Starting phenix.real_space_refine on Thu Jul 24 13:44:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w8o_21576/07_2025/6w8o_21576.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w8o_21576/07_2025/6w8o_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6w8o_21576/07_2025/6w8o_21576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w8o_21576/07_2025/6w8o_21576.map" model { file = "/net/cci-nas-00/data/ceres_data/6w8o_21576/07_2025/6w8o_21576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w8o_21576/07_2025/6w8o_21576.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'PHE:plan': 1, 'ARG:plan': 6, 'HIS:plan': 2} 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: {'PHE:plan': 1, 'ARG:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 46 Time building chain proxies: 4.85, per 1000 atoms: 0.77 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: 2.30 Conformation dependent library (CDL) restraints added in 867.2 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: 0.74 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: 1.85 Time building geometry restraints manager: 2.23 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: 0.03 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: 1.260 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 19.760 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.540 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP B 324 HIS 0.006 0.001 HIS A 449 PHE 0.009 0.001 PHE B 99 TYR 0.016 0.002 TYR B 313 ARG 0.003 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.19401 ( 447) hydrogen bonds : angle 7.30135 ( 1311) SS BOND : bond 0.00475 ( 2) SS BOND : angle 0.74542 ( 4) covalent geometry : bond 0.02857 ( 6482) covalent geometry : angle 1.19783 ( 8848) *********************** 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 : 0.727 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: 0.7871 (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: 0.1618 time to fit residues: 61.2675 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 : 0.723 ------------------------------------------------------------------------------- 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 69 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN B 166 HIS B 345 ASN B 390 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.103055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.082221 restraints weight = 15594.772| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 4.50 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6484 Z= 0.181 Angle : 0.821 15.183 8852 Z= 0.392 Chirality : 0.044 0.210 1096 Planarity : 0.005 0.044 1080 Dihedral : 11.232 87.082 971 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.67 % Favored : 93.97 % Rotamer: Outliers : 10.60 % Allowed : 27.61 % Favored : 61.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.29), residues: 812 helix: -0.19 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -2.18 (0.50), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 410 HIS 0.009 0.001 HIS B 166 PHE 0.012 0.001 PHE B 122 TYR 0.020 0.002 TYR B 160 ARG 0.006 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.06128 ( 447) hydrogen bonds : angle 5.22955 ( 1311) SS BOND : bond 0.00959 ( 2) SS BOND : angle 1.02214 ( 4) covalent geometry : bond 0.00394 ( 6482) covalent geometry : angle 0.82096 ( 8848) *********************** 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: 71 poor density : 260 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASN cc_start: 0.9506 (t0) cc_final: 0.8690 (t0) REVERT: A 117 MET cc_start: 0.9356 (OUTLIER) cc_final: 0.8212 (mpp) REVERT: A 160 TYR cc_start: 0.9311 (t80) cc_final: 0.9011 (t80) REVERT: A 171 GLN cc_start: 0.9165 (mm110) cc_final: 0.8744 (mm110) REVERT: A 191 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8833 (pp30) REVERT: A 206 PHE cc_start: 0.6287 (OUTLIER) cc_final: 0.5873 (m-10) REVERT: A 254 GLU cc_start: 0.8859 (mm-30) cc_final: 0.7741 (mm-30) REVERT: A 284 ASN cc_start: 0.7843 (m110) cc_final: 0.7431 (m110) REVERT: A 322 LEU cc_start: 0.9398 (mm) cc_final: 0.9051 (mm) REVERT: A 374 GLU cc_start: 0.8799 (tp30) cc_final: 0.8536 (tp30) REVERT: A 393 MET cc_start: 0.9159 (mtm) cc_final: 0.8938 (ttm) REVERT: A 460 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7828 (mm) REVERT: B 106 ASP cc_start: 0.8877 (t0) cc_final: 0.8647 (t70) REVERT: B 160 TYR cc_start: 0.9298 (t80) cc_final: 0.9075 (t80) REVERT: B 191 GLN cc_start: 0.9095 (pp30) cc_final: 0.8844 (pp30) REVERT: B 254 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8618 (tm-30) REVERT: B 262 GLU cc_start: 0.8576 (tt0) cc_final: 0.8142 (tp30) REVERT: B 284 ASN cc_start: 0.7565 (m110) cc_final: 0.7135 (m110) REVERT: B 322 LEU cc_start: 0.9442 (mm) cc_final: 0.9085 (mm) REVERT: B 374 GLU cc_start: 0.8737 (tt0) cc_final: 0.7989 (tp30) outliers start: 71 outliers final: 50 residues processed: 284 average time/residue: 0.1662 time to fit residues: 66.3629 Evaluate side-chains 277 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 223 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 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 222 TYR 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 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 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 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 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 222 TYR 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 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 44 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 166 HIS B 390 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.105035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.083593 restraints weight = 15730.740| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 4.63 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6484 Z= 0.175 Angle : 0.797 13.913 8852 Z= 0.381 Chirality : 0.044 0.209 1096 Planarity : 0.004 0.041 1080 Dihedral : 9.888 59.852 944 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 11.34 % Allowed : 28.51 % Favored : 60.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.30), residues: 812 helix: 0.33 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.78 (0.53), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 324 HIS 0.014 0.002 HIS B 166 PHE 0.010 0.001 PHE B 389 TYR 0.023 0.003 TYR A 211 ARG 0.003 0.000 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.05684 ( 447) hydrogen bonds : angle 4.97111 ( 1311) SS BOND : bond 0.00222 ( 2) SS BOND : angle 1.20933 ( 4) covalent geometry : bond 0.00385 ( 6482) covalent geometry : angle 0.79724 ( 8848) *********************** 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: 76 poor density : 249 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASN cc_start: 0.9480 (t0) cc_final: 0.8577 (t0) REVERT: A 117 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.8141 (mpp) REVERT: A 130 MET cc_start: 0.9356 (tmm) cc_final: 0.8934 (tmm) REVERT: A 160 TYR cc_start: 0.9320 (t80) cc_final: 0.9033 (t80) REVERT: A 171 GLN cc_start: 0.9046 (mm110) cc_final: 0.8689 (mm110) REVERT: A 181 TYR cc_start: 0.8610 (m-80) cc_final: 0.8254 (m-80) REVERT: A 191 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8793 (pp30) REVERT: A 254 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8552 (tm-30) REVERT: A 262 GLU cc_start: 0.8458 (tt0) cc_final: 0.7719 (tp30) REVERT: A 284 ASN cc_start: 0.7552 (m110) cc_final: 0.7199 (m110) REVERT: A 322 LEU cc_start: 0.9375 (mm) cc_final: 0.9081 (mm) REVERT: A 341 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8488 (tpp) REVERT: A 374 GLU cc_start: 0.8770 (tp30) cc_final: 0.8438 (tp30) REVERT: A 415 GLU cc_start: 0.8981 (pm20) cc_final: 0.8730 (pm20) REVERT: B 113 ASN cc_start: 0.9040 (t0) cc_final: 0.8259 (t0) REVERT: B 117 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8098 (mpp) REVERT: B 154 GLN cc_start: 0.9654 (mt0) cc_final: 0.9448 (mt0) REVERT: B 160 TYR cc_start: 0.9290 (t80) cc_final: 0.9064 (t80) REVERT: B 171 GLN cc_start: 0.9033 (mm110) cc_final: 0.8612 (mm-40) REVERT: B 181 TYR cc_start: 0.8548 (m-80) cc_final: 0.8180 (m-80) REVERT: B 191 GLN cc_start: 0.9091 (pp30) cc_final: 0.8844 (pp30) REVERT: B 254 GLU cc_start: 0.8870 (mm-30) cc_final: 0.7778 (mm-30) REVERT: B 262 GLU cc_start: 0.8538 (tt0) cc_final: 0.8060 (tp30) REVERT: B 284 ASN cc_start: 0.7480 (m110) cc_final: 0.7055 (m110) REVERT: B 314 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8431 (m-80) REVERT: B 322 LEU cc_start: 0.9427 (mm) cc_final: 0.9064 (mm) REVERT: B 393 MET cc_start: 0.9283 (ttm) cc_final: 0.9053 (ttm) outliers start: 76 outliers final: 46 residues processed: 277 average time/residue: 0.1764 time to fit residues: 68.2607 Evaluate side-chains 288 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 237 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 341 MET 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 440 LEU 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 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 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 411 PHE Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 432 LEU 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 54 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 81 optimal weight: 0.0670 chunk 43 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.106865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085840 restraints weight = 15635.983| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 4.61 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6484 Z= 0.162 Angle : 0.778 13.376 8852 Z= 0.370 Chirality : 0.043 0.207 1096 Planarity : 0.004 0.040 1080 Dihedral : 9.076 58.890 932 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 10.90 % Allowed : 30.75 % Favored : 58.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.30), residues: 812 helix: 0.67 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -1.81 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 324 HIS 0.005 0.001 HIS A 449 PHE 0.010 0.001 PHE B 389 TYR 0.026 0.003 TYR A 211 ARG 0.002 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.05278 ( 447) hydrogen bonds : angle 4.82571 ( 1311) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.90116 ( 4) covalent geometry : bond 0.00354 ( 6482) covalent geometry : angle 0.77815 ( 8848) *********************** 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 320 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 247 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASN cc_start: 0.9427 (t0) cc_final: 0.8532 (t0) REVERT: A 117 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.8108 (mpp) REVERT: A 160 TYR cc_start: 0.9331 (t80) cc_final: 0.9088 (t80) REVERT: A 181 TYR cc_start: 0.8640 (m-80) cc_final: 0.8279 (m-80) REVERT: A 184 HIS cc_start: 0.8972 (t70) cc_final: 0.8761 (t-90) REVERT: A 188 ILE cc_start: 0.9331 (tp) cc_final: 0.9012 (tp) REVERT: A 191 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8694 (pp30) REVERT: A 254 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8544 (tm-30) REVERT: A 284 ASN cc_start: 0.7429 (m110) cc_final: 0.7035 (m110) REVERT: A 322 LEU cc_start: 0.9349 (mm) cc_final: 0.9007 (mm) REVERT: A 336 LYS cc_start: 0.8917 (ttpp) cc_final: 0.8629 (mtpp) REVERT: A 374 GLU cc_start: 0.8753 (tp30) cc_final: 0.8470 (tp30) REVERT: A 403 GLU cc_start: 0.8460 (mp0) cc_final: 0.8248 (mp0) REVERT: A 415 GLU cc_start: 0.8966 (pm20) cc_final: 0.8735 (pm20) REVERT: B 113 ASN cc_start: 0.8983 (t0) cc_final: 0.8319 (t0) REVERT: B 117 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.7855 (mpp) REVERT: B 160 TYR cc_start: 0.9304 (t80) cc_final: 0.9065 (t80) REVERT: B 171 GLN cc_start: 0.9056 (mm110) cc_final: 0.8656 (mm110) REVERT: B 181 TYR cc_start: 0.8635 (m-80) cc_final: 0.8284 (m-80) REVERT: B 254 GLU cc_start: 0.8869 (mm-30) cc_final: 0.7806 (mm-30) REVERT: B 262 GLU cc_start: 0.8563 (tt0) cc_final: 0.7871 (tm-30) REVERT: B 284 ASN cc_start: 0.7069 (m110) cc_final: 0.6529 (m110) REVERT: B 314 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8541 (m-80) REVERT: B 322 LEU cc_start: 0.9378 (mm) cc_final: 0.9015 (mm) REVERT: B 336 LYS cc_start: 0.8897 (ttpp) cc_final: 0.8624 (mtpp) REVERT: B 403 GLU cc_start: 0.8418 (mp0) cc_final: 0.8201 (mp0) outliers start: 73 outliers final: 48 residues processed: 270 average time/residue: 0.1577 time to fit residues: 58.6961 Evaluate side-chains 291 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 239 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 140 ILE Chi-restraints excluded: chain A residue 146 CYS 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 215 VAL 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 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 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 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 362 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 70 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.108667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087213 restraints weight = 15481.623| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 4.68 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6484 Z= 0.162 Angle : 0.773 12.481 8852 Z= 0.368 Chirality : 0.044 0.225 1096 Planarity : 0.004 0.038 1080 Dihedral : 8.733 55.469 927 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 11.19 % Allowed : 31.34 % Favored : 57.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.30), residues: 812 helix: 0.72 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.55 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 324 HIS 0.005 0.001 HIS A 449 PHE 0.009 0.001 PHE B 389 TYR 0.017 0.002 TYR B 313 ARG 0.002 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.05179 ( 447) hydrogen bonds : angle 4.74842 ( 1311) SS BOND : bond 0.00147 ( 2) SS BOND : angle 1.17809 ( 4) covalent geometry : bond 0.00362 ( 6482) covalent geometry : angle 0.77285 ( 8848) *********************** 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 327 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 252 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASN cc_start: 0.9413 (t0) cc_final: 0.8544 (t0) REVERT: A 117 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.8210 (mpp) REVERT: A 160 TYR cc_start: 0.9321 (t80) cc_final: 0.9076 (t80) REVERT: A 181 TYR cc_start: 0.8678 (m-80) cc_final: 0.8414 (m-80) REVERT: A 188 ILE cc_start: 0.9223 (tp) cc_final: 0.8930 (tp) REVERT: A 206 PHE cc_start: 0.6216 (OUTLIER) cc_final: 0.5999 (m-10) REVERT: A 208 PRO cc_start: 0.7388 (Cg_endo) cc_final: 0.7109 (Cg_exo) REVERT: A 254 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8423 (tm-30) REVERT: A 259 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8686 (mp0) REVERT: A 284 ASN cc_start: 0.7382 (m110) cc_final: 0.6942 (m110) REVERT: A 322 LEU cc_start: 0.9340 (mm) cc_final: 0.9027 (mm) REVERT: A 336 LYS cc_start: 0.8865 (ttpp) cc_final: 0.8632 (mtpp) REVERT: A 341 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8495 (tpp) REVERT: A 374 GLU cc_start: 0.8670 (tp30) cc_final: 0.8387 (tp30) REVERT: A 403 GLU cc_start: 0.8468 (mp0) cc_final: 0.8258 (mp0) REVERT: A 415 GLU cc_start: 0.8970 (pm20) cc_final: 0.8743 (pm20) REVERT: B 59 GLU cc_start: 0.8896 (mp0) cc_final: 0.8488 (tm-30) REVERT: B 113 ASN cc_start: 0.9043 (t0) cc_final: 0.8323 (t0) REVERT: B 117 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.7873 (mpp) REVERT: B 160 TYR cc_start: 0.9306 (t80) cc_final: 0.9090 (t80) REVERT: B 181 TYR cc_start: 0.8653 (m-80) cc_final: 0.8391 (m-80) REVERT: B 184 HIS cc_start: 0.8830 (t70) cc_final: 0.8608 (t-90) REVERT: B 254 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8469 (tm-30) REVERT: B 259 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8630 (mp0) REVERT: B 262 GLU cc_start: 0.8519 (tt0) cc_final: 0.7748 (tm-30) REVERT: B 284 ASN cc_start: 0.7143 (m110) cc_final: 0.6682 (m110) REVERT: B 314 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8708 (m-80) REVERT: B 336 LYS cc_start: 0.8872 (ttpp) cc_final: 0.8625 (mtpp) REVERT: B 359 TYR cc_start: 0.8938 (m-80) cc_final: 0.8670 (m-10) REVERT: B 374 GLU cc_start: 0.8646 (tt0) cc_final: 0.7975 (tp30) REVERT: B 403 GLU cc_start: 0.8439 (mp0) cc_final: 0.8237 (mp0) outliers start: 75 outliers final: 50 residues processed: 278 average time/residue: 0.1399 time to fit residues: 54.0901 Evaluate side-chains 297 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 240 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU 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 140 ILE Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 206 PHE 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 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 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 43 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 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 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 25 optimal weight: 8.9990 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.108545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.086961 restraints weight = 15389.668| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 4.67 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6484 Z= 0.164 Angle : 0.788 12.451 8852 Z= 0.376 Chirality : 0.044 0.232 1096 Planarity : 0.005 0.046 1080 Dihedral : 8.297 58.779 922 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 9.85 % Allowed : 33.13 % Favored : 57.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.30), residues: 812 helix: 0.68 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.44 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.005 0.001 HIS A 449 PHE 0.009 0.001 PHE A 443 TYR 0.017 0.002 TYR B 313 ARG 0.010 0.000 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.05207 ( 447) hydrogen bonds : angle 4.77791 ( 1311) SS BOND : bond 0.00173 ( 2) SS BOND : angle 1.31281 ( 4) covalent geometry : bond 0.00368 ( 6482) covalent geometry : angle 0.78782 ( 8848) *********************** 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 312 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 246 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8783 (mp0) cc_final: 0.8385 (tm-30) REVERT: A 83 MET cc_start: 0.8701 (mtm) cc_final: 0.8176 (mtm) REVERT: A 113 ASN cc_start: 0.9445 (t0) cc_final: 0.8556 (t0) REVERT: A 117 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.8216 (mpp) REVERT: A 130 MET cc_start: 0.9308 (tmm) cc_final: 0.8799 (tmm) REVERT: A 160 TYR cc_start: 0.9322 (t80) cc_final: 0.9107 (t80) REVERT: A 181 TYR cc_start: 0.8700 (m-80) cc_final: 0.8332 (m-80) REVERT: A 184 HIS cc_start: 0.8958 (t70) cc_final: 0.8663 (t-90) REVERT: A 188 ILE cc_start: 0.9200 (tp) cc_final: 0.8941 (tp) REVERT: A 208 PRO cc_start: 0.7484 (Cg_endo) cc_final: 0.7222 (Cg_exo) REVERT: A 254 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8373 (tm-30) REVERT: A 259 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8665 (mp0) REVERT: A 284 ASN cc_start: 0.7424 (m110) cc_final: 0.6977 (m110) REVERT: A 322 LEU cc_start: 0.9325 (mm) cc_final: 0.8995 (mm) REVERT: A 336 LYS cc_start: 0.8859 (ttpp) cc_final: 0.8606 (mtpp) REVERT: A 341 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8579 (tpp) REVERT: A 374 GLU cc_start: 0.8654 (tp30) cc_final: 0.8370 (tp30) REVERT: A 393 MET cc_start: 0.8778 (tpp) cc_final: 0.8385 (tpp) REVERT: A 415 GLU cc_start: 0.8948 (pm20) cc_final: 0.8733 (pm20) REVERT: B 59 GLU cc_start: 0.8865 (mp0) cc_final: 0.8521 (tm-30) REVERT: B 83 MET cc_start: 0.8739 (mtm) cc_final: 0.8142 (mtm) REVERT: B 113 ASN cc_start: 0.9062 (t0) cc_final: 0.8377 (t0) REVERT: B 117 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.7958 (mpp) REVERT: B 160 TYR cc_start: 0.9308 (t80) cc_final: 0.9061 (t80) REVERT: B 171 GLN cc_start: 0.9046 (mm110) cc_final: 0.8747 (mm-40) REVERT: B 181 TYR cc_start: 0.8693 (m-80) cc_final: 0.8355 (m-80) REVERT: B 184 HIS cc_start: 0.8922 (t70) cc_final: 0.8628 (t-90) REVERT: B 254 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8471 (tm-30) REVERT: B 259 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8662 (mp0) REVERT: B 262 GLU cc_start: 0.8542 (tt0) cc_final: 0.7779 (tm-30) REVERT: B 284 ASN cc_start: 0.7060 (m110) cc_final: 0.6606 (m110) REVERT: B 314 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8752 (m-80) REVERT: B 336 LYS cc_start: 0.8878 (ttpp) cc_final: 0.8642 (mtpp) REVERT: B 393 MET cc_start: 0.9232 (ttm) cc_final: 0.9023 (tpp) outliers start: 66 outliers final: 51 residues processed: 268 average time/residue: 0.2063 time to fit residues: 76.3135 Evaluate side-chains 289 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU 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 140 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 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 316 SER 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 440 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 43 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 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 362 THR Chi-restraints excluded: chain B residue 390 GLN 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 453 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 60 optimal weight: 0.0870 chunk 8 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.110521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.088843 restraints weight = 15415.770| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 4.76 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6484 Z= 0.163 Angle : 0.798 11.978 8852 Z= 0.379 Chirality : 0.044 0.248 1096 Planarity : 0.004 0.034 1080 Dihedral : 8.093 59.145 922 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 9.70 % Allowed : 34.63 % Favored : 55.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.30), residues: 812 helix: 0.65 (0.20), residues: 628 sheet: None (None), residues: 0 loop : -1.37 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 324 HIS 0.005 0.001 HIS A 184 PHE 0.009 0.001 PHE B 351 TYR 0.017 0.002 TYR B 313 ARG 0.006 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.05127 ( 447) hydrogen bonds : angle 4.73961 ( 1311) SS BOND : bond 0.00245 ( 2) SS BOND : angle 1.48295 ( 4) covalent geometry : bond 0.00361 ( 6482) covalent geometry : angle 0.79741 ( 8848) *********************** 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 318 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 253 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8737 (mp0) cc_final: 0.8368 (tm-30) REVERT: A 83 MET cc_start: 0.8662 (mtm) cc_final: 0.8168 (mtm) REVERT: A 113 ASN cc_start: 0.9453 (t0) cc_final: 0.8582 (t0) REVERT: A 117 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.8207 (mpp) REVERT: A 181 TYR cc_start: 0.8639 (m-80) cc_final: 0.8273 (m-80) REVERT: A 184 HIS cc_start: 0.8969 (t70) cc_final: 0.8623 (t-90) REVERT: A 188 ILE cc_start: 0.9174 (tp) cc_final: 0.8923 (tp) REVERT: A 206 PHE cc_start: 0.6191 (OUTLIER) cc_final: 0.5910 (m-10) REVERT: A 208 PRO cc_start: 0.7377 (Cg_endo) cc_final: 0.7149 (Cg_exo) REVERT: A 254 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8368 (tm-30) REVERT: A 259 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8596 (mp0) REVERT: A 262 GLU cc_start: 0.8273 (tt0) cc_final: 0.7409 (tm-30) REVERT: A 284 ASN cc_start: 0.7433 (m110) cc_final: 0.7009 (m110) REVERT: A 322 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9068 (mm) REVERT: A 336 LYS cc_start: 0.8876 (ttpp) cc_final: 0.8616 (mtpp) REVERT: A 341 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8457 (tpp) REVERT: A 374 GLU cc_start: 0.8594 (tp30) cc_final: 0.8303 (tp30) REVERT: B 59 GLU cc_start: 0.8809 (mp0) cc_final: 0.8410 (tm-30) REVERT: B 83 MET cc_start: 0.8743 (mtm) cc_final: 0.8216 (mtm) REVERT: B 113 ASN cc_start: 0.9094 (t0) cc_final: 0.8463 (t0) REVERT: B 117 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.7954 (mpp) REVERT: B 160 TYR cc_start: 0.9306 (t80) cc_final: 0.9070 (t80) REVERT: B 181 TYR cc_start: 0.8639 (m-80) cc_final: 0.8317 (m-80) REVERT: B 254 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8396 (tm-30) REVERT: B 259 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8546 (mp0) REVERT: B 262 GLU cc_start: 0.8410 (tt0) cc_final: 0.7920 (tm-30) REVERT: B 284 ASN cc_start: 0.6956 (m110) cc_final: 0.6547 (m110) REVERT: B 314 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8823 (m-80) REVERT: B 336 LYS cc_start: 0.8856 (ttpp) cc_final: 0.8625 (mtpp) REVERT: B 374 GLU cc_start: 0.8545 (tt0) cc_final: 0.7834 (tp30) outliers start: 65 outliers final: 44 residues processed: 276 average time/residue: 0.1319 time to fit residues: 51.3499 Evaluate side-chains 285 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 233 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU 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 206 PHE 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 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 440 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 43 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 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 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 453 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN B 184 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.108703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.086031 restraints weight = 15435.907| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 4.74 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4206 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 : 0.831 11.756 8852 Z= 0.400 Chirality : 0.046 0.264 1096 Planarity : 0.004 0.035 1080 Dihedral : 7.824 59.063 918 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 9.85 % Allowed : 35.82 % Favored : 54.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.30), residues: 812 helix: 0.68 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.30 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 324 HIS 0.005 0.001 HIS A 449 PHE 0.009 0.001 PHE B 351 TYR 0.020 0.002 TYR A 160 ARG 0.004 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.05216 ( 447) hydrogen bonds : angle 4.75813 ( 1311) SS BOND : bond 0.00203 ( 2) SS BOND : angle 1.49464 ( 4) covalent geometry : bond 0.00413 ( 6482) covalent geometry : angle 0.83044 ( 8848) *********************** 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 311 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 245 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8737 (mp0) cc_final: 0.8314 (tm-30) REVERT: A 113 ASN cc_start: 0.9436 (t0) cc_final: 0.8574 (t0) REVERT: A 117 MET cc_start: 0.9368 (OUTLIER) cc_final: 0.8110 (mpp) REVERT: A 130 MET cc_start: 0.9290 (tmm) cc_final: 0.8793 (tmm) REVERT: A 181 TYR cc_start: 0.8657 (m-80) cc_final: 0.8291 (m-80) REVERT: A 184 HIS cc_start: 0.9020 (t70) cc_final: 0.8655 (t-90) REVERT: A 188 ILE cc_start: 0.9152 (tp) cc_final: 0.8893 (tp) REVERT: A 208 PRO cc_start: 0.7439 (Cg_endo) cc_final: 0.7170 (Cg_exo) REVERT: A 254 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8321 (tm-30) REVERT: A 259 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8567 (mp0) REVERT: A 284 ASN cc_start: 0.7444 (m110) cc_final: 0.6998 (m110) REVERT: A 322 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9058 (mm) REVERT: A 336 LYS cc_start: 0.8891 (ttpp) cc_final: 0.8619 (mtpp) REVERT: A 341 MET cc_start: 0.9044 (tpp) cc_final: 0.8534 (tpp) REVERT: A 374 GLU cc_start: 0.8615 (tp30) cc_final: 0.8330 (tp30) REVERT: B 37 LEU cc_start: 0.8433 (mt) cc_final: 0.8221 (mt) REVERT: B 59 GLU cc_start: 0.8887 (mp0) cc_final: 0.8480 (tm-30) REVERT: B 83 MET cc_start: 0.8748 (mtm) cc_final: 0.8293 (mtm) REVERT: B 113 ASN cc_start: 0.9097 (t0) cc_final: 0.8412 (t0) REVERT: B 117 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.7964 (mpp) REVERT: B 154 GLN cc_start: 0.9639 (mt0) cc_final: 0.9431 (mt0) REVERT: B 181 TYR cc_start: 0.8695 (m-80) cc_final: 0.8374 (m-80) REVERT: B 254 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8386 (tm-30) REVERT: B 259 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: B 262 GLU cc_start: 0.8399 (tt0) cc_final: 0.7984 (tm-30) REVERT: B 284 ASN cc_start: 0.7005 (m110) cc_final: 0.6569 (m110) REVERT: B 336 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8634 (mtpp) REVERT: B 341 MET cc_start: 0.8846 (tpp) cc_final: 0.8443 (tpp) outliers start: 66 outliers final: 50 residues processed: 268 average time/residue: 0.1812 time to fit residues: 67.0932 Evaluate side-chains 283 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 228 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU 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 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 258 LYS 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 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 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 43 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 111 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 258 LYS 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 362 THR 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 25 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 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 = 0.3649 r_free = 0.3649 target = 0.109417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.086598 restraints weight = 15338.446| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 4.80 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6484 Z= 0.171 Angle : 0.858 16.097 8852 Z= 0.401 Chirality : 0.045 0.193 1096 Planarity : 0.004 0.034 1080 Dihedral : 7.707 57.598 918 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 9.10 % Allowed : 36.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.30), residues: 812 helix: 0.69 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.26 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 324 HIS 0.005 0.001 HIS A 449 PHE 0.009 0.001 PHE B 351 TYR 0.016 0.002 TYR B 125 ARG 0.008 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.05178 ( 447) hydrogen bonds : angle 4.78387 ( 1311) SS BOND : bond 0.00210 ( 2) SS BOND : angle 2.23366 ( 4) covalent geometry : bond 0.00389 ( 6482) covalent geometry : angle 0.85697 ( 8848) *********************** 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 304 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 243 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9072 (pp30) cc_final: 0.8808 (pp30) REVERT: A 59 GLU cc_start: 0.8737 (mp0) cc_final: 0.8411 (tm-30) REVERT: A 113 ASN cc_start: 0.9380 (t0) cc_final: 0.8528 (t0) REVERT: A 117 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.8064 (mpp) REVERT: A 181 TYR cc_start: 0.8676 (m-80) cc_final: 0.8285 (m-80) REVERT: A 188 ILE cc_start: 0.9122 (tp) cc_final: 0.8889 (tp) REVERT: A 208 PRO cc_start: 0.7504 (Cg_endo) cc_final: 0.7231 (Cg_exo) REVERT: A 254 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8271 (tm-30) REVERT: A 259 GLU cc_start: 0.9012 (pt0) cc_final: 0.8531 (mp0) REVERT: A 284 ASN cc_start: 0.7365 (m110) cc_final: 0.6937 (m110) REVERT: A 322 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9050 (mm) REVERT: A 336 LYS cc_start: 0.8862 (ttpp) cc_final: 0.8583 (mtpp) REVERT: A 341 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8461 (tpp) REVERT: A 374 GLU cc_start: 0.8634 (tp30) cc_final: 0.8371 (tp30) REVERT: B 59 GLU cc_start: 0.8892 (mp0) cc_final: 0.8490 (tm-30) REVERT: B 83 MET cc_start: 0.8780 (mtm) cc_final: 0.8348 (mtm) REVERT: B 113 ASN cc_start: 0.9076 (t0) cc_final: 0.8370 (t0) REVERT: B 117 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.7798 (mpp) REVERT: B 181 TYR cc_start: 0.8711 (m-80) cc_final: 0.8388 (m-80) REVERT: B 254 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8365 (tm-30) REVERT: B 259 GLU cc_start: 0.8957 (pt0) cc_final: 0.8506 (mp0) REVERT: B 262 GLU cc_start: 0.8433 (tt0) cc_final: 0.7973 (tm-30) REVERT: B 284 ASN cc_start: 0.6914 (m110) cc_final: 0.6487 (m110) REVERT: B 336 LYS cc_start: 0.8848 (ttpp) cc_final: 0.8558 (mtpp) REVERT: B 341 MET cc_start: 0.8833 (tpp) cc_final: 0.8436 (tpp) REVERT: B 374 GLU cc_start: 0.8436 (tt0) cc_final: 0.7670 (tp30) REVERT: B 415 GLU cc_start: 0.8810 (pm20) cc_final: 0.8418 (pm20) outliers start: 61 outliers final: 48 residues processed: 265 average time/residue: 0.2508 time to fit residues: 93.2586 Evaluate side-chains 291 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 239 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 112 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 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 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 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 43 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 111 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 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 362 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 0.0270 chunk 65 optimal weight: 3.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.111069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.088530 restraints weight = 15298.500| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 4.84 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6484 Z= 0.172 Angle : 0.885 15.951 8852 Z= 0.414 Chirality : 0.047 0.187 1096 Planarity : 0.004 0.034 1080 Dihedral : 7.385 53.596 910 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 7.91 % Allowed : 37.61 % Favored : 54.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.30), residues: 812 helix: 0.74 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.16 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 324 HIS 0.005 0.001 HIS A 449 PHE 0.011 0.001 PHE A 122 TYR 0.016 0.002 TYR B 313 ARG 0.007 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.05198 ( 447) hydrogen bonds : angle 4.79810 ( 1311) SS BOND : bond 0.00210 ( 2) SS BOND : angle 1.92115 ( 4) covalent geometry : bond 0.00381 ( 6482) covalent geometry : angle 0.88461 ( 8848) ********************** 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 297 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9057 (pp30) cc_final: 0.8746 (pp30) REVERT: A 181 TYR cc_start: 0.8666 (m-80) cc_final: 0.8331 (m-80) REVERT: A 184 HIS cc_start: 0.9026 (t70) cc_final: 0.8781 (t-90) REVERT: A 188 ILE cc_start: 0.9070 (tp) cc_final: 0.8831 (tp) REVERT: A 208 PRO cc_start: 0.7411 (Cg_endo) cc_final: 0.7136 (Cg_exo) REVERT: A 254 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8259 (tm-30) REVERT: A 259 GLU cc_start: 0.8957 (pt0) cc_final: 0.8515 (mp0) REVERT: A 284 ASN cc_start: 0.7306 (m110) cc_final: 0.6870 (m110) REVERT: A 322 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9069 (mm) REVERT: A 336 LYS cc_start: 0.8864 (ttpp) cc_final: 0.8573 (mtpp) REVERT: A 341 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8426 (tpp) REVERT: A 374 GLU cc_start: 0.8584 (tp30) cc_final: 0.8326 (tp30) REVERT: A 415 GLU cc_start: 0.8945 (pm20) cc_final: 0.8463 (pm20) REVERT: B 113 ASN cc_start: 0.9014 (t0) cc_final: 0.8551 (t0) REVERT: B 117 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8162 (mpp) REVERT: B 181 TYR cc_start: 0.8705 (m-80) cc_final: 0.8381 (m-80) REVERT: B 254 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8361 (tm-30) REVERT: B 259 GLU cc_start: 0.8916 (pt0) cc_final: 0.8489 (mp0) REVERT: B 262 GLU cc_start: 0.8423 (tt0) cc_final: 0.7926 (tm-30) REVERT: B 283 ASP cc_start: 0.8128 (t0) cc_final: 0.7877 (t0) REVERT: B 284 ASN cc_start: 0.6799 (m110) cc_final: 0.6430 (m110) REVERT: B 314 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8943 (m-80) REVERT: B 336 LYS cc_start: 0.8866 (ttpp) cc_final: 0.8584 (mtpp) REVERT: B 341 MET cc_start: 0.8824 (tpp) cc_final: 0.8420 (tpp) REVERT: B 374 GLU cc_start: 0.8345 (tt0) cc_final: 0.7520 (tp30) REVERT: B 415 GLU cc_start: 0.8853 (pm20) cc_final: 0.8469 (pm20) outliers start: 53 outliers final: 45 residues processed: 262 average time/residue: 0.2557 time to fit residues: 95.1550 Evaluate side-chains 290 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 112 LEU 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 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 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 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 52 ILE Chi-restraints excluded: chain B residue 111 LEU 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 362 THR 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 47 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 23 optimal weight: 0.0770 chunk 78 optimal weight: 10.0000 chunk 75 optimal weight: 0.0470 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.0370 chunk 24 optimal weight: 0.8980 overall best weight: 0.2114 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.115370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.091907 restraints weight = 15415.668| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 5.12 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6484 Z= 0.171 Angle : 0.893 15.455 8852 Z= 0.413 Chirality : 0.046 0.241 1096 Planarity : 0.004 0.036 1080 Dihedral : 7.078 59.657 906 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 7.46 % Allowed : 38.96 % Favored : 53.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.30), residues: 812 helix: 0.78 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -1.07 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 324 HIS 0.006 0.001 HIS A 449 PHE 0.009 0.001 PHE A 264 TYR 0.043 0.002 TYR A 211 ARG 0.007 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.04923 ( 447) hydrogen bonds : angle 4.72616 ( 1311) SS BOND : bond 0.00334 ( 2) SS BOND : angle 1.89746 ( 4) covalent geometry : bond 0.00362 ( 6482) covalent geometry : angle 0.89196 ( 8848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3186.13 seconds wall clock time: 59 minutes 47.46 seconds (3587.46 seconds total)