Starting phenix.real_space_refine on Tue Feb 11 16:40:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w8o_21576/02_2025/6w8o_21576.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w8o_21576/02_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_21576/02_2025/6w8o_21576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w8o_21576/02_2025/6w8o_21576.map" model { file = "/net/cci-nas-00/data/ceres_data/6w8o_21576/02_2025/6w8o_21576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w8o_21576/02_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-5592/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: 4.40, per 1000 atoms: 0.69 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: 1.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.62 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: 1.79 Time building geometry restraints manager: 2.03 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: 1.120 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.690 Find NCS groups from input model: 0.380 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: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.210 ------------------------------------------------------------------------------- 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 6482 Z= 1.217 Angle : 1.198 50.741 8848 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 *********************** 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 : 0.740 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: 0.1746 time to fit residues: 65.8313 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 : 0.702 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS 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 = 0.3563 r_free = 0.3563 target = 0.103380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.082179 restraints weight = 15546.117| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 4.53 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6482 Z= 0.246 Angle : 0.820 15.048 8848 Z= 0.392 Chirality : 0.044 0.212 1096 Planarity : 0.005 0.044 1080 Dihedral : 11.243 87.186 971 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.79 % Favored : 93.84 % Rotamer: Outliers : 10.45 % Allowed : 27.46 % Favored : 62.09 % 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: -1.05 (0.29), residues: 812 helix: -0.20 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -2.17 (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 A 166 PHE 0.012 0.001 PHE B 122 TYR 0.020 0.002 TYR B 160 ARG 0.005 0.000 ARG B 35 *********************** 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 330 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 260 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASN cc_start: 0.9510 (t0) cc_final: 0.8676 (t0) REVERT: A 117 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.8198 (mpp) REVERT: A 160 TYR cc_start: 0.9316 (t80) cc_final: 0.9022 (t80) REVERT: A 171 GLN cc_start: 0.9158 (mm110) cc_final: 0.8734 (mm110) REVERT: A 191 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8834 (pp30) REVERT: A 206 PHE cc_start: 0.6265 (OUTLIER) cc_final: 0.5850 (m-10) REVERT: A 254 GLU cc_start: 0.8869 (mm-30) cc_final: 0.7761 (mm-30) REVERT: A 284 ASN cc_start: 0.7863 (m110) cc_final: 0.7460 (m110) REVERT: A 322 LEU cc_start: 0.9398 (mm) cc_final: 0.9041 (mm) REVERT: A 374 GLU cc_start: 0.8776 (tp30) cc_final: 0.8478 (tp30) REVERT: A 393 MET cc_start: 0.9153 (mtm) cc_final: 0.8952 (ttm) REVERT: A 460 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7840 (mm) REVERT: B 106 ASP cc_start: 0.8899 (t0) cc_final: 0.8681 (t70) REVERT: B 160 TYR cc_start: 0.9294 (t80) cc_final: 0.9077 (t80) REVERT: B 191 GLN cc_start: 0.9096 (pp30) cc_final: 0.8847 (pp30) REVERT: B 254 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8639 (tm-30) REVERT: B 262 GLU cc_start: 0.8590 (tt0) cc_final: 0.8159 (tp30) REVERT: B 284 ASN cc_start: 0.7598 (m110) cc_final: 0.7178 (m110) REVERT: B 322 LEU cc_start: 0.9439 (mm) cc_final: 0.9080 (mm) REVERT: B 374 GLU cc_start: 0.8732 (tt0) cc_final: 0.7991 (tp30) outliers start: 70 outliers final: 48 residues processed: 284 average time/residue: 0.1450 time to fit residues: 56.9054 Evaluate side-chains 275 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 223 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 65 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.104167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.082751 restraints weight = 15870.831| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 4.58 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6482 Z= 0.250 Angle : 0.805 13.939 8848 Z= 0.386 Chirality : 0.044 0.207 1096 Planarity : 0.004 0.041 1080 Dihedral : 9.796 59.931 942 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 11.94 % Allowed : 27.76 % Favored : 60.30 % 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: 0.31 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.72 (0.54), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 324 HIS 0.013 0.002 HIS B 166 PHE 0.010 0.001 PHE A 351 TYR 0.023 0.003 TYR A 313 ARG 0.002 0.000 ARG B 335 *********************** 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 331 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 251 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASN cc_start: 0.9485 (t0) cc_final: 0.8586 (t0) REVERT: A 117 MET cc_start: 0.9406 (OUTLIER) cc_final: 0.8138 (mpp) REVERT: A 130 MET cc_start: 0.9374 (tmm) cc_final: 0.8780 (tmm) REVERT: A 160 TYR cc_start: 0.9328 (t80) cc_final: 0.9054 (t80) REVERT: A 171 GLN cc_start: 0.9040 (mm110) cc_final: 0.8675 (mm110) REVERT: A 181 TYR cc_start: 0.8621 (m-80) cc_final: 0.8263 (m-80) REVERT: A 191 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8822 (pp30) REVERT: A 254 GLU cc_start: 0.8900 (mm-30) cc_final: 0.7772 (mm-30) REVERT: A 262 GLU cc_start: 0.8478 (tt0) cc_final: 0.7783 (tp30) REVERT: A 284 ASN cc_start: 0.7632 (m110) cc_final: 0.7270 (m110) REVERT: A 322 LEU cc_start: 0.9362 (mm) cc_final: 0.9059 (mm) REVERT: A 374 GLU cc_start: 0.8774 (tp30) cc_final: 0.8453 (tp30) REVERT: A 415 GLU cc_start: 0.8979 (pm20) cc_final: 0.8715 (pm20) REVERT: A 460 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7898 (mm) REVERT: B 113 ASN cc_start: 0.9091 (t0) cc_final: 0.8288 (t0) REVERT: B 117 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.8100 (mpp) REVERT: B 154 GLN cc_start: 0.9661 (mt0) cc_final: 0.9450 (mt0) REVERT: B 160 TYR cc_start: 0.9301 (t80) cc_final: 0.9055 (t80) REVERT: B 171 GLN cc_start: 0.9040 (mm110) cc_final: 0.8622 (mm-40) REVERT: B 181 TYR cc_start: 0.8558 (m-80) cc_final: 0.8227 (m-80) REVERT: B 191 GLN cc_start: 0.9108 (pp30) cc_final: 0.8869 (pp30) REVERT: B 254 GLU cc_start: 0.8888 (mm-30) cc_final: 0.7793 (mm-30) REVERT: B 260 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8374 (mmm-85) REVERT: B 262 GLU cc_start: 0.8575 (tt0) cc_final: 0.8116 (tp30) REVERT: B 284 ASN cc_start: 0.7512 (m110) cc_final: 0.7095 (m110) REVERT: B 314 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8460 (m-80) REVERT: B 322 LEU cc_start: 0.9434 (mm) cc_final: 0.9075 (mm) REVERT: B 393 MET cc_start: 0.9283 (ttm) cc_final: 0.9065 (ttm) outliers start: 80 outliers final: 51 residues processed: 277 average time/residue: 0.1419 time to fit residues: 54.3026 Evaluate side-chains 294 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 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 280 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 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 201 ILE Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 411 PHE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 54 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.106782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.085608 restraints weight = 15591.949| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 4.67 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6482 Z= 0.221 Angle : 0.775 13.389 8848 Z= 0.368 Chirality : 0.043 0.217 1096 Planarity : 0.004 0.039 1080 Dihedral : 9.358 59.392 937 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 11.19 % Allowed : 30.60 % Favored : 58.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.09 (0.30), residues: 812 helix: 0.66 (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 0.011 0.001 PHE B 389 TYR 0.022 0.003 TYR A 313 ARG 0.002 0.000 ARG A 335 *********************** 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 326 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 251 time to evaluate : 0.677 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: 0.8535 (t0) REVERT: A 117 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8087 (mpp) REVERT: A 160 TYR cc_start: 0.9331 (t80) cc_final: 0.9099 (t80) REVERT: A 181 TYR cc_start: 0.8627 (m-80) cc_final: 0.8268 (m-80) REVERT: A 184 HIS cc_start: 0.8954 (t70) cc_final: 0.8753 (t-90) REVERT: A 188 ILE cc_start: 0.9315 (tp) cc_final: 0.8994 (tp) REVERT: A 191 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8704 (pp30) REVERT: A 254 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8552 (tm-30) REVERT: A 284 ASN cc_start: 0.7471 (m110) cc_final: 0.7079 (m110) REVERT: A 322 LEU cc_start: 0.9331 (mm) cc_final: 0.8999 (mm) REVERT: A 336 LYS cc_start: 0.8913 (ttpp) cc_final: 0.8620 (mtpp) REVERT: A 374 GLU cc_start: 0.8745 (tp30) cc_final: 0.8455 (tp30) REVERT: A 403 GLU cc_start: 0.8493 (mp0) cc_final: 0.8289 (mp0) REVERT: A 415 GLU cc_start: 0.8923 (pm20) cc_final: 0.8700 (pm20) REVERT: B 59 GLU cc_start: 0.8867 (mp0) cc_final: 0.8575 (tm-30) REVERT: B 113 ASN cc_start: 0.8976 (t0) cc_final: 0.8243 (t0) REVERT: B 117 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.7824 (mpp) REVERT: B 160 TYR cc_start: 0.9311 (t80) cc_final: 0.9072 (t80) REVERT: B 171 GLN cc_start: 0.8994 (mm110) cc_final: 0.8596 (mm110) REVERT: B 181 TYR cc_start: 0.8606 (m-80) cc_final: 0.8254 (m-80) REVERT: B 188 ILE cc_start: 0.9280 (tp) cc_final: 0.9079 (tp) REVERT: B 254 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8573 (tm-30) REVERT: B 262 GLU cc_start: 0.8556 (tt0) cc_final: 0.7871 (tm-30) REVERT: B 284 ASN cc_start: 0.7081 (m110) cc_final: 0.6526 (m110) REVERT: B 314 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8536 (m-80) REVERT: B 322 LEU cc_start: 0.9373 (mm) cc_final: 0.9002 (mm) REVERT: B 336 LYS cc_start: 0.8911 (ttpp) cc_final: 0.8616 (mtpp) REVERT: B 393 MET cc_start: 0.9230 (ttm) cc_final: 0.9030 (ttm) REVERT: B 403 GLU cc_start: 0.8405 (mp0) cc_final: 0.8190 (mp0) outliers start: 75 outliers final: 46 residues processed: 279 average time/residue: 0.1507 time to fit residues: 58.4218 Evaluate side-chains 289 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 239 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 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 395 THR 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 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 411 PHE 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: 3.9990 chunk 2 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.108234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.086561 restraints weight = 15502.336| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 4.66 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6482 Z= 0.219 Angle : 0.767 12.163 8848 Z= 0.366 Chirality : 0.044 0.221 1096 Planarity : 0.004 0.043 1080 Dihedral : 8.703 55.486 927 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 10.90 % Allowed : 31.79 % Favored : 57.31 % 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: 0.75 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -1.55 (0.49), residues: 186 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 A 351 TYR 0.017 0.002 TYR A 125 ARG 0.009 0.000 ARG A 260 *********************** 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 321 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 248 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8768 (mtm) cc_final: 0.8189 (mtm) REVERT: A 113 ASN cc_start: 0.9437 (t0) cc_final: 0.8533 (t0) REVERT: A 117 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.8219 (mpp) REVERT: A 160 TYR cc_start: 0.9328 (t80) cc_final: 0.9123 (t80) REVERT: A 181 TYR cc_start: 0.8645 (m-80) cc_final: 0.8322 (m-80) REVERT: A 184 HIS cc_start: 0.8938 (t70) cc_final: 0.8643 (t-90) REVERT: A 188 ILE cc_start: 0.9234 (tp) cc_final: 0.8939 (tp) REVERT: A 208 PRO cc_start: 0.7396 (Cg_endo) cc_final: 0.7151 (Cg_exo) REVERT: A 254 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8457 (tm-30) REVERT: A 259 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8676 (mp0) REVERT: A 262 GLU cc_start: 0.8379 (tt0) cc_final: 0.7496 (tm-30) REVERT: A 284 ASN cc_start: 0.7421 (m110) cc_final: 0.6973 (m110) REVERT: A 322 LEU cc_start: 0.9330 (mm) cc_final: 0.9012 (mm) REVERT: A 336 LYS cc_start: 0.8900 (ttpp) cc_final: 0.8654 (mtpp) REVERT: A 341 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8483 (tpp) REVERT: A 374 GLU cc_start: 0.8662 (tp30) cc_final: 0.8377 (tp30) REVERT: A 415 GLU cc_start: 0.8948 (pm20) cc_final: 0.8707 (pm20) REVERT: B 59 GLU cc_start: 0.8861 (mp0) cc_final: 0.8526 (tm-30) REVERT: B 113 ASN cc_start: 0.9046 (t0) cc_final: 0.8298 (t0) REVERT: B 117 MET cc_start: 0.9332 (OUTLIER) cc_final: 0.7869 (mpp) REVERT: B 160 TYR cc_start: 0.9316 (t80) cc_final: 0.9099 (t80) REVERT: B 171 GLN cc_start: 0.9062 (mm110) cc_final: 0.8701 (mm-40) REVERT: B 181 TYR cc_start: 0.8635 (m-80) cc_final: 0.8335 (m-80) REVERT: B 184 HIS cc_start: 0.8858 (t70) cc_final: 0.8622 (t-90) REVERT: B 188 ILE cc_start: 0.9214 (tp) cc_final: 0.9011 (tp) REVERT: B 254 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8494 (tm-30) REVERT: B 259 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8644 (mp0) REVERT: B 262 GLU cc_start: 0.8523 (tt0) cc_final: 0.7766 (tm-30) REVERT: B 284 ASN cc_start: 0.7187 (m110) cc_final: 0.6742 (m110) REVERT: B 314 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8700 (m-80) REVERT: B 336 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8636 (mtpp) REVERT: B 374 GLU cc_start: 0.8664 (tt0) cc_final: 0.7976 (tp30) REVERT: B 393 MET cc_start: 0.9267 (ttm) cc_final: 0.9032 (ttm) REVERT: B 403 GLU cc_start: 0.8410 (mp0) cc_final: 0.8193 (mp0) outliers start: 73 outliers final: 48 residues processed: 275 average time/residue: 0.1383 time to fit residues: 52.5648 Evaluate side-chains 286 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 146 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 275 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 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 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: 9.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.107764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.085955 restraints weight = 15389.158| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 4.64 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6482 Z= 0.237 Angle : 0.781 12.770 8848 Z= 0.373 Chirality : 0.044 0.213 1096 Planarity : 0.004 0.035 1080 Dihedral : 8.306 58.561 920 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 10.45 % Allowed : 32.54 % 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: 0.33 (0.30), residues: 812 helix: 0.77 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -1.47 (0.48), residues: 186 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 0.007 0.000 ARG B 260 *********************** 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 314 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 244 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8782 (mp0) cc_final: 0.8392 (tm-30) REVERT: A 83 MET cc_start: 0.8754 (mtm) cc_final: 0.8222 (mtm) REVERT: A 113 ASN cc_start: 0.9458 (t0) cc_final: 0.8575 (t0) REVERT: A 117 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.8191 (mpp) REVERT: A 130 MET cc_start: 0.9301 (tmm) cc_final: 0.8813 (tmm) REVERT: A 160 TYR cc_start: 0.9336 (t80) cc_final: 0.9136 (t80) REVERT: A 181 TYR cc_start: 0.8615 (m-80) cc_final: 0.8360 (m-80) REVERT: A 208 PRO cc_start: 0.7569 (Cg_endo) cc_final: 0.7298 (Cg_exo) REVERT: A 254 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8407 (tm-30) REVERT: A 259 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8611 (mp0) REVERT: A 260 ARG cc_start: 0.8517 (mmm-85) cc_final: 0.8268 (mmm-85) REVERT: A 284 ASN cc_start: 0.7443 (m110) cc_final: 0.6992 (m110) REVERT: A 322 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9002 (mm) REVERT: A 336 LYS cc_start: 0.8890 (ttpp) cc_final: 0.8630 (mtpp) REVERT: A 341 MET cc_start: 0.9075 (tpp) cc_final: 0.8738 (tpp) REVERT: A 359 TYR cc_start: 0.9037 (m-80) cc_final: 0.8812 (m-80) REVERT: A 374 GLU cc_start: 0.8658 (tp30) cc_final: 0.8378 (tp30) REVERT: A 393 MET cc_start: 0.8777 (tpp) cc_final: 0.8442 (tpp) REVERT: A 415 GLU cc_start: 0.8947 (pm20) cc_final: 0.8740 (pm20) REVERT: B 59 GLU cc_start: 0.8834 (mp0) cc_final: 0.8502 (tm-30) REVERT: B 113 ASN cc_start: 0.9077 (t0) cc_final: 0.8354 (t0) REVERT: B 117 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.7947 (mpp) REVERT: B 181 TYR cc_start: 0.8667 (m-80) cc_final: 0.8422 (m-80) REVERT: B 184 HIS cc_start: 0.8898 (t70) cc_final: 0.8630 (t-90) REVERT: B 188 ILE cc_start: 0.9179 (tp) cc_final: 0.8971 (tp) REVERT: B 254 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8479 (tm-30) REVERT: B 259 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8666 (mp0) REVERT: B 262 GLU cc_start: 0.8413 (tt0) cc_final: 0.7695 (tm-30) REVERT: B 284 ASN cc_start: 0.7043 (m110) cc_final: 0.6595 (m110) REVERT: B 336 LYS cc_start: 0.8914 (ttpp) cc_final: 0.8657 (mtpp) REVERT: B 393 MET cc_start: 0.9192 (ttm) cc_final: 0.8992 (ttm) outliers start: 70 outliers final: 49 residues processed: 269 average time/residue: 0.1487 time to fit residues: 55.1703 Evaluate side-chains 290 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 236 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 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 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 VAL 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 50 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN B 416 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.107893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.086530 restraints weight = 15478.415| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 4.65 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6482 Z= 0.239 Angle : 0.806 11.264 8848 Z= 0.386 Chirality : 0.045 0.254 1096 Planarity : 0.004 0.034 1080 Dihedral : 8.066 57.931 918 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 10.00 % Allowed : 35.52 % 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: 0.28 (0.30), residues: 812 helix: 0.70 (0.20), residues: 628 sheet: None (None), residues: 0 loop : -1.39 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 324 HIS 0.006 0.001 HIS A 184 PHE 0.009 0.001 PHE A 351 TYR 0.022 0.002 TYR B 160 ARG 0.008 0.000 ARG B 260 *********************** 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 312 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 245 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8744 (mp0) cc_final: 0.8375 (tm-30) REVERT: A 83 MET cc_start: 0.8736 (mtm) cc_final: 0.8213 (mtm) REVERT: A 113 ASN cc_start: 0.9451 (t0) cc_final: 0.8565 (t0) REVERT: A 117 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.8201 (mpp) REVERT: A 181 TYR cc_start: 0.8664 (m-80) cc_final: 0.8296 (m-80) REVERT: A 184 HIS cc_start: 0.8948 (t70) cc_final: 0.8670 (t-90) REVERT: A 188 ILE cc_start: 0.9164 (tp) cc_final: 0.8910 (tp) REVERT: A 208 PRO cc_start: 0.7466 (Cg_endo) cc_final: 0.7199 (Cg_exo) REVERT: A 254 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8360 (tm-30) REVERT: A 259 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8597 (mp0) REVERT: A 284 ASN cc_start: 0.7457 (m110) cc_final: 0.7021 (m110) REVERT: A 322 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9062 (mm) REVERT: A 336 LYS cc_start: 0.8886 (ttpp) cc_final: 0.8616 (mtpp) REVERT: A 341 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8584 (tpp) REVERT: A 374 GLU cc_start: 0.8646 (tp30) cc_final: 0.8356 (tp30) REVERT: A 415 GLU cc_start: 0.8943 (pm20) cc_final: 0.8726 (pm20) REVERT: B 59 GLU cc_start: 0.8773 (mp0) cc_final: 0.8493 (tm-30) REVERT: B 83 MET cc_start: 0.8774 (mtm) cc_final: 0.8224 (mtm) REVERT: B 113 ASN cc_start: 0.9064 (t0) cc_final: 0.8322 (t0) REVERT: B 117 MET cc_start: 0.9318 (OUTLIER) cc_final: 0.7934 (mpp) REVERT: B 181 TYR cc_start: 0.8721 (m-80) cc_final: 0.8392 (m-80) REVERT: B 184 HIS cc_start: 0.8953 (t70) cc_final: 0.8595 (t-90) REVERT: B 188 ILE cc_start: 0.9138 (tp) cc_final: 0.8919 (tp) REVERT: B 254 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8452 (tm-30) REVERT: B 259 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8605 (mp0) REVERT: B 262 GLU cc_start: 0.8404 (tt0) cc_final: 0.7859 (tm-30) REVERT: B 284 ASN cc_start: 0.7015 (m110) cc_final: 0.6570 (m110) REVERT: B 336 LYS cc_start: 0.8911 (ttpp) cc_final: 0.8624 (mtpp) REVERT: B 374 GLU cc_start: 0.8619 (tt0) cc_final: 0.7898 (tp30) outliers start: 67 outliers final: 52 residues processed: 270 average time/residue: 0.1494 time to fit residues: 56.3842 Evaluate side-chains 290 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 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 316 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 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 50 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.108123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.086043 restraints weight = 15338.614| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 4.69 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6482 Z= 0.245 Angle : 0.820 10.853 8848 Z= 0.395 Chirality : 0.046 0.273 1096 Planarity : 0.004 0.034 1080 Dihedral : 8.000 59.109 918 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 10.00 % Allowed : 35.97 % Favored : 54.03 % 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: 0.22 (0.30), residues: 812 helix: 0.66 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.43 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 324 HIS 0.006 0.001 HIS A 184 PHE 0.009 0.001 PHE A 443 TYR 0.017 0.002 TYR B 125 ARG 0.007 0.000 ARG A 260 *********************** 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 315 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 248 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8733 (mp0) cc_final: 0.8332 (tm-30) REVERT: A 83 MET cc_start: 0.8762 (mtm) cc_final: 0.8301 (mtm) REVERT: A 113 ASN cc_start: 0.9463 (t0) cc_final: 0.8622 (t0) REVERT: A 117 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.8200 (mpp) REVERT: A 130 MET cc_start: 0.9276 (tmm) cc_final: 0.8867 (tmm) REVERT: A 181 TYR cc_start: 0.8679 (m-80) cc_final: 0.8297 (m-80) REVERT: A 184 HIS cc_start: 0.8987 (t70) cc_final: 0.8662 (t-90) REVERT: A 188 ILE cc_start: 0.9136 (tp) cc_final: 0.8885 (tp) REVERT: A 208 PRO cc_start: 0.7473 (Cg_endo) cc_final: 0.7177 (Cg_exo) REVERT: A 254 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8316 (tm-30) REVERT: A 259 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8607 (mp0) REVERT: A 284 ASN cc_start: 0.7480 (m110) cc_final: 0.7048 (m110) REVERT: A 322 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8972 (mm) REVERT: A 336 LYS cc_start: 0.8881 (ttpp) cc_final: 0.8607 (mtpp) REVERT: A 341 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8588 (tpp) REVERT: A 374 GLU cc_start: 0.8598 (tp30) cc_final: 0.8311 (tp30) REVERT: A 403 GLU cc_start: 0.8326 (mp0) cc_final: 0.8104 (mp0) REVERT: A 415 GLU cc_start: 0.8943 (pm20) cc_final: 0.8707 (pm20) REVERT: B 59 GLU cc_start: 0.8818 (mp0) cc_final: 0.8503 (tm-30) REVERT: B 83 MET cc_start: 0.8758 (mtm) cc_final: 0.8299 (mtm) REVERT: B 113 ASN cc_start: 0.9050 (t0) cc_final: 0.8282 (t0) REVERT: B 117 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.7898 (mpp) REVERT: B 154 GLN cc_start: 0.9642 (mt0) cc_final: 0.9433 (mt0) REVERT: B 181 TYR cc_start: 0.8733 (m-80) cc_final: 0.8386 (m-80) REVERT: B 184 HIS cc_start: 0.8989 (t70) cc_final: 0.8648 (t-90) REVERT: B 254 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8428 (tm-30) REVERT: B 259 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8581 (mp0) REVERT: B 262 GLU cc_start: 0.8427 (tt0) cc_final: 0.7983 (tm-30) REVERT: B 284 ASN cc_start: 0.7026 (m110) cc_final: 0.6583 (m110) REVERT: B 336 LYS cc_start: 0.8910 (ttpp) cc_final: 0.8610 (mtpp) REVERT: B 374 GLU cc_start: 0.8532 (tt0) cc_final: 0.7785 (tp30) outliers start: 67 outliers final: 51 residues processed: 272 average time/residue: 0.1340 time to fit residues: 51.0661 Evaluate side-chains 301 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 244 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 111 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 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 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 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 50 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 98 LEU 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 140 ILE Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 25 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 16 optimal weight: 0.0270 chunk 60 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.110229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.087693 restraints weight = 15302.420| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 4.83 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6482 Z= 0.234 Angle : 0.873 17.057 8848 Z= 0.407 Chirality : 0.046 0.280 1096 Planarity : 0.004 0.034 1080 Dihedral : 7.635 59.473 916 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 9.70 % Allowed : 35.82 % 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: 0.26 (0.30), residues: 812 helix: 0.69 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.39 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 324 HIS 0.005 0.001 HIS A 449 PHE 0.008 0.001 PHE A 443 TYR 0.037 0.002 TYR A 211 ARG 0.006 0.000 ARG A 260 *********************** 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 315 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 250 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8766 (mp0) cc_final: 0.8426 (tm-30) REVERT: A 83 MET cc_start: 0.8735 (mtm) cc_final: 0.8311 (mtm) REVERT: A 113 ASN cc_start: 0.9401 (t0) cc_final: 0.8580 (t0) REVERT: A 117 MET cc_start: 0.9332 (OUTLIER) cc_final: 0.8061 (mpp) REVERT: A 181 TYR cc_start: 0.8670 (m-80) cc_final: 0.8284 (m-80) REVERT: A 184 HIS cc_start: 0.9016 (t70) cc_final: 0.8668 (t-90) REVERT: A 188 ILE cc_start: 0.9088 (tp) cc_final: 0.8852 (tp) REVERT: A 208 PRO cc_start: 0.7447 (Cg_endo) cc_final: 0.7173 (Cg_exo) REVERT: A 254 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8263 (tm-30) REVERT: A 259 GLU cc_start: 0.9009 (pt0) cc_final: 0.8548 (mp0) REVERT: A 262 GLU cc_start: 0.8268 (tt0) cc_final: 0.7396 (tm-30) REVERT: A 284 ASN cc_start: 0.7351 (m110) cc_final: 0.6907 (m110) REVERT: A 322 LEU cc_start: 0.9329 (mm) cc_final: 0.8986 (mm) REVERT: A 341 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8483 (tpp) REVERT: A 374 GLU cc_start: 0.8601 (tp30) cc_final: 0.8337 (tp30) REVERT: A 415 GLU cc_start: 0.8967 (pm20) cc_final: 0.8745 (pm20) REVERT: B 34 GLN cc_start: 0.9198 (pp30) cc_final: 0.8976 (pp30) REVERT: B 59 GLU cc_start: 0.8810 (mp0) cc_final: 0.8435 (tm-30) REVERT: B 83 MET cc_start: 0.8787 (mtm) cc_final: 0.8338 (mtm) REVERT: B 113 ASN cc_start: 0.9026 (t0) cc_final: 0.8297 (t0) REVERT: B 117 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.7883 (mpp) REVERT: B 181 TYR cc_start: 0.8718 (m-80) cc_final: 0.8371 (m-80) REVERT: B 254 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8354 (tm-30) REVERT: B 259 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8544 (mp0) REVERT: B 262 GLU cc_start: 0.8416 (tt0) cc_final: 0.7934 (tm-30) REVERT: B 284 ASN cc_start: 0.6884 (m110) cc_final: 0.6476 (m110) REVERT: B 314 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8943 (m-80) REVERT: B 336 LYS cc_start: 0.8883 (ttpp) cc_final: 0.8574 (mtpp) REVERT: B 374 GLU cc_start: 0.8448 (tt0) cc_final: 0.7689 (tp30) outliers start: 65 outliers final: 48 residues processed: 274 average time/residue: 0.1434 time to fit residues: 54.7141 Evaluate side-chains 301 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 248 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 111 LEU 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 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 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 341 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 VAL 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 50 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 405 LEU 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: 2.9990 chunk 47 optimal weight: 0.2980 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.0870 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.111880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.089356 restraints weight = 15379.691| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 4.87 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6482 Z= 0.235 Angle : 0.899 16.119 8848 Z= 0.421 Chirality : 0.047 0.294 1096 Planarity : 0.004 0.035 1080 Dihedral : 7.496 59.238 913 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 9.10 % Allowed : 37.76 % Favored : 53.13 % Cbeta Deviations : 0.13 % 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: 626 sheet: None (None), residues: 0 loop : -1.16 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 324 HIS 0.006 0.001 HIS A 184 PHE 0.009 0.001 PHE B 264 TYR 0.017 0.002 TYR B 313 ARG 0.005 0.000 ARG B 260 ********************** 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 311 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 250 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9087 (pp30) cc_final: 0.8796 (pp30) REVERT: A 113 ASN cc_start: 0.9412 (t0) cc_final: 0.8552 (t0) REVERT: A 117 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.8089 (mpp) REVERT: A 181 TYR cc_start: 0.8693 (m-80) cc_final: 0.8357 (m-80) REVERT: A 184 HIS cc_start: 0.9009 (t70) cc_final: 0.8669 (t-90) REVERT: A 188 ILE cc_start: 0.9044 (tp) cc_final: 0.8804 (tp) REVERT: A 208 PRO cc_start: 0.7391 (Cg_endo) cc_final: 0.7137 (Cg_exo) REVERT: A 254 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8265 (tm-30) REVERT: A 259 GLU cc_start: 0.8954 (pt0) cc_final: 0.8503 (mp0) REVERT: A 284 ASN cc_start: 0.7288 (m110) cc_final: 0.6859 (m110) REVERT: A 322 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8970 (mm) REVERT: A 341 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8480 (tpp) REVERT: A 374 GLU cc_start: 0.8575 (tp30) cc_final: 0.8314 (tp30) REVERT: A 415 GLU cc_start: 0.8925 (pm20) cc_final: 0.8715 (pm20) REVERT: B 34 GLN cc_start: 0.9170 (pp30) cc_final: 0.8945 (pp30) REVERT: B 83 MET cc_start: 0.8736 (mtm) cc_final: 0.8266 (mtm) REVERT: B 113 ASN cc_start: 0.9054 (t0) cc_final: 0.8279 (t0) REVERT: B 117 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.7881 (mpp) REVERT: B 154 GLN cc_start: 0.9629 (mt0) cc_final: 0.9427 (mt0) REVERT: B 181 TYR cc_start: 0.8723 (m-80) cc_final: 0.8415 (m-80) REVERT: B 254 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8314 (tm-30) REVERT: B 259 GLU cc_start: 0.8930 (pt0) cc_final: 0.8538 (mp0) REVERT: B 262 GLU cc_start: 0.8395 (tt0) cc_final: 0.7937 (tm-30) REVERT: B 283 ASP cc_start: 0.8092 (t0) cc_final: 0.7845 (t0) REVERT: B 284 ASN cc_start: 0.6834 (m110) cc_final: 0.6460 (m110) REVERT: B 314 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8980 (m-80) REVERT: B 322 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8866 (mm) REVERT: B 336 LYS cc_start: 0.8876 (ttpp) cc_final: 0.8580 (mtpp) REVERT: B 341 MET cc_start: 0.8870 (tpp) cc_final: 0.8589 (tpp) REVERT: B 374 GLU cc_start: 0.8303 (tt0) cc_final: 0.7495 (tp30) outliers start: 61 outliers final: 49 residues processed: 272 average time/residue: 0.1444 time to fit residues: 55.0897 Evaluate side-chains 298 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 243 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 111 LEU 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 216 THR 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 281 CYS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 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 50 VAL 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 271 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 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: 0.9990 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.111756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.088574 restraints weight = 15599.075| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 4.98 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6482 Z= 0.242 Angle : 0.896 15.669 8848 Z= 0.415 Chirality : 0.047 0.201 1096 Planarity : 0.004 0.034 1080 Dihedral : 7.091 55.743 908 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 8.36 % Allowed : 38.36 % Favored : 53.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.41 (0.30), residues: 812 helix: 0.75 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -1.15 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 324 HIS 0.006 0.001 HIS A 184 PHE 0.016 0.001 PHE B 162 TYR 0.037 0.002 TYR A 313 ARG 0.005 0.000 ARG B 260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2471.21 seconds wall clock time: 45 minutes 1.93 seconds (2701.93 seconds total)