Starting phenix.real_space_refine on Wed Sep 17 17:07:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yas_39106/09_2025/8yas_39106.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yas_39106/09_2025/8yas_39106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yas_39106/09_2025/8yas_39106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yas_39106/09_2025/8yas_39106.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yas_39106/09_2025/8yas_39106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yas_39106/09_2025/8yas_39106.map" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.050 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: 8 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 46 5.16 5 Be 1 3.05 5 C 6323 2.51 5 N 1693 2.21 5 O 1825 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9894 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 6107 Classifications: {'peptide': 765} Link IDs: {'PTRANS': 15, 'TRANS': 749} Chain: "Y" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3275 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Chain: "E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 480 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.27, per 1000 atoms: 0.23 Number of scatterers: 9894 At special positions: 0 Unit cell: (93.74, 113.36, 116.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 46 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 1825 8.00 N 1693 7.00 C 6323 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 363.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 66.7% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 4.033A pdb=" N ARG A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 removed outlier: 4.270A pdb=" N ILE A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY A 55 " --> pdb=" O ARG A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 77 Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.540A pdb=" N THR A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 130 through 149 Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 177 through 188 removed outlier: 3.536A pdb=" N ASN A 188 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 215 through 218 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 377 through 384 Processing helix chain 'A' and resid 410 through 427 Processing helix chain 'A' and resid 438 through 451 removed outlier: 3.595A pdb=" N SER A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN A 451 " --> pdb=" O LYS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 466 through 474 removed outlier: 3.659A pdb=" N GLU A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.776A pdb=" N ASP A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG A 528 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.625A pdb=" N MET A 557 " --> pdb=" O THR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 619 removed outlier: 3.851A pdb=" N ARG A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 642 removed outlier: 3.640A pdb=" N TYR A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.579A pdb=" N LEU A 657 " --> pdb=" O LYS A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 704 removed outlier: 3.646A pdb=" N GLY A 704 " --> pdb=" O GLU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 742 removed outlier: 3.665A pdb=" N ARG A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N HIS A 739 " --> pdb=" O ARG A 735 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU A 740 " --> pdb=" O GLN A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 745 No H-bonds generated for 'chain 'A' and resid 743 through 745' Processing helix chain 'A' and resid 747 through 777 Processing helix chain 'Y' and resid 3 through 9 removed outlier: 3.604A pdb=" N MET Y 9 " --> pdb=" O ILE Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 33 Processing helix chain 'Y' and resid 40 through 47 removed outlier: 3.928A pdb=" N LEU Y 44 " --> pdb=" O ASN Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 74 through 89 removed outlier: 3.920A pdb=" N MET Y 89 " --> pdb=" O GLN Y 85 " (cutoff:3.500A) Processing helix chain 'Y' and resid 92 through 102 removed outlier: 4.156A pdb=" N GLY Y 102 " --> pdb=" O TRP Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 137 Processing helix chain 'Y' and resid 145 through 173 Processing helix chain 'Y' and resid 177 through 202 removed outlier: 3.688A pdb=" N ILE Y 181 " --> pdb=" O ASN Y 177 " (cutoff:3.500A) Proline residue: Y 192 - end of helix Processing helix chain 'Y' and resid 213 through 236 Processing helix chain 'Y' and resid 271 through 290 removed outlier: 3.705A pdb=" N ILE Y 275 " --> pdb=" O VAL Y 271 " (cutoff:3.500A) Proline residue: Y 284 - end of helix Processing helix chain 'Y' and resid 294 through 304 removed outlier: 3.696A pdb=" N LEU Y 298 " --> pdb=" O ASN Y 294 " (cutoff:3.500A) Processing helix chain 'Y' and resid 308 through 331 Processing helix chain 'Y' and resid 332 through 344 Processing helix chain 'Y' and resid 353 through 388 removed outlier: 3.912A pdb=" N GLN Y 357 " --> pdb=" O GLY Y 353 " (cutoff:3.500A) Proline residue: Y 382 - end of helix Processing helix chain 'Y' and resid 399 through 421 removed outlier: 3.982A pdb=" N LEU Y 403 " --> pdb=" O GLY Y 399 " (cutoff:3.500A) Processing helix chain 'Y' and resid 422 through 424 No H-bonds generated for 'chain 'Y' and resid 422 through 424' Processing helix chain 'E' and resid 3 through 16 removed outlier: 3.643A pdb=" N LYS E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 154 removed outlier: 6.353A pdb=" N ALA A 204 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N MET A 370 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE A 206 " --> pdb=" O MET A 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 220 through 226 removed outlier: 6.791A pdb=" N LEU A 221 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR A 354 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 223 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 250 through 253 removed outlier: 3.527A pdb=" N ALA A 258 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 306 through 309 removed outlier: 3.955A pdb=" N ILE A 315 " --> pdb=" O MET A 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 400 through 402 Processing sheet with id=AA6, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.426A pdb=" N LEU A 433 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 432 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA A 483 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL A 434 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLN A 457 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Y' and resid 57 through 60 Processing sheet with id=AA8, first strand: chain 'Y' and resid 238 through 242 Processing sheet with id=AA9, first strand: chain 'Y' and resid 244 through 245 632 hydrogen bonds defined for protein. 1860 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: 1.75 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2140 1.32 - 1.44: 2147 1.44 - 1.56: 5680 1.56 - 1.68: 3 1.68 - 1.80: 94 Bond restraints: 10064 Sorted by residual: bond pdb=" F3 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.762 -0.286 2.00e-02 2.50e+03 2.05e+02 bond pdb=" F2 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.761 -0.285 2.00e-02 2.50e+03 2.02e+02 bond pdb=" F1 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.751 -0.275 2.00e-02 2.50e+03 1.88e+02 bond pdb=" CG1 ILE A 764 " pdb=" CD1 ILE A 764 " ideal model delta sigma weight residual 1.513 1.364 0.149 3.90e-02 6.57e+02 1.47e+01 bond pdb=" CB VAL A 69 " pdb=" CG2 VAL A 69 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.01e+01 ... (remaining 10059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 13121 2.69 - 5.38: 418 5.38 - 8.07: 45 8.07 - 10.76: 9 10.76 - 13.44: 1 Bond angle restraints: 13594 Sorted by residual: angle pdb=" N VAL A 399 " pdb=" CA VAL A 399 " pdb=" C VAL A 399 " ideal model delta sigma weight residual 112.29 106.63 5.66 9.40e-01 1.13e+00 3.62e+01 angle pdb=" C ASP A 38 " pdb=" N ASP A 39 " pdb=" CA ASP A 39 " ideal model delta sigma weight residual 121.54 131.11 -9.57 1.91e+00 2.74e-01 2.51e+01 angle pdb=" CA GLN A 529 " pdb=" CB GLN A 529 " pdb=" CG GLN A 529 " ideal model delta sigma weight residual 114.10 123.40 -9.30 2.00e+00 2.50e-01 2.16e+01 angle pdb=" C THR A 394 " pdb=" N ASN A 395 " pdb=" CA ASN A 395 " ideal model delta sigma weight residual 121.54 129.72 -8.18 1.91e+00 2.74e-01 1.83e+01 angle pdb=" CA THR A 643 " pdb=" C THR A 643 " pdb=" N PRO A 644 " ideal model delta sigma weight residual 118.16 121.05 -2.89 7.00e-01 2.04e+00 1.71e+01 ... (remaining 13589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 5612 24.23 - 48.46: 390 48.46 - 72.69: 69 72.69 - 96.92: 4 96.92 - 121.16: 1 Dihedral angle restraints: 6076 sinusoidal: 2485 harmonic: 3591 Sorted by residual: dihedral pdb=" O2A ADP A1003 " pdb=" O3A ADP A1003 " pdb=" PA ADP A1003 " pdb=" PB ADP A1003 " ideal model delta sinusoidal sigma weight residual -60.00 61.16 -121.16 1 2.00e+01 2.50e-03 3.64e+01 dihedral pdb=" CA ASP A 667 " pdb=" C ASP A 667 " pdb=" N GLU A 668 " pdb=" CA GLU A 668 " ideal model delta harmonic sigma weight residual 180.00 150.23 29.77 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA ASN A 451 " pdb=" C ASN A 451 " pdb=" N LYS A 452 " pdb=" CA LYS A 452 " ideal model delta harmonic sigma weight residual -180.00 -152.02 -27.98 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 6073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 887 0.056 - 0.113: 506 0.113 - 0.169: 131 0.169 - 0.225: 24 0.225 - 0.281: 7 Chirality restraints: 1555 Sorted by residual: chirality pdb=" CB VAL A 127 " pdb=" CA VAL A 127 " pdb=" CG1 VAL A 127 " pdb=" CG2 VAL A 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB ILE Y 397 " pdb=" CA ILE Y 397 " pdb=" CG1 ILE Y 397 " pdb=" CG2 ILE Y 397 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB VAL A 307 " pdb=" CA VAL A 307 " pdb=" CG1 VAL A 307 " pdb=" CG2 VAL A 307 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 1552 not shown) Planarity restraints: 1740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL Y 36 " -0.060 5.00e-02 4.00e+02 9.04e-02 1.31e+01 pdb=" N PRO Y 37 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO Y 37 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO Y 37 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 32 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.98e+00 pdb=" CG ASP A 32 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASP A 32 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 32 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 365 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.83e+00 pdb=" C GLU A 365 " -0.048 2.00e-02 2.50e+03 pdb=" O GLU A 365 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS A 366 " 0.016 2.00e-02 2.50e+03 ... (remaining 1737 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 68 2.51 - 3.11: 7195 3.11 - 3.71: 15143 3.71 - 4.30: 22037 4.30 - 4.90: 37202 Nonbonded interactions: 81645 Sorted by model distance: nonbonded pdb="MG MG A1001 " pdb=" F3 BEF A1002 " model vdw 1.919 2.120 nonbonded pdb="MG MG A1001 " pdb=" O1B ADP A1003 " model vdw 2.109 2.170 nonbonded pdb=" F3 BEF A1002 " pdb=" O1B ADP A1003 " model vdw 2.164 2.990 nonbonded pdb=" CD1 LEU A 740 " pdb=" OH TYR Y 245 " model vdw 2.196 3.460 nonbonded pdb=" CD1 PHE A 757 " pdb=" CE1 TYR Y 425 " model vdw 2.202 3.640 ... (remaining 81640 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.540 Find NCS groups from input model: 0.040 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 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 : 0.020 0.900 10065 Z= 1.164 Angle : 1.107 13.444 13594 Z= 0.611 Chirality : 0.071 0.281 1555 Planarity : 0.008 0.090 1740 Dihedral : 16.480 121.156 3766 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.66 % Allowed : 16.02 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.32 (0.19), residues: 1235 helix: -1.97 (0.14), residues: 786 sheet: -1.32 (0.55), residues: 81 loop : -2.51 (0.27), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 30 TYR 0.027 0.004 TYR Y 306 PHE 0.023 0.004 PHE A 703 TRP 0.010 0.002 TRP Y 165 HIS 0.006 0.002 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.01774 (10064) covalent geometry : angle 1.10693 (13594) hydrogen bonds : bond 0.14450 ( 630) hydrogen bonds : angle 6.43374 ( 1860) Misc. bond : bond 0.89972 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 409 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 THR cc_start: 0.8701 (p) cc_final: 0.8414 (t) REVERT: A 30 ARG cc_start: 0.1581 (OUTLIER) cc_final: 0.0954 (ppt90) REVERT: A 66 PHE cc_start: 0.8081 (m-10) cc_final: 0.7795 (m-10) REVERT: A 145 PHE cc_start: 0.7223 (m-80) cc_final: 0.6979 (m-80) REVERT: A 196 MET cc_start: 0.8149 (mtp) cc_final: 0.7264 (mtm) REVERT: A 222 ILE cc_start: 0.9068 (mt) cc_final: 0.8356 (mp) REVERT: A 244 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6335 (mt) REVERT: A 257 LYS cc_start: 0.9093 (mttp) cc_final: 0.8663 (mppt) REVERT: A 305 ASP cc_start: 0.8554 (m-30) cc_final: 0.8092 (m-30) REVERT: A 327 ARG cc_start: 0.8146 (mtp180) cc_final: 0.7692 (mmm160) REVERT: A 377 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7743 (mp0) REVERT: A 387 MET cc_start: 0.7641 (mtm) cc_final: 0.6798 (mtm) REVERT: A 411 MET cc_start: 0.8038 (mtp) cc_final: 0.7652 (mtp) REVERT: A 454 ILE cc_start: 0.8599 (mt) cc_final: 0.8046 (mt) REVERT: A 493 ILE cc_start: 0.8703 (mt) cc_final: 0.8487 (mp) REVERT: A 617 VAL cc_start: 0.7798 (t) cc_final: 0.7527 (t) REVERT: A 630 MET cc_start: 0.7885 (mtt) cc_final: 0.7202 (mmm) REVERT: A 711 PHE cc_start: 0.7803 (t80) cc_final: 0.7587 (t80) REVERT: A 731 MET cc_start: 0.9233 (tpt) cc_final: 0.9000 (mmm) REVERT: A 763 MET cc_start: 0.8017 (tmm) cc_final: 0.7543 (tmm) REVERT: A 765 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7631 (mt-10) REVERT: Y 18 ILE cc_start: 0.8587 (mt) cc_final: 0.8379 (mt) REVERT: Y 217 LEU cc_start: 0.9079 (mt) cc_final: 0.8582 (tp) REVERT: Y 233 TYR cc_start: 0.8374 (t80) cc_final: 0.8019 (t80) REVERT: Y 298 LEU cc_start: 0.8257 (mt) cc_final: 0.8016 (mm) REVERT: Y 381 LEU cc_start: 0.8590 (tp) cc_final: 0.8218 (tt) REVERT: E 24 LYS cc_start: 0.9297 (mmtt) cc_final: 0.9077 (ttpp) outliers start: 7 outliers final: 1 residues processed: 413 average time/residue: 0.1162 time to fit residues: 63.6816 Evaluate side-chains 244 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 241 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 364 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 238 ASN A 291 ASN A 297 HIS A 347 ASN A 383 ASN A 464 HIS A 513 HIS A 529 GLN A 536 GLN A 613 GLN A 736 GLN A 739 HIS Y 88 GLN Y 101 GLN Y 124 GLN ** Y 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 134 ASN Y 143 ASN Y 177 ASN Y 213 ASN ** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 267 ASN Y 343 GLN Y 387 ASN Y 415 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.143626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.113073 restraints weight = 24633.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.116125 restraints weight = 14640.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.118154 restraints weight = 8747.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.119354 restraints weight = 7371.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.119713 restraints weight = 6466.195| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10065 Z= 0.195 Angle : 0.776 12.478 13594 Z= 0.411 Chirality : 0.046 0.223 1555 Planarity : 0.006 0.074 1740 Dihedral : 7.234 113.476 1372 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.71 % Allowed : 20.17 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.23), residues: 1235 helix: 0.07 (0.17), residues: 798 sheet: -0.85 (0.60), residues: 77 loop : -1.92 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 750 TYR 0.017 0.002 TYR A 385 PHE 0.041 0.002 PHE Y 67 TRP 0.011 0.002 TRP Y 299 HIS 0.006 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00417 (10064) covalent geometry : angle 0.77597 (13594) hydrogen bonds : bond 0.06355 ( 630) hydrogen bonds : angle 4.85237 ( 1860) Misc. bond : bond 0.00115 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 253 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7647 (pt0) cc_final: 0.7402 (pt0) REVERT: A 30 ARG cc_start: 0.1260 (OUTLIER) cc_final: 0.0628 (ppt170) REVERT: A 79 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6576 (mtt) REVERT: A 87 MET cc_start: 0.8484 (mmm) cc_final: 0.8275 (mmp) REVERT: A 305 ASP cc_start: 0.8584 (m-30) cc_final: 0.8008 (m-30) REVERT: A 365 GLU cc_start: 0.7880 (tt0) cc_final: 0.7541 (tm-30) REVERT: A 367 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8317 (tt) REVERT: A 380 GLU cc_start: 0.8592 (mp0) cc_final: 0.8210 (mp0) REVERT: A 384 ILE cc_start: 0.9147 (mp) cc_final: 0.8908 (pt) REVERT: A 411 MET cc_start: 0.7932 (mtp) cc_final: 0.7634 (mtp) REVERT: A 600 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7685 (t0) REVERT: A 725 MET cc_start: 0.8658 (ptm) cc_final: 0.8057 (ptm) REVERT: A 759 MET cc_start: 0.8518 (mmm) cc_final: 0.8189 (mmm) REVERT: A 763 MET cc_start: 0.8405 (tmm) cc_final: 0.7931 (tmm) REVERT: Y 24 MET cc_start: 0.7994 (mmp) cc_final: 0.7210 (mmp) REVERT: Y 164 MET cc_start: 0.8754 (ptp) cc_final: 0.8440 (ptp) REVERT: Y 217 LEU cc_start: 0.9067 (mt) cc_final: 0.8538 (tp) REVERT: Y 233 TYR cc_start: 0.8428 (t80) cc_final: 0.8034 (t80) REVERT: Y 298 LEU cc_start: 0.8287 (mt) cc_final: 0.8012 (tt) REVERT: Y 343 GLN cc_start: 0.7964 (tp40) cc_final: 0.7710 (tp40) REVERT: E 24 LYS cc_start: 0.9284 (mmtt) cc_final: 0.8791 (ttpp) outliers start: 50 outliers final: 20 residues processed: 287 average time/residue: 0.0915 time to fit residues: 37.0089 Evaluate side-chains 237 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 647 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 156 LEU Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 370 VAL Chi-restraints excluded: chain Y residue 383 VAL Chi-restraints excluded: chain Y residue 420 LEU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 23 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 GLN ** Y 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 142 GLN ** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.131393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.102519 restraints weight = 24324.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.103566 restraints weight = 13433.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.104808 restraints weight = 9887.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.105287 restraints weight = 8115.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.105657 restraints weight = 7296.206| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10065 Z= 0.189 Angle : 0.726 9.089 13594 Z= 0.379 Chirality : 0.045 0.169 1555 Planarity : 0.005 0.064 1740 Dihedral : 6.546 108.889 1368 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.00 % Allowed : 21.21 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.23), residues: 1235 helix: 0.83 (0.18), residues: 791 sheet: -0.80 (0.57), residues: 79 loop : -1.77 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 70 TYR 0.020 0.002 TYR A 385 PHE 0.028 0.002 PHE Y 184 TRP 0.009 0.002 TRP A 652 HIS 0.005 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00416 (10064) covalent geometry : angle 0.72604 (13594) hydrogen bonds : bond 0.06052 ( 630) hydrogen bonds : angle 4.55794 ( 1860) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 234 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7871 (pt0) cc_final: 0.7591 (pt0) REVERT: A 30 ARG cc_start: 0.1702 (OUTLIER) cc_final: 0.1012 (ppt170) REVERT: A 79 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.7107 (mtt) REVERT: A 189 MET cc_start: 0.8265 (ttm) cc_final: 0.7897 (mtp) REVERT: A 213 LEU cc_start: 0.9355 (mp) cc_final: 0.9155 (tp) REVERT: A 305 ASP cc_start: 0.8554 (m-30) cc_final: 0.7836 (m-30) REVERT: A 327 ARG cc_start: 0.6122 (mmm160) cc_final: 0.5493 (mmm160) REVERT: A 329 TYR cc_start: 0.8824 (m-10) cc_final: 0.8584 (m-10) REVERT: A 363 MET cc_start: 0.8827 (ttm) cc_final: 0.8495 (ttm) REVERT: A 365 GLU cc_start: 0.8121 (tt0) cc_final: 0.7804 (tm-30) REVERT: A 411 MET cc_start: 0.8098 (mtp) cc_final: 0.7799 (mtp) REVERT: A 586 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8195 (mm-30) REVERT: A 666 LEU cc_start: 0.7816 (tp) cc_final: 0.7357 (tt) REVERT: A 711 PHE cc_start: 0.7722 (t80) cc_final: 0.7516 (t80) REVERT: A 725 MET cc_start: 0.8505 (ptm) cc_final: 0.8134 (ptm) REVERT: A 759 MET cc_start: 0.8646 (mmm) cc_final: 0.8366 (mmm) REVERT: A 763 MET cc_start: 0.8745 (tmm) cc_final: 0.8258 (tmm) REVERT: Y 30 ILE cc_start: 0.9017 (tp) cc_final: 0.8708 (pt) REVERT: Y 164 MET cc_start: 0.8718 (ptp) cc_final: 0.8228 (ptp) REVERT: Y 184 PHE cc_start: 0.9372 (t80) cc_final: 0.9160 (t80) REVERT: Y 217 LEU cc_start: 0.9106 (mt) cc_final: 0.8645 (tp) REVERT: Y 218 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8297 (mm) REVERT: Y 233 TYR cc_start: 0.8479 (t80) cc_final: 0.8073 (t80) REVERT: E 9 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8794 (mtmm) REVERT: E 24 LYS cc_start: 0.9323 (mmtt) cc_final: 0.9085 (ttpp) outliers start: 53 outliers final: 26 residues processed: 258 average time/residue: 0.0744 time to fit residues: 28.8162 Evaluate side-chains 240 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Y residue 156 LEU Chi-restraints excluded: chain Y residue 166 LEU Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 181 ILE Chi-restraints excluded: chain Y residue 218 LEU Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 378 ILE Chi-restraints excluded: chain Y residue 383 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 18 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 21 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 29 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 HIS ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 133 ASN ** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 343 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.132148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.103193 restraints weight = 24366.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.104098 restraints weight = 14159.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.105278 restraints weight = 10338.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.106105 restraints weight = 8405.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.106207 restraints weight = 7547.393| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10065 Z= 0.159 Angle : 0.687 10.761 13594 Z= 0.355 Chirality : 0.043 0.165 1555 Planarity : 0.004 0.062 1740 Dihedral : 6.243 106.191 1368 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.00 % Allowed : 22.90 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.24), residues: 1235 helix: 1.18 (0.18), residues: 785 sheet: -1.00 (0.52), residues: 96 loop : -1.62 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 750 TYR 0.014 0.001 TYR A 599 PHE 0.019 0.001 PHE E 7 TRP 0.006 0.001 TRP E 20 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00346 (10064) covalent geometry : angle 0.68680 (13594) hydrogen bonds : bond 0.05676 ( 630) hydrogen bonds : angle 4.37557 ( 1860) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 222 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7626 (mtp) REVERT: A 189 MET cc_start: 0.8119 (ttm) cc_final: 0.7915 (mtp) REVERT: A 305 ASP cc_start: 0.8515 (m-30) cc_final: 0.7875 (m-30) REVERT: A 411 MET cc_start: 0.8169 (mtp) cc_final: 0.7936 (mtp) REVERT: A 443 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7669 (tm-30) REVERT: A 586 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8153 (mm-30) REVERT: A 600 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7659 (t0) REVERT: A 632 LYS cc_start: 0.8788 (ptpt) cc_final: 0.8312 (ptpt) REVERT: A 666 LEU cc_start: 0.7918 (tp) cc_final: 0.7559 (tp) REVERT: A 684 MET cc_start: 0.8037 (mtt) cc_final: 0.7799 (mtt) REVERT: A 725 MET cc_start: 0.8380 (ptm) cc_final: 0.8175 (ptm) REVERT: A 759 MET cc_start: 0.8560 (mmm) cc_final: 0.8316 (mmm) REVERT: A 763 MET cc_start: 0.8855 (tmm) cc_final: 0.7997 (tmm) REVERT: Y 24 MET cc_start: 0.8018 (mmm) cc_final: 0.7561 (mmm) REVERT: Y 30 ILE cc_start: 0.8934 (tp) cc_final: 0.8661 (pt) REVERT: Y 217 LEU cc_start: 0.8998 (mt) cc_final: 0.8549 (tt) REVERT: Y 233 TYR cc_start: 0.8454 (t80) cc_final: 0.8023 (t80) REVERT: E 23 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7892 (mpt180) REVERT: E 24 LYS cc_start: 0.9305 (mmtt) cc_final: 0.8984 (ttpp) outliers start: 53 outliers final: 31 residues processed: 251 average time/residue: 0.0800 time to fit residues: 29.0534 Evaluate side-chains 236 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Y residue 128 MET Chi-restraints excluded: chain Y residue 156 LEU Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 181 ILE Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 287 ILE Chi-restraints excluded: chain Y residue 383 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain E residue 23 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 10 optimal weight: 0.0670 chunk 69 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 29 optimal weight: 0.0020 chunk 17 optimal weight: 1.9990 overall best weight: 0.5930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN A 613 GLN Y 66 ASN ** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.130038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.100365 restraints weight = 24294.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.101702 restraints weight = 14738.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.103165 restraints weight = 10287.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104352 restraints weight = 8551.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.104777 restraints weight = 7343.789| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.6744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10065 Z= 0.152 Angle : 0.675 9.692 13594 Z= 0.349 Chirality : 0.043 0.195 1555 Planarity : 0.005 0.060 1740 Dihedral : 6.040 103.969 1368 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.62 % Allowed : 24.88 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.24), residues: 1235 helix: 1.44 (0.18), residues: 779 sheet: -0.42 (0.59), residues: 83 loop : -1.52 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 13 TYR 0.013 0.001 TYR A 250 PHE 0.031 0.001 PHE Y 184 TRP 0.007 0.001 TRP Y 299 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00327 (10064) covalent geometry : angle 0.67513 (13594) hydrogen bonds : bond 0.05472 ( 630) hydrogen bonds : angle 4.28110 ( 1860) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 219 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.7190 (p0) cc_final: 0.6718 (t0) REVERT: A 146 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7719 (tm-30) REVERT: A 305 ASP cc_start: 0.8372 (m-30) cc_final: 0.7674 (m-30) REVERT: A 324 MET cc_start: 0.7699 (mtp) cc_final: 0.7187 (ttp) REVERT: A 327 ARG cc_start: 0.5976 (mmm160) cc_final: 0.3574 (tpt170) REVERT: A 380 GLU cc_start: 0.8779 (mp0) cc_final: 0.8307 (pm20) REVERT: A 411 MET cc_start: 0.8194 (mtp) cc_final: 0.7879 (mtt) REVERT: A 443 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7656 (tm-30) REVERT: A 561 PHE cc_start: 0.7732 (m-80) cc_final: 0.7417 (m-80) REVERT: A 586 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8265 (mm-30) REVERT: A 600 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7513 (t0) REVERT: A 630 MET cc_start: 0.7713 (mmt) cc_final: 0.7437 (mmt) REVERT: A 666 LEU cc_start: 0.7656 (tp) cc_final: 0.7232 (tp) REVERT: A 759 MET cc_start: 0.8658 (mmm) cc_final: 0.8453 (mmm) REVERT: A 763 MET cc_start: 0.8746 (tmm) cc_final: 0.7847 (tmm) REVERT: Y 24 MET cc_start: 0.8178 (mmm) cc_final: 0.7818 (mmm) REVERT: Y 30 ILE cc_start: 0.8896 (tp) cc_final: 0.8666 (pt) REVERT: Y 164 MET cc_start: 0.8763 (ptp) cc_final: 0.8303 (ptp) REVERT: Y 217 LEU cc_start: 0.8986 (mt) cc_final: 0.8571 (tt) REVERT: Y 218 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8340 (mm) REVERT: Y 233 TYR cc_start: 0.8410 (t80) cc_final: 0.8039 (t80) REVERT: Y 391 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8270 (tt) REVERT: E 14 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8641 (mm-30) REVERT: E 23 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7947 (mpt180) REVERT: E 24 LYS cc_start: 0.9255 (mmtt) cc_final: 0.8942 (ttpp) outliers start: 49 outliers final: 29 residues processed: 246 average time/residue: 0.0777 time to fit residues: 27.9033 Evaluate side-chains 238 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain Y residue 128 MET Chi-restraints excluded: chain Y residue 156 LEU Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 181 ILE Chi-restraints excluded: chain Y residue 218 LEU Chi-restraints excluded: chain Y residue 261 HIS Chi-restraints excluded: chain Y residue 378 ILE Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 420 LEU Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain E residue 23 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 25 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.126808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.097686 restraints weight = 24527.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.098760 restraints weight = 14488.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.100005 restraints weight = 10418.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.100360 restraints weight = 8736.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.100616 restraints weight = 7840.877| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.7275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10065 Z= 0.161 Angle : 0.679 11.439 13594 Z= 0.348 Chirality : 0.043 0.204 1555 Planarity : 0.004 0.061 1740 Dihedral : 5.974 102.064 1368 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.43 % Allowed : 26.01 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.24), residues: 1235 helix: 1.61 (0.18), residues: 774 sheet: -0.51 (0.56), residues: 94 loop : -1.48 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 13 TYR 0.013 0.001 TYR A 250 PHE 0.024 0.001 PHE Y 184 TRP 0.006 0.001 TRP E 20 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00349 (10064) covalent geometry : angle 0.67899 (13594) hydrogen bonds : bond 0.05522 ( 630) hydrogen bonds : angle 4.25333 ( 1860) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.9470 (t) cc_final: 0.9140 (m) REVERT: A 146 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7510 (tm-30) REVERT: A 173 THR cc_start: 0.9266 (m) cc_final: 0.8885 (p) REVERT: A 305 ASP cc_start: 0.8394 (m-30) cc_final: 0.7702 (m-30) REVERT: A 324 MET cc_start: 0.7745 (mtp) cc_final: 0.7370 (ttt) REVERT: A 327 ARG cc_start: 0.6035 (mmm160) cc_final: 0.3447 (tpt170) REVERT: A 380 GLU cc_start: 0.8763 (mp0) cc_final: 0.8302 (pm20) REVERT: A 443 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7673 (tm-30) REVERT: A 541 MET cc_start: 0.8541 (tpp) cc_final: 0.8198 (tpp) REVERT: A 561 PHE cc_start: 0.7998 (m-80) cc_final: 0.7621 (m-80) REVERT: A 586 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8337 (mm-30) REVERT: A 600 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7535 (t0) REVERT: A 630 MET cc_start: 0.8108 (mmt) cc_final: 0.7822 (mmt) REVERT: A 666 LEU cc_start: 0.7663 (tp) cc_final: 0.7162 (tp) REVERT: A 689 MET cc_start: 0.8075 (tpp) cc_final: 0.7612 (mmt) REVERT: A 763 MET cc_start: 0.8846 (tmm) cc_final: 0.8342 (tmm) REVERT: Y 8 PHE cc_start: 0.8328 (m-10) cc_final: 0.7786 (m-10) REVERT: Y 24 MET cc_start: 0.8354 (mmm) cc_final: 0.7971 (mmm) REVERT: Y 30 ILE cc_start: 0.8890 (tp) cc_final: 0.8652 (pt) REVERT: Y 75 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8219 (ttm) REVERT: Y 164 MET cc_start: 0.8883 (ptp) cc_final: 0.8360 (ptp) REVERT: Y 217 LEU cc_start: 0.9009 (mt) cc_final: 0.8644 (tt) REVERT: Y 218 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8341 (pp) REVERT: Y 233 TYR cc_start: 0.8439 (t80) cc_final: 0.8018 (t80) REVERT: Y 417 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7859 (mt-10) REVERT: E 14 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8607 (mm-30) REVERT: E 23 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8029 (mpt180) REVERT: E 24 LYS cc_start: 0.9248 (mmtt) cc_final: 0.8920 (ttpp) outliers start: 47 outliers final: 33 residues processed: 237 average time/residue: 0.0813 time to fit residues: 28.5251 Evaluate side-chains 240 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 75 MET Chi-restraints excluded: chain Y residue 128 MET Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 181 ILE Chi-restraints excluded: chain Y residue 218 LEU Chi-restraints excluded: chain Y residue 370 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 97 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 0.0010 chunk 17 optimal weight: 0.0870 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 739 HIS ** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.125715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.098206 restraints weight = 23635.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.098841 restraints weight = 13098.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.100220 restraints weight = 9731.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.100562 restraints weight = 7847.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.100859 restraints weight = 7183.064| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.7638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10065 Z= 0.144 Angle : 0.690 11.007 13594 Z= 0.345 Chirality : 0.043 0.288 1555 Planarity : 0.004 0.058 1740 Dihedral : 5.805 97.030 1368 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.77 % Allowed : 28.18 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.24), residues: 1235 helix: 1.67 (0.18), residues: 769 sheet: -0.47 (0.59), residues: 83 loop : -1.26 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 13 TYR 0.018 0.001 TYR A 385 PHE 0.039 0.001 PHE Y 184 TRP 0.016 0.001 TRP Y 299 HIS 0.003 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00308 (10064) covalent geometry : angle 0.69040 (13594) hydrogen bonds : bond 0.05301 ( 630) hydrogen bonds : angle 4.17545 ( 1860) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.9514 (t) cc_final: 0.9178 (m) REVERT: A 146 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7709 (tp30) REVERT: A 173 THR cc_start: 0.9287 (m) cc_final: 0.8913 (p) REVERT: A 305 ASP cc_start: 0.8327 (m-30) cc_final: 0.7670 (m-30) REVERT: A 380 GLU cc_start: 0.8750 (mp0) cc_final: 0.8323 (pm20) REVERT: A 443 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7596 (tm-30) REVERT: A 541 MET cc_start: 0.8569 (tpp) cc_final: 0.7778 (tpp) REVERT: A 559 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7391 (m-30) REVERT: A 586 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8411 (mm-30) REVERT: A 600 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7439 (t0) REVERT: A 630 MET cc_start: 0.8186 (mmt) cc_final: 0.7850 (mmt) REVERT: A 632 LYS cc_start: 0.8927 (mtmm) cc_final: 0.8641 (pttm) REVERT: A 666 LEU cc_start: 0.7519 (tp) cc_final: 0.7132 (tp) REVERT: A 689 MET cc_start: 0.8158 (tpp) cc_final: 0.7737 (mmt) REVERT: A 763 MET cc_start: 0.8868 (tmm) cc_final: 0.8361 (tmm) REVERT: Y 24 MET cc_start: 0.8411 (mmm) cc_final: 0.8033 (mmm) REVERT: Y 30 ILE cc_start: 0.8861 (tp) cc_final: 0.8606 (pt) REVERT: Y 75 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8224 (ttm) REVERT: Y 164 MET cc_start: 0.8804 (ptp) cc_final: 0.8301 (ptp) REVERT: Y 217 LEU cc_start: 0.8988 (mt) cc_final: 0.8644 (tt) REVERT: Y 233 TYR cc_start: 0.8424 (t80) cc_final: 0.8011 (t80) REVERT: Y 413 MET cc_start: 0.8850 (tpp) cc_final: 0.7938 (tpp) REVERT: Y 417 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7825 (mt-10) REVERT: E 9 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8568 (mtmm) REVERT: E 23 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7977 (mpt180) REVERT: E 24 LYS cc_start: 0.9209 (mmtt) cc_final: 0.8907 (ttpp) outliers start: 40 outliers final: 31 residues processed: 244 average time/residue: 0.0886 time to fit residues: 31.1840 Evaluate side-chains 243 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 75 MET Chi-restraints excluded: chain Y residue 128 MET Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 181 ILE Chi-restraints excluded: chain Y residue 370 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 23 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 89 optimal weight: 0.2980 chunk 38 optimal weight: 0.4980 chunk 95 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 0.0270 chunk 20 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.125369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.097902 restraints weight = 23665.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.098417 restraints weight = 13885.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.099567 restraints weight = 10135.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.100302 restraints weight = 7999.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.100655 restraints weight = 7356.668| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.7963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10065 Z= 0.144 Angle : 0.742 14.655 13594 Z= 0.361 Chirality : 0.045 0.337 1555 Planarity : 0.004 0.056 1740 Dihedral : 5.748 96.870 1368 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.20 % Allowed : 29.31 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.24), residues: 1235 helix: 1.65 (0.18), residues: 769 sheet: -0.46 (0.55), residues: 93 loop : -1.25 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 13 TYR 0.022 0.001 TYR A 385 PHE 0.035 0.001 PHE Y 184 TRP 0.011 0.001 TRP Y 299 HIS 0.002 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00310 (10064) covalent geometry : angle 0.74155 (13594) hydrogen bonds : bond 0.05233 ( 630) hydrogen bonds : angle 4.17616 ( 1860) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.9521 (t) cc_final: 0.9172 (m) REVERT: A 173 THR cc_start: 0.9290 (m) cc_final: 0.8918 (p) REVERT: A 305 ASP cc_start: 0.8335 (m-30) cc_final: 0.7554 (m-30) REVERT: A 324 MET cc_start: 0.7674 (mtp) cc_final: 0.7240 (ttt) REVERT: A 327 ARG cc_start: 0.6022 (mmp-170) cc_final: 0.2983 (tpt170) REVERT: A 380 GLU cc_start: 0.8777 (mp0) cc_final: 0.8458 (mp0) REVERT: A 385 TYR cc_start: 0.9052 (m-10) cc_final: 0.8544 (m-10) REVERT: A 443 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7600 (tm-30) REVERT: A 541 MET cc_start: 0.8551 (tpp) cc_final: 0.8111 (tpp) REVERT: A 559 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7355 (m-30) REVERT: A 586 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8366 (mm-30) REVERT: A 600 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7455 (t0) REVERT: A 630 MET cc_start: 0.8308 (mmt) cc_final: 0.7941 (mmt) REVERT: A 666 LEU cc_start: 0.7718 (tp) cc_final: 0.7221 (tp) REVERT: A 689 MET cc_start: 0.8232 (tpp) cc_final: 0.7707 (mmt) REVERT: A 763 MET cc_start: 0.8911 (tmm) cc_final: 0.8386 (tmm) REVERT: Y 24 MET cc_start: 0.8340 (mmm) cc_final: 0.8008 (mmm) REVERT: Y 164 MET cc_start: 0.8720 (ptp) cc_final: 0.8240 (ptp) REVERT: Y 217 LEU cc_start: 0.9047 (mt) cc_final: 0.8646 (tt) REVERT: Y 218 LEU cc_start: 0.9247 (pp) cc_final: 0.8864 (mm) REVERT: Y 233 TYR cc_start: 0.8427 (t80) cc_final: 0.7998 (t80) REVERT: Y 391 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8238 (tt) REVERT: Y 413 MET cc_start: 0.8748 (tpp) cc_final: 0.7789 (tmm) REVERT: E 9 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8584 (mtmm) REVERT: E 24 LYS cc_start: 0.9208 (mmtt) cc_final: 0.8906 (ttpp) outliers start: 34 outliers final: 26 residues processed: 233 average time/residue: 0.0878 time to fit residues: 29.8348 Evaluate side-chains 230 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 128 MET Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 181 ILE Chi-restraints excluded: chain Y residue 261 HIS Chi-restraints excluded: chain Y residue 370 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 18 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.121092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092710 restraints weight = 24644.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.093425 restraints weight = 14647.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.094511 restraints weight = 10749.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.094981 restraints weight = 8922.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.095240 restraints weight = 8046.339| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.8496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10065 Z= 0.173 Angle : 0.783 13.655 13594 Z= 0.384 Chirality : 0.047 0.412 1555 Planarity : 0.005 0.058 1740 Dihedral : 5.807 98.885 1368 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.11 % Allowed : 29.50 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.24), residues: 1235 helix: 1.65 (0.18), residues: 775 sheet: -0.40 (0.56), residues: 86 loop : -1.29 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Y 366 TYR 0.020 0.002 TYR Y 326 PHE 0.032 0.001 PHE E 43 TRP 0.006 0.001 TRP E 20 HIS 0.002 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00382 (10064) covalent geometry : angle 0.78268 (13594) hydrogen bonds : bond 0.05682 ( 630) hydrogen bonds : angle 4.25053 ( 1860) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.9433 (t) cc_final: 0.9110 (m) REVERT: A 173 THR cc_start: 0.9346 (m) cc_final: 0.9036 (p) REVERT: A 183 ASP cc_start: 0.8871 (t0) cc_final: 0.8625 (t70) REVERT: A 305 ASP cc_start: 0.8291 (m-30) cc_final: 0.7599 (m-30) REVERT: A 324 MET cc_start: 0.7656 (mtp) cc_final: 0.7366 (ttt) REVERT: A 327 ARG cc_start: 0.6106 (mmp-170) cc_final: 0.3527 (tpt170) REVERT: A 443 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7588 (tm-30) REVERT: A 541 MET cc_start: 0.8622 (tpp) cc_final: 0.8023 (tpp) REVERT: A 559 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7536 (m-30) REVERT: A 586 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8479 (mm-30) REVERT: A 600 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7668 (t0) REVERT: A 630 MET cc_start: 0.8449 (mmt) cc_final: 0.8128 (mmt) REVERT: A 632 LYS cc_start: 0.8924 (pttm) cc_final: 0.8618 (mtmm) REVERT: A 666 LEU cc_start: 0.7770 (tp) cc_final: 0.7179 (tp) REVERT: A 689 MET cc_start: 0.8353 (tpp) cc_final: 0.7899 (mmt) REVERT: A 763 MET cc_start: 0.8884 (tmm) cc_final: 0.8312 (tmm) REVERT: A 769 ASP cc_start: 0.9049 (t0) cc_final: 0.8805 (t0) REVERT: Y 24 MET cc_start: 0.8435 (mmm) cc_final: 0.8098 (mmm) REVERT: Y 164 MET cc_start: 0.8661 (ptp) cc_final: 0.8238 (ptp) REVERT: Y 217 LEU cc_start: 0.9027 (mt) cc_final: 0.8660 (tt) REVERT: Y 218 LEU cc_start: 0.9145 (pp) cc_final: 0.8812 (mm) REVERT: Y 233 TYR cc_start: 0.8408 (t80) cc_final: 0.7964 (t80) REVERT: Y 338 ASP cc_start: 0.7657 (m-30) cc_final: 0.7305 (m-30) REVERT: Y 413 MET cc_start: 0.8764 (tpp) cc_final: 0.7939 (tmm) REVERT: E 9 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8634 (mmtp) REVERT: E 23 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8043 (mpt180) REVERT: E 24 LYS cc_start: 0.9226 (mmtt) cc_final: 0.8909 (ttpp) outliers start: 33 outliers final: 23 residues processed: 228 average time/residue: 0.0872 time to fit residues: 29.0447 Evaluate side-chains 219 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain Y residue 30 ILE Chi-restraints excluded: chain Y residue 128 MET Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 261 HIS Chi-restraints excluded: chain Y residue 370 VAL Chi-restraints excluded: chain Y residue 400 THR Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 4 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 463 ASN Y 101 GLN ** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.121676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.093598 restraints weight = 24267.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.094245 restraints weight = 14267.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.095542 restraints weight = 10387.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.096177 restraints weight = 8469.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.096391 restraints weight = 7570.119| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.8736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10065 Z= 0.155 Angle : 0.798 13.937 13594 Z= 0.386 Chirality : 0.046 0.411 1555 Planarity : 0.004 0.058 1740 Dihedral : 5.744 92.782 1368 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.02 % Allowed : 30.91 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.24), residues: 1235 helix: 1.59 (0.18), residues: 775 sheet: -0.28 (0.56), residues: 86 loop : -1.28 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 382 TYR 0.019 0.001 TYR A 385 PHE 0.027 0.001 PHE E 8 TRP 0.055 0.003 TRP Y 98 HIS 0.002 0.001 HIS A 762 Details of bonding type rmsd covalent geometry : bond 0.00339 (10064) covalent geometry : angle 0.79775 (13594) hydrogen bonds : bond 0.05467 ( 630) hydrogen bonds : angle 4.19880 ( 1860) Misc. bond : bond 0.00001 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.9405 (t) cc_final: 0.9042 (m) REVERT: A 173 THR cc_start: 0.9334 (m) cc_final: 0.8968 (p) REVERT: A 266 MET cc_start: 0.8597 (ptt) cc_final: 0.8307 (ptt) REVERT: A 305 ASP cc_start: 0.8249 (m-30) cc_final: 0.7565 (m-30) REVERT: A 324 MET cc_start: 0.7622 (mtp) cc_final: 0.7304 (ttt) REVERT: A 327 ARG cc_start: 0.6045 (mmp-170) cc_final: 0.3490 (tpt170) REVERT: A 443 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7535 (tm-30) REVERT: A 541 MET cc_start: 0.8601 (tpp) cc_final: 0.8035 (tpp) REVERT: A 559 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7535 (m-30) REVERT: A 586 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8441 (mm-30) REVERT: A 600 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7469 (t0) REVERT: A 630 MET cc_start: 0.8480 (mmt) cc_final: 0.8157 (mmt) REVERT: A 666 LEU cc_start: 0.7655 (tp) cc_final: 0.7067 (tp) REVERT: A 685 LEU cc_start: 0.8505 (mm) cc_final: 0.8286 (pp) REVERT: A 689 MET cc_start: 0.8420 (tpp) cc_final: 0.8036 (mmt) REVERT: A 738 ILE cc_start: 0.8919 (tp) cc_final: 0.8642 (tp) REVERT: A 759 MET cc_start: 0.8786 (mtt) cc_final: 0.8558 (mmm) REVERT: A 763 MET cc_start: 0.8817 (tmm) cc_final: 0.8278 (tmm) REVERT: A 776 MET cc_start: 0.8101 (tpp) cc_final: 0.7708 (tpp) REVERT: Y 24 MET cc_start: 0.8461 (mmm) cc_final: 0.8087 (mmm) REVERT: Y 164 MET cc_start: 0.8551 (ptp) cc_final: 0.8100 (ptp) REVERT: Y 217 LEU cc_start: 0.9016 (mt) cc_final: 0.8656 (tt) REVERT: Y 218 LEU cc_start: 0.9159 (pp) cc_final: 0.8821 (mm) REVERT: Y 233 TYR cc_start: 0.8412 (t80) cc_final: 0.7960 (t80) REVERT: Y 299 TRP cc_start: 0.8484 (t-100) cc_final: 0.8248 (t60) REVERT: Y 338 ASP cc_start: 0.7654 (m-30) cc_final: 0.7373 (m-30) REVERT: Y 413 MET cc_start: 0.8763 (tpp) cc_final: 0.7929 (tmm) REVERT: E 9 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8434 (mmtt) REVERT: E 23 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8031 (mpt180) REVERT: E 24 LYS cc_start: 0.9190 (mmtt) cc_final: 0.8892 (ttpp) outliers start: 32 outliers final: 24 residues processed: 226 average time/residue: 0.0845 time to fit residues: 27.5896 Evaluate side-chains 224 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 774 PHE Chi-restraints excluded: chain Y residue 128 MET Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 261 HIS Chi-restraints excluded: chain Y residue 370 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 400 THR Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 23 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.0370 chunk 88 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 18 optimal weight: 0.3980 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN ** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.121391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.094208 restraints weight = 24732.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.094487 restraints weight = 14396.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.095762 restraints weight = 10508.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.096556 restraints weight = 8219.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.097782 restraints weight = 7490.694| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.8949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10065 Z= 0.155 Angle : 0.813 13.776 13594 Z= 0.393 Chirality : 0.045 0.401 1555 Planarity : 0.004 0.058 1740 Dihedral : 5.697 91.516 1368 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.02 % Allowed : 30.82 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.24), residues: 1235 helix: 1.63 (0.18), residues: 773 sheet: -0.21 (0.57), residues: 86 loop : -1.36 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 382 TYR 0.021 0.001 TYR A 385 PHE 0.031 0.001 PHE E 8 TRP 0.006 0.001 TRP Y 98 HIS 0.002 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00342 (10064) covalent geometry : angle 0.81261 (13594) hydrogen bonds : bond 0.05392 ( 630) hydrogen bonds : angle 4.17301 ( 1860) Misc. bond : bond 0.00007 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1677.66 seconds wall clock time: 29 minutes 44.57 seconds (1784.57 seconds total)