc_final: 0.8592 (t0) REVERT: B 117 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.7954 (mpp) REVERT: B 160 TYR cc_start: 0.9313 (t80) cc_final: 0.9078 (t80) REVERT: B 171 GLN cc_start: 0.9073 (mm110) cc_final: 0.8662 (mm110) REVERT: B 181 TYR cc_start: 0.8586 (m-80) cc_final: 0.8244 (m-80) REVERT: B 191 GLN cc_start: 0.9152 (pp30) cc_final: 0.8903 (pp30) REVERT: B 254 GLU cc_start: 0.8885 (mm-30) cc_final: 0.7793 (mm-30) REVERT: B 260 ARG cc_start: 0.8769 (mmm-85) cc_final: 0.8400 (mmm-85) REVERT: B 262 GLU cc_start: 0.8602 (tt0) cc_final: 0.8104 (tp30) REVERT: B 284 ASN cc_start: 0.7568 (m110) cc_final: 0.7150 (m110) REVERT: B 322 LEU cc_start: 0.9439 (mm) cc_final: 0.9079 (mm) outliers start: 81 outliers final: 50 residues processed: 270 average time/residue: 0.0565 time to fit residues: 21.8106 Evaluate side-chains 290 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 236 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN B 416 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.106142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.084287 restraints weight = 15740.542| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 4.67 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6484 Z= 0.164 Angle : 0.784 13.465 8852 Z= 0.372 Chirality : 0.043 0.219 1096 Planarity : 0.004 0.038 1080 Dihedral : 9.447 59.875 934 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 11.64 % Allowed : 30.15 % Favored : 58.21 % 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 are not related in a simple way. whole: 0.01 (0.30), residues: 812 helix: 0.52 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.68 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 335 TYR 0.020 0.003 TYR A 211 PHE 0.011 0.001 PHE B 389 TRP 0.008 0.001 TRP B 324 HIS 0.008 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6482) covalent geometry : angle 0.78387 ( 8848) SS BOND : bond 0.00042 ( 2) SS BOND : angle 0.99074 ( 4) hydrogen bonds : bond 0.05388 ( 447) hydrogen bonds : angle 4.88403 ( 1311) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 254 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASN cc_start: 0.9431 (t0) cc_final: 0.8536 (t0) REVERT: A 117 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.8076 (mpp) REVERT: A 160 TYR cc_start: 0.9337 (t80) cc_final: 0.9095 (t80) REVERT: A 181 TYR cc_start: 0.8630 (m-80) cc_final: 0.8290 (m-80) REVERT: A 191 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8740 (pp30) REVERT: A 254 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8508 (tm-30) REVERT: A 284 ASN cc_start: 0.7546 (m110) cc_final: 0.7086 (m110) REVERT: A 336 LYS cc_start: 0.8908 (ttpp) cc_final: 0.8617 (mtpp) REVERT: A 341 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.8817 (mmp) REVERT: A 374 GLU cc_start: 0.8731 (tp30) cc_final: 0.8447 (tp30) REVERT: A 403 GLU cc_start: 0.8498 (mp0) cc_final: 0.8291 (mp0) REVERT: A 415 GLU cc_start: 0.8967 (pm20) cc_final: 0.8733 (pm20) REVERT: B 59 GLU cc_start: 0.8888 (mp0) cc_final: 0.8526 (tm-30) REVERT: B 113 ASN cc_start: 0.8667 (t0) cc_final: 0.8272 (t0) REVERT: B 117 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.7899 (mpp) REVERT: B 160 TYR cc_start: 0.9308 (t80) cc_final: 0.8998 (t80) REVERT: B 171 GLN cc_start: 0.9056 (mm110) cc_final: 0.8645 (mm110) REVERT: B 181 TYR cc_start: 0.8637 (m-80) cc_final: 0.8297 (m-80) REVERT: B 254 GLU cc_start: 0.8894 (mm-30) cc_final: 0.7862 (mm-30) REVERT: B 262 GLU cc_start: 0.8572 (tt0) cc_final: 0.7903 (tm-30) REVERT: B 284 ASN cc_start: 0.7169 (m110) cc_final: 0.6786 (m110) REVERT: B 314 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8540 (m-80) REVERT: B 322 LEU cc_start: 0.9389 (mm) cc_final: 0.9028 (mm) REVERT: B 336 LYS cc_start: 0.8916 (ttpp) cc_final: 0.8615 (mtpp) REVERT: B 403 GLU cc_start: 0.8414 (mp0) cc_final: 0.8195 (mp0) REVERT: B 415 GLU cc_start: 0.8978 (pm20) cc_final: 0.8773 (pm20) outliers start: 78 outliers final: 52 residues processed: 280 average time/residue: 0.0572 time to fit residues: 22.6349 Evaluate side-chains 298 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 72 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.105827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.084294 restraints weight = 15825.755| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 4.66 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6484 Z= 0.166 Angle : 0.770 12.338 8852 Z= 0.369 Chirality : 0.044 0.211 1096 Planarity : 0.004 0.037 1080 Dihedral : 9.078 56.305 931 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 12.24 % Allowed : 30.90 % Favored : 56.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.30), residues: 812 helix: 0.67 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -1.59 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 335 TYR 0.026 0.002 TYR A 211 PHE 0.009 0.001 PHE A 443 TRP 0.015 0.001 TRP A 324 HIS 0.008 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6482) covalent geometry : angle 0.76950 ( 8848) SS BOND : bond 0.00524 ( 2) SS BOND : angle 1.07566 ( 4) hydrogen bonds : bond 0.05286 ( 447) hydrogen bonds : angle 4.84626 ( 1311) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 253 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8765 (mtm) cc_final: 0.8154 (mtm) REVERT: A 113 ASN cc_start: 0.9419 (t0) cc_final: 0.8551 (t0) REVERT: A 117 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8220 (mpp) REVERT: A 130 MET cc_start: 0.9264 (tmm) cc_final: 0.8809 (tmm) REVERT: A 160 TYR cc_start: 0.9330 (t80) cc_final: 0.9117 (t80) REVERT: A 181 TYR cc_start: 0.8655 (m-80) cc_final: 0.8321 (m-80) REVERT: A 188 ILE cc_start: 0.9247 (tp) cc_final: 0.8943 (tp) REVERT: A 191 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8719 (pp30) REVERT: A 208 PRO cc_start: 0.7410 (Cg_endo) cc_final: 0.7134 (Cg_exo) REVERT: A 254 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8513 (tm-30) REVERT: A 259 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8692 (mp0) REVERT: A 284 ASN cc_start: 0.7477 (m110) cc_final: 0.7015 (m110) REVERT: A 322 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9060 (mm) REVERT: A 336 LYS cc_start: 0.8927 (ttpp) cc_final: 0.8656 (mtpp) REVERT: A 341 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8693 (tpp) REVERT: A 374 GLU cc_start: 0.8696 (tp30) cc_final: 0.8411 (tp30) REVERT: A 403 GLU cc_start: 0.8538 (mp0) cc_final: 0.8337 (mp0) REVERT: A 415 GLU cc_start: 0.8977 (pm20) cc_final: 0.8725 (pm20) REVERT: B 59 GLU cc_start: 0.8843 (mp0) cc_final: 0.8488 (tm-30) REVERT: B 113 ASN cc_start: 0.8787 (t0) cc_final: 0.8421 (t0) REVERT: B 117 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.7865 (mpp) REVERT: B 160 TYR cc_start: 0.9275 (t80) cc_final: 0.9069 (t80) REVERT: B 171 GLN cc_start: 0.9065 (mm110) cc_final: 0.8690 (mm-40) REVERT: B 181 TYR cc_start: 0.8653 (m-80) cc_final: 0.8390 (m-80) REVERT: B 184 HIS cc_start: 0.8855 (t70) cc_final: 0.8610 (t-90) REVERT: B 254 GLU cc_start: 0.8886 (mm-30) cc_final: 0.7800 (mm-30) REVERT: B 262 GLU cc_start: 0.8550 (tt0) cc_final: 0.7833 (tp30) REVERT: B 284 ASN cc_start: 0.7011 (m110) cc_final: 0.6559 (m110) REVERT: B 314 PHE cc_start: 0.9220 (OUTLIER) cc_final: 0.8691 (m-80) REVERT: B 336 LYS cc_start: 0.8910 (ttpp) cc_final: 0.8640 (mtpp) REVERT: B 403 GLU cc_start: 0.8415 (mp0) cc_final: 0.8201 (mp0) REVERT: B 415 GLU cc_start: 0.8939 (pm20) cc_final: 0.8719 (pm20) outliers start: 82 outliers final: 56 residues processed: 279 average time/residue: 0.0596 time to fit residues: 23.7634 Evaluate side-chains 311 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 248 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 28 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.107316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.086089 restraints weight = 15532.092| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 4.63 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6484 Z= 0.166 Angle : 0.782 12.339 8852 Z= 0.373 Chirality : 0.044 0.239 1096 Planarity : 0.004 0.048 1080 Dihedral : 8.769 57.975 927 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 10.00 % Allowed : 33.28 % Favored : 56.72 % 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 are not related in a simple way. whole: 0.21 (0.30), residues: 812 helix: 0.68 (0.20), residues: 626 sheet: None (None), residues: 0 loop : -1.53 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 260 TYR 0.035 0.003 TYR A 211 PHE 0.009 0.001 PHE A 443 TRP 0.007 0.001 TRP A 324 HIS 0.008 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 6482) covalent geometry : angle 0.78168 ( 8848) SS BOND : bond 0.00109 ( 2) SS BOND : angle 1.30795 ( 4) hydrogen bonds : bond 0.05304 ( 447) hydrogen bonds : angle 4.82428 ( 1311) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 246 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8821 (mp0) cc_final: 0.8461 (tm-30) REVERT: A 83 MET cc_start: 0.8735 (mtm) cc_final: 0.8207 (mtm) REVERT: A 113 ASN cc_start: 0.9448 (t0) cc_final: 0.8582 (t0) REVERT: A 117 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.8213 (mpp) REVERT: A 130 MET cc_start: 0.9241 (tmm) cc_final: 0.8811 (tmm) REVERT: A 181 TYR cc_start: 0.8648 (m-80) cc_final: 0.8378 (m-80) REVERT: A 208 PRO cc_start: 0.7468 (Cg_endo) cc_final: 0.7163 (Cg_exo) REVERT: A 254 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8428 (tm-30) REVERT: A 259 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8673 (mp0) REVERT: A 279 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8357 (p0) REVERT: A 284 ASN cc_start: 0.7492 (m110) cc_final: 0.7056 (m110) REVERT: A 322 LEU cc_start: 0.9365 (mm) cc_final: 0.9030 (mm) REVERT: A 336 LYS cc_start: 0.8892 (ttpp) cc_final: 0.8630 (mtpp) REVERT: A 341 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8372 (mmp) REVERT: A 374 GLU cc_start: 0.8698 (tp30) cc_final: 0.8420 (tp30) REVERT: A 415 GLU cc_start: 0.8983 (pm20) cc_final: 0.8754 (pm20) REVERT: B 59 GLU cc_start: 0.8867 (mp0) cc_final: 0.8540 (tm-30) REVERT: B 113 ASN cc_start: 0.8829 (t0) cc_final: 0.8270 (t0) REVERT: B 117 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.7743 (mpp) REVERT: B 160 TYR cc_start: 0.9307 (t80) cc_final: 0.9087 (t80) REVERT: B 181 TYR cc_start: 0.8726 (m-80) cc_final: 0.8382 (m-80) REVERT: B 184 HIS cc_start: 0.8850 (t70) cc_final: 0.8612 (t-90) REVERT: B 254 GLU cc_start: 0.8899 (mm-30) cc_final: 0.7799 (mm-30) REVERT: B 259 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8641 (mp0) REVERT: B 262 GLU cc_start: 0.8417 (tt0) cc_final: 0.7695 (tm-30) REVERT: B 284 ASN cc_start: 0.6909 (m110) cc_final: 0.6369 (m110) REVERT: B 336 LYS cc_start: 0.8929 (ttpp) cc_final: 0.8652 (mtpp) REVERT: B 415 GLU cc_start: 0.8956 (pm20) cc_final: 0.8727 (pm20) outliers start: 67 outliers final: 48 residues processed: 268 average time/residue: 0.0574 time to fit residues: 21.8754 Evaluate side-chains 292 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 238 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.108449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.086928 restraints weight = 15550.953| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 4.69 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6484 Z= 0.167 Angle : 0.806 11.691 8852 Z= 0.386 Chirality : 0.045 0.248 1096 Planarity : 0.004 0.034 1080 Dihedral : 8.368 58.431 920 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 10.90 % Allowed : 34.33 % Favored : 54.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.30), residues: 812 helix: 0.65 (0.20), residues: 626 sheet: None (None), residues: 0 loop : -1.45 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 260 TYR 0.020 0.002 TYR A 160 PHE 0.009 0.001 PHE A 443 TRP 0.019 0.001 TRP A 324 HIS 0.007 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6482) covalent geometry : angle 0.80567 ( 8848) SS BOND : bond 0.00639 ( 2) SS BOND : angle 1.50404 ( 4) hydrogen bonds : bond 0.05229 ( 447) hydrogen bonds : angle 4.79796 ( 1311) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 252 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8782 (mp0) cc_final: 0.8447 (tm-30) REVERT: A 83 MET cc_start: 0.8776 (mtm) cc_final: 0.8278 (mtm) REVERT: A 113 ASN cc_start: 0.9437 (t0) cc_final: 0.8555 (t0) REVERT: A 117 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.8209 (mpp) REVERT: A 130 MET cc_start: 0.9251 (tmm) cc_final: 0.8809 (tmm) REVERT: A 154 GLN cc_start: 0.9695 (mt0) cc_final: 0.9337 (mm-40) REVERT: A 160 TYR cc_start: 0.9293 (t80) cc_final: 0.8982 (t80) REVERT: A 181 TYR cc_start: 0.8669 (m-80) cc_final: 0.8296 (m-80) REVERT: A 188 ILE cc_start: 0.9146 (tp) cc_final: 0.8904 (tp) REVERT: A 208 PRO cc_start: 0.7365 (Cg_endo) cc_final: 0.7069 (Cg_exo) REVERT: A 254 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8399 (tm-30) REVERT: A 259 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8594 (mp0) REVERT: A 284 ASN cc_start: 0.7410 (m110) cc_final: 0.6949 (m110) REVERT: A 322 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8981 (mm) REVERT: A 336 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8613 (mtpp) REVERT: A 341 MET cc_start: 0.9066 (tpp) cc_final: 0.8522 (tpp) REVERT: A 374 GLU cc_start: 0.8674 (tp30) cc_final: 0.8390 (tp30) REVERT: A 415 GLU cc_start: 0.8937 (pm20) cc_final: 0.8718 (pm20) REVERT: B 59 GLU cc_start: 0.8836 (mp0) cc_final: 0.8471 (tm-30) REVERT: B 113 ASN cc_start: 0.8891 (t0) cc_final: 0.8448 (t0) REVERT: B 117 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.7787 (mpp) REVERT: B 160 TYR cc_start: 0.9321 (t80) cc_final: 0.9110 (t80) REVERT: B 181 TYR cc_start: 0.8720 (m-80) cc_final: 0.8362 (m-80) REVERT: B 188 ILE cc_start: 0.9385 (tp) cc_final: 0.9173 (mm) REVERT: B 254 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8480 (tm-30) REVERT: B 259 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8551 (mp0) REVERT: B 262 GLU cc_start: 0.8422 (tt0) cc_final: 0.7894 (tm-30) REVERT: B 284 ASN cc_start: 0.7020 (m110) cc_final: 0.6578 (m110) REVERT: B 322 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8912 (mm) REVERT: B 336 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8653 (mtpp) REVERT: B 374 GLU cc_start: 0.8597 (tt0) cc_final: 0.7885 (tp30) REVERT: B 415 GLU cc_start: 0.8916 (pm20) cc_final: 0.8704 (pm20) outliers start: 73 outliers final: 52 residues processed: 279 average time/residue: 0.0542 time to fit residues: 21.9576 Evaluate side-chains 296 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 238 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 10 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.109353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.086727 restraints weight = 15534.333| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 4.84 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6484 Z= 0.166 Angle : 0.834 16.081 8852 Z= 0.392 Chirality : 0.046 0.226 1096 Planarity : 0.004 0.034 1080 Dihedral : 7.983 59.700 918 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 10.60 % Allowed : 35.22 % Favored : 54.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.30), residues: 812 helix: 0.62 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -1.34 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 260 TYR 0.035 0.003 TYR A 211 PHE 0.010 0.001 PHE B 127 TRP 0.011 0.001 TRP A 324 HIS 0.007 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 6482) covalent geometry : angle 0.83296 ( 8848) SS BOND : bond 0.00036 ( 2) SS BOND : angle 1.67271 ( 4) hydrogen bonds : bond 0.05152 ( 447) hydrogen bonds : angle 4.78684 ( 1311) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 248 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8822 (mp0) cc_final: 0.8399 (tm-30) REVERT: A 113 ASN cc_start: 0.9395 (t0) cc_final: 0.8542 (t0) REVERT: A 117 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8155 (mpp) REVERT: A 130 MET cc_start: 0.9269 (tmm) cc_final: 0.8896 (tmm) REVERT: A 154 GLN cc_start: 0.9696 (mt0) cc_final: 0.9372 (mm-40) REVERT: A 160 TYR cc_start: 0.9393 (t80) cc_final: 0.9087 (t80) REVERT: A 181 TYR cc_start: 0.8666 (m-80) cc_final: 0.8292 (m-80) REVERT: A 184 HIS cc_start: 0.9016 (t70) cc_final: 0.8746 (t-90) REVERT: A 188 ILE cc_start: 0.9136 (tp) cc_final: 0.8895 (tp) REVERT: A 208 PRO cc_start: 0.7520 (Cg_endo) cc_final: 0.7214 (Cg_exo) REVERT: A 250 PHE cc_start: 0.6280 (OUTLIER) cc_final: 0.6035 (m-10) REVERT: A 254 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8337 (tm-30) REVERT: A 259 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8559 (mp0) REVERT: A 260 ARG cc_start: 0.8469 (mmm-85) cc_final: 0.8232 (mmm-85) REVERT: A 284 ASN cc_start: 0.7404 (m110) cc_final: 0.6958 (m110) REVERT: A 322 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8833 (mm) REVERT: A 336 LYS cc_start: 0.8857 (ttpp) cc_final: 0.8591 (mtpp) REVERT: A 341 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8479 (tpp) REVERT: A 374 GLU cc_start: 0.8596 (tp30) cc_final: 0.8302 (tp30) REVERT: A 403 GLU cc_start: 0.8255 (mp0) cc_final: 0.8028 (mp0) REVERT: A 415 GLU cc_start: 0.8995 (pm20) cc_final: 0.8737 (pm20) REVERT: B 59 GLU cc_start: 0.8902 (mp0) cc_final: 0.8523 (tm-30) REVERT: B 113 ASN cc_start: 0.8918 (t0) cc_final: 0.8322 (t0) REVERT: B 117 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.7688 (mpp) REVERT: B 181 TYR cc_start: 0.8714 (m-80) cc_final: 0.8350 (m-80) REVERT: B 184 HIS cc_start: 0.8933 (t70) cc_final: 0.8729 (t-90) REVERT: B 254 GLU cc_start: 0.8834 (mm-30) cc_final: 0.7706 (mm-30) REVERT: B 259 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8539 (mp0) REVERT: B 262 GLU cc_start: 0.8415 (tt0) cc_final: 0.7888 (tm-30) REVERT: B 284 ASN cc_start: 0.6921 (m110) cc_final: 0.6496 (m110) REVERT: B 322 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8885 (mm) REVERT: B 336 LYS cc_start: 0.8880 (ttpp) cc_final: 0.8625 (mtpp) REVERT: B 341 MET cc_start: 0.8676 (tpp) cc_final: 0.8346 (mmp) REVERT: B 374 GLU cc_start: 0.8490 (tt0) cc_final: 0.7714 (tp30) REVERT: B 415 GLU cc_start: 0.8925 (pm20) cc_final: 0.8724 (pm20) outliers start: 71 outliers final: 52 residues processed: 274 average time/residue: 0.0563 time to fit residues: 22.0046 Evaluate side-chains 297 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 237 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.0030 chunk 60 optimal weight: 0.0020 overall best weight: 0.2976 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.114220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.091423 restraints weight = 15542.829| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 5.00 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6484 Z= 0.165 Angle : 0.866 16.432 8852 Z= 0.401 Chirality : 0.046 0.253 1096 Planarity : 0.004 0.035 1080 Dihedral : 7.662 56.156 916 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 8.96 % Allowed : 37.31 % Favored : 53.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.30), residues: 812 helix: 0.70 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -1.25 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 260 TYR 0.017 0.002 TYR B 313 PHE 0.015 0.001 PHE A 127 TRP 0.036 0.002 TRP B 324 HIS 0.008 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6482) covalent geometry : angle 0.86499 ( 8848) SS BOND : bond 0.00153 ( 2) SS BOND : angle 1.88602 ( 4) hydrogen bonds : bond 0.04960 ( 447) hydrogen bonds : angle 4.75398 ( 1311) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 254 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8800 (mp0) cc_final: 0.8501 (tm-30) REVERT: A 113 ASN cc_start: 0.9362 (t0) cc_final: 0.8541 (t0) REVERT: A 117 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.8093 (mpp) REVERT: A 154 GLN cc_start: 0.9669 (mt0) cc_final: 0.9449 (mm-40) REVERT: A 160 TYR cc_start: 0.9389 (t80) cc_final: 0.9086 (t80) REVERT: A 181 TYR cc_start: 0.8645 (m-80) cc_final: 0.8310 (m-80) REVERT: A 184 HIS cc_start: 0.9050 (t70) cc_final: 0.8740 (t-90) REVERT: A 188 ILE cc_start: 0.9016 (tp) cc_final: 0.8782 (tp) REVERT: A 208 PRO cc_start: 0.7338 (Cg_endo) cc_final: 0.7072 (Cg_exo) REVERT: A 250 PHE cc_start: 0.6288 (OUTLIER) cc_final: 0.6012 (m-10) REVERT: A 254 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8282 (tm-30) REVERT: A 259 GLU cc_start: 0.8955 (pt0) cc_final: 0.8527 (mp0) REVERT: A 284 ASN cc_start: 0.7287 (m110) cc_final: 0.6864 (m110) REVERT: A 336 LYS cc_start: 0.8876 (ttpp) cc_final: 0.8606 (mtpp) REVERT: A 341 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8323 (mmp) REVERT: A 374 GLU cc_start: 0.8602 (tp30) cc_final: 0.8332 (tp30) REVERT: A 403 GLU cc_start: 0.8202 (mp0) cc_final: 0.7978 (mp0) REVERT: A 415 GLU cc_start: 0.8957 (pm20) cc_final: 0.8753 (pm20) REVERT: B 34 GLN cc_start: 0.9194 (pp30) cc_final: 0.8972 (pp30) REVERT: B 113 ASN cc_start: 0.8868 (t0) cc_final: 0.8607 (t0) REVERT: B 117 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.7999 (mpp) REVERT: B 181 TYR cc_start: 0.8650 (m-80) cc_final: 0.8307 (m-80) REVERT: B 184 HIS cc_start: 0.8936 (t70) cc_final: 0.8715 (t-90) REVERT: B 254 GLU cc_start: 0.8826 (mm-30) cc_final: 0.7694 (mm-30) REVERT: B 259 GLU cc_start: 0.8914 (pt0) cc_final: 0.8470 (mp0) REVERT: B 262 GLU cc_start: 0.8337 (tt0) cc_final: 0.7841 (tm-30) REVERT: B 284 ASN cc_start: 0.6814 (m110) cc_final: 0.6422 (m110) REVERT: B 314 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8889 (m-80) REVERT: B 322 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8836 (mm) REVERT: B 336 LYS cc_start: 0.8815 (ttpp) cc_final: 0.8571 (mtpp) REVERT: B 341 MET cc_start: 0.8647 (tpp) cc_final: 0.8296 (mmp) REVERT: B 374 GLU cc_start: 0.8301 (tt0) cc_final: 0.7507 (tp30) REVERT: B 415 GLU cc_start: 0.8925 (pm20) cc_final: 0.8725 (pm20) outliers start: 60 outliers final: 44 residues processed: 273 average time/residue: 0.0582 time to fit residues: 22.7575 Evaluate side-chains 295 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 245 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 60 optimal weight: 0.4980 chunk 35 optimal weight: 0.0870 chunk 68 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.114120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.091870 restraints weight = 15417.097| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 4.95 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6484 Z= 0.169 Angle : 0.892 16.343 8852 Z= 0.415 Chirality : 0.047 0.259 1096 Planarity : 0.004 0.035 1080 Dihedral : 7.283 57.394 908 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 7.91 % Allowed : 39.55 % Favored : 52.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.30), residues: 812 helix: 0.75 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.12 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 260 TYR 0.040 0.003 TYR A 211 PHE 0.021 0.001 PHE A 127 TRP 0.026 0.002 TRP B 324 HIS 0.008 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6482) covalent geometry : angle 0.89177 ( 8848) SS BOND : bond 0.00109 ( 2) SS BOND : angle 1.71357 ( 4) hydrogen bonds : bond 0.04999 ( 447) hydrogen bonds : angle 4.76699 ( 1311) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9037 (pp30) cc_final: 0.8741 (pp30) REVERT: A 83 MET cc_start: 0.8755 (mtm) cc_final: 0.8316 (mtm) REVERT: A 154 GLN cc_start: 0.9687 (mt0) cc_final: 0.9438 (mm-40) REVERT: A 160 TYR cc_start: 0.9415 (t80) cc_final: 0.9162 (t80) REVERT: A 181 TYR cc_start: 0.8641 (m-80) cc_final: 0.8331 (m-80) REVERT: A 184 HIS cc_start: 0.9030 (t70) cc_final: 0.8732 (t-90) REVERT: A 188 ILE cc_start: 0.9014 (tp) cc_final: 0.8770 (tp) REVERT: A 208 PRO cc_start: 0.7385 (Cg_endo) cc_final: 0.7106 (Cg_exo) REVERT: A 254 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8262 (tm-30) REVERT: A 259 GLU cc_start: 0.8951 (pt0) cc_final: 0.8542 (mp0) REVERT: A 284 ASN cc_start: 0.7272 (m110) cc_final: 0.6847 (m110) REVERT: A 322 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8848 (mm) REVERT: A 336 LYS cc_start: 0.8872 (ttpp) cc_final: 0.8591 (mtpp) REVERT: A 341 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8355 (mmp) REVERT: A 374 GLU cc_start: 0.8599 (tp30) cc_final: 0.8336 (tp30) REVERT: B 113 ASN cc_start: 0.8866 (t0) cc_final: 0.8429 (t0) REVERT: B 117 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.7750 (mpp) REVERT: B 181 TYR cc_start: 0.8669 (m-80) cc_final: 0.8368 (m-80) REVERT: B 184 HIS cc_start: 0.8974 (t70) cc_final: 0.8759 (t-90) REVERT: B 254 GLU cc_start: 0.8878 (mm-30) cc_final: 0.7741 (mm-30) REVERT: B 259 GLU cc_start: 0.8897 (pt0) cc_final: 0.8492 (mp0) REVERT: B 262 GLU cc_start: 0.8405 (tt0) cc_final: 0.7874 (tm-30) REVERT: B 284 ASN cc_start: 0.6657 (m110) cc_final: 0.6321 (m110) REVERT: B 314 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8944 (m-80) REVERT: B 322 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8897 (mm) REVERT: B 336 LYS cc_start: 0.8809 (ttpp) cc_final: 0.8557 (mtpp) REVERT: B 374 GLU cc_start: 0.8319 (tt0) cc_final: 0.7588 (tp30) outliers start: 53 outliers final: 43 residues processed: 262 average time/residue: 0.0560 time to fit residues: 21.1598 Evaluate side-chains 290 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 38 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 39 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.107736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.085547 restraints weight = 15395.920| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 4.77 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6484 Z= 0.200 Angle : 0.918 15.419 8852 Z= 0.434 Chirality : 0.048 0.220 1096 Planarity : 0.005 0.037 1080 Dihedral : 6.979 57.505 906 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 8.51 % Allowed : 38.36 % Favored : 53.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.30), residues: 812 helix: 0.74 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -0.97 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 260 TYR 0.022 0.002 TYR A 313 PHE 0.021 0.001 PHE A 127 TRP 0.027 0.002 TRP A 324 HIS 0.007 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 6482) covalent geometry : angle 0.91795 ( 8848) SS BOND : bond 0.00169 ( 2) SS BOND : angle 1.41348 ( 4) hydrogen bonds : bond 0.05391 ( 447) hydrogen bonds : angle 4.86885 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1209.07 seconds wall clock time: 21 minutes 31.67 seconds (1291.67 seconds total)