Starting phenix.real_space_refine on Tue May 13 09:36:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yas_39106/05_2025/8yas_39106.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yas_39106/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yas_39106/05_2025/8yas_39106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yas_39106/05_2025/8yas_39106.map" model { file = "/net/cci-nas-00/data/ceres_data/8yas_39106/05_2025/8yas_39106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yas_39106/05_2025/8yas_39106.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.91, per 1000 atoms: 0.60 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: 2.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.01 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: 3.14 Time building geometry restraints manager: 2.81 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: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.110 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (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 TRP 0.010 0.002 TRP Y 165 HIS 0.006 0.002 HIS A 93 PHE 0.023 0.004 PHE A 703 TYR 0.027 0.004 TYR Y 306 ARG 0.005 0.001 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.14450 ( 630) hydrogen bonds : angle 6.43374 ( 1860) covalent geometry : bond 0.01774 (10064) covalent geometry : angle 1.10693 (13594) 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 : 1.186 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: 0.2619 time to fit residues: 142.6178 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 : 1.008 ------------------------------------------------------------------------------- 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 103 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 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 267 ASN Y 343 GLN Y 387 ASN Y 415 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.142985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.112718 restraints weight = 24401.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.115562 restraints weight = 14777.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.116921 restraints weight = 8903.957| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 10065 Z= 0.205 Angle : 0.791 14.292 13594 Z= 0.419 Chirality : 0.046 0.202 1555 Planarity : 0.006 0.075 1740 Dihedral : 7.319 114.466 1372 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.52 % Allowed : 20.64 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.23), residues: 1235 helix: 0.11 (0.18), residues: 798 sheet: -0.93 (0.60), residues: 77 loop : -1.92 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Y 299 HIS 0.006 0.001 HIS A 93 PHE 0.041 0.002 PHE Y 67 TYR 0.017 0.002 TYR A 385 ARG 0.010 0.001 ARG A 750 Details of bonding type rmsd hydrogen bonds : bond 0.06453 ( 630) hydrogen bonds : angle 4.90511 ( 1860) covalent geometry : bond 0.00445 (10064) covalent geometry : angle 0.79117 (13594) Misc. bond : bond 0.00044 ( 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 300 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 252 time to evaluate : 1.098 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 20 GLU cc_start: 0.7785 (pt0) cc_final: 0.7508 (pt0) REVERT: A 30 ARG cc_start: 0.1418 (OUTLIER) cc_final: 0.0640 (ppt170) REVERT: A 87 MET cc_start: 0.8486 (mmm) cc_final: 0.8260 (mmp) REVERT: A 305 ASP cc_start: 0.8595 (m-30) cc_final: 0.8035 (m-30) REVERT: A 365 GLU cc_start: 0.7867 (tt0) cc_final: 0.7596 (tm-30) REVERT: A 367 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8394 (tt) REVERT: A 380 GLU cc_start: 0.8511 (mp0) cc_final: 0.8080 (mp0) REVERT: A 411 MET cc_start: 0.7975 (mtp) cc_final: 0.7657 (mtp) REVERT: A 600 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7637 (t0) REVERT: A 725 MET cc_start: 0.8601 (ptm) cc_final: 0.7954 (ptm) REVERT: A 759 MET cc_start: 0.8539 (mmm) cc_final: 0.8217 (mmm) REVERT: A 763 MET cc_start: 0.8464 (tmm) cc_final: 0.7932 (tmm) REVERT: Y 24 MET cc_start: 0.8036 (mmp) cc_final: 0.7248 (mmp) REVERT: Y 164 MET cc_start: 0.8699 (ptp) cc_final: 0.8443 (ptp) REVERT: Y 217 LEU cc_start: 0.9095 (mt) cc_final: 0.8552 (tp) REVERT: Y 233 TYR cc_start: 0.8420 (t80) cc_final: 0.8079 (t80) REVERT: Y 298 LEU cc_start: 0.8306 (mt) cc_final: 0.8066 (tp) REVERT: Y 343 GLN cc_start: 0.8007 (tp40) cc_final: 0.7731 (tp40) REVERT: E 24 LYS cc_start: 0.9304 (mmtt) cc_final: 0.8802 (ttpp) outliers start: 48 outliers final: 20 residues processed: 284 average time/residue: 0.2015 time to fit residues: 80.7748 Evaluate side-chains 236 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG 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 4 optimal weight: 5.9990 chunk 48 optimal weight: 0.0010 chunk 70 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 202 HIS ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 HIS A 753 GLN ** Y 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3922 r_free = 0.3922 target = 0.131073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.101000 restraints weight = 24207.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.102900 restraints weight = 13853.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.104725 restraints weight = 9105.429| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5552 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= 0.183 Angle : 0.730 9.921 13594 Z= 0.382 Chirality : 0.045 0.171 1555 Planarity : 0.005 0.067 1740 Dihedral : 6.534 107.080 1368 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.56 % Allowed : 20.26 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1235 helix: 0.78 (0.18), residues: 791 sheet: -0.78 (0.57), residues: 79 loop : -1.76 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 652 HIS 0.006 0.001 HIS A 93 PHE 0.027 0.002 PHE E 8 TYR 0.024 0.002 TYR A 385 ARG 0.006 0.001 ARG Y 29 Details of bonding type rmsd hydrogen bonds : bond 0.06095 ( 630) hydrogen bonds : angle 4.60580 ( 1860) covalent geometry : bond 0.00393 (10064) covalent geometry : angle 0.73003 (13594) Misc. bond : bond 0.00058 ( 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 296 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 237 time to evaluate : 1.078 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 20 GLU cc_start: 0.7895 (pt0) cc_final: 0.7597 (pt0) REVERT: A 70 ARG cc_start: 0.7428 (mmm160) cc_final: 0.7095 (ttt180) REVERT: A 189 MET cc_start: 0.8291 (ttm) cc_final: 0.7931 (mtp) REVERT: A 305 ASP cc_start: 0.8542 (m-30) cc_final: 0.7810 (m-30) REVERT: A 327 ARG cc_start: 0.6143 (mmm160) cc_final: 0.5940 (mmm160) REVERT: A 329 TYR cc_start: 0.8848 (m-10) cc_final: 0.8613 (m-10) REVERT: A 363 MET cc_start: 0.8896 (ttm) cc_final: 0.8579 (ttm) REVERT: A 365 GLU cc_start: 0.8153 (tt0) cc_final: 0.7852 (tm-30) REVERT: A 384 ILE cc_start: 0.9257 (mp) cc_final: 0.9041 (mm) REVERT: A 411 MET cc_start: 0.8126 (mtp) cc_final: 0.7870 (mtp) REVERT: A 555 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8578 (mtp) REVERT: A 559 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6867 (m-30) REVERT: A 586 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8190 (mm-30) REVERT: A 612 LYS cc_start: 0.9307 (tmmt) cc_final: 0.9101 (tmmt) REVERT: A 666 LEU cc_start: 0.7805 (tp) cc_final: 0.7441 (tp) REVERT: A 689 MET cc_start: 0.7074 (tpt) cc_final: 0.6839 (tpt) REVERT: A 725 MET cc_start: 0.8508 (ptm) cc_final: 0.8155 (ptm) REVERT: A 759 MET cc_start: 0.8696 (mmm) cc_final: 0.8399 (mmm) REVERT: A 763 MET cc_start: 0.8657 (tmm) cc_final: 0.8168 (tmm) REVERT: Y 24 MET cc_start: 0.8235 (mmp) cc_final: 0.7908 (mmm) REVERT: Y 30 ILE cc_start: 0.8993 (tp) cc_final: 0.8730 (pt) REVERT: Y 164 MET cc_start: 0.8718 (ptp) cc_final: 0.8260 (ptp) REVERT: Y 184 PHE cc_start: 0.9424 (t80) cc_final: 0.9201 (t80) REVERT: Y 217 LEU cc_start: 0.9118 (mt) cc_final: 0.8671 (tp) REVERT: Y 218 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8451 (mm) REVERT: Y 233 TYR cc_start: 0.8459 (t80) cc_final: 0.8034 (t80) REVERT: E 9 LYS cc_start: 0.8936 (mtmm) cc_final: 0.8695 (mtmm) REVERT: E 24 LYS cc_start: 0.9345 (mmtt) cc_final: 0.9106 (ttpp) outliers start: 59 outliers final: 30 residues processed: 268 average time/residue: 0.1895 time to fit residues: 73.7273 Evaluate side-chains 249 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 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 555 MET Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 618 ILE 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 Y residue 74 VAL 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 Y residue 420 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 86 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 109 optimal weight: 0.0070 chunk 117 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** Y 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.131218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.102126 restraints weight = 24352.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.103388 restraints weight = 14390.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.105032 restraints weight = 10165.355| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10065 Z= 0.160 Angle : 0.682 9.493 13594 Z= 0.356 Chirality : 0.043 0.160 1555 Planarity : 0.004 0.061 1740 Dihedral : 6.257 104.060 1368 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.18 % Allowed : 22.62 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.24), residues: 1235 helix: 1.17 (0.18), residues: 785 sheet: -0.52 (0.58), residues: 79 loop : -1.70 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 20 HIS 0.008 0.001 HIS A 283 PHE 0.023 0.001 PHE E 7 TYR 0.019 0.001 TYR A 385 ARG 0.005 0.000 ARG A 750 Details of bonding type rmsd hydrogen bonds : bond 0.05718 ( 630) hydrogen bonds : angle 4.42393 ( 1860) covalent geometry : bond 0.00345 (10064) covalent geometry : angle 0.68196 (13594) Misc. bond : bond 0.00027 ( 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 280 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 225 time to evaluate : 1.108 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 70 ARG cc_start: 0.7657 (mmm160) cc_final: 0.7289 (ttt180) REVERT: A 189 MET cc_start: 0.8164 (ttm) cc_final: 0.7956 (mtp) REVERT: A 213 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8772 (tp) REVERT: A 305 ASP cc_start: 0.8427 (m-30) cc_final: 0.7798 (m-30) REVERT: A 380 GLU cc_start: 0.8871 (mp0) cc_final: 0.8574 (mp0) REVERT: A 384 ILE cc_start: 0.9345 (mp) cc_final: 0.9063 (mm) REVERT: A 411 MET cc_start: 0.8173 (mtp) cc_final: 0.7923 (mtp) REVERT: A 443 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7747 (tm-30) REVERT: A 541 MET cc_start: 0.8648 (tpp) cc_final: 0.8124 (tmm) REVERT: A 557 MET cc_start: 0.8092 (mpp) cc_final: 0.7839 (pmm) REVERT: A 559 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7175 (m-30) REVERT: A 586 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8143 (mm-30) REVERT: A 600 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7679 (t0) REVERT: A 630 MET cc_start: 0.7635 (mmt) cc_final: 0.7385 (mmt) REVERT: A 666 LEU cc_start: 0.7821 (tp) cc_final: 0.7460 (tp) REVERT: A 684 MET cc_start: 0.8062 (mtt) cc_final: 0.7820 (mtt) REVERT: A 759 MET cc_start: 0.8679 (mmm) cc_final: 0.8377 (mmm) REVERT: A 763 MET cc_start: 0.8893 (tmm) cc_final: 0.7952 (tmm) REVERT: Y 30 ILE cc_start: 0.8921 (tp) cc_final: 0.8670 (pt) REVERT: Y 217 LEU cc_start: 0.9052 (mt) cc_final: 0.8585 (tt) REVERT: Y 233 TYR cc_start: 0.8433 (t80) cc_final: 0.8049 (t80) REVERT: E 14 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8855 (mm-30) REVERT: E 17 LYS cc_start: 0.9233 (mtmm) cc_final: 0.8902 (mtmm) REVERT: E 23 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7941 (mpt180) REVERT: E 24 LYS cc_start: 0.9310 (mmtt) cc_final: 0.9066 (ttpp) outliers start: 55 outliers final: 29 residues processed: 254 average time/residue: 0.1997 time to fit residues: 72.6873 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 : 1.174 ------------------------------------------------------------------------------- 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 85 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 559 ASP 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 642 TYR 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 75 MET 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 5 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 ASN ** 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 = 0.3882 r_free = 0.3882 target = 0.126742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.098749 restraints weight = 23448.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.099677 restraints weight = 13360.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.100970 restraints weight = 9869.197| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10065 Z= 0.165 Angle : 0.690 11.563 13594 Z= 0.359 Chirality : 0.045 0.227 1555 Planarity : 0.005 0.061 1740 Dihedral : 6.068 101.771 1368 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.43 % Allowed : 24.22 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.24), residues: 1235 helix: 1.40 (0.18), residues: 778 sheet: -0.69 (0.54), residues: 96 loop : -1.60 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 299 HIS 0.004 0.001 HIS A 283 PHE 0.034 0.001 PHE Y 184 TYR 0.019 0.001 TYR A 385 ARG 0.005 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.05830 ( 630) hydrogen bonds : angle 4.32049 ( 1860) covalent geometry : bond 0.00353 (10064) covalent geometry : angle 0.69033 (13594) Misc. bond : bond 0.00008 ( 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 267 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 1.061 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 146 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7762 (tm-30) REVERT: A 173 THR cc_start: 0.9256 (m) cc_final: 0.8864 (p) REVERT: A 213 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8786 (tp) REVERT: A 305 ASP cc_start: 0.8419 (m-30) cc_final: 0.7675 (m-30) REVERT: A 324 MET cc_start: 0.7832 (mtp) cc_final: 0.7386 (ttt) REVERT: A 327 ARG cc_start: 0.6076 (mmm160) cc_final: 0.3344 (tpt170) REVERT: A 380 GLU cc_start: 0.8833 (mp0) cc_final: 0.8577 (mp0) REVERT: A 411 MET cc_start: 0.8301 (mtp) cc_final: 0.8073 (mtt) REVERT: A 443 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7661 (tm-30) REVERT: A 561 PHE cc_start: 0.7951 (m-80) cc_final: 0.7596 (m-80) REVERT: A 586 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8284 (mm-30) REVERT: A 600 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7564 (t0) REVERT: A 612 LYS cc_start: 0.9289 (tmmt) cc_final: 0.8994 (tmmt) REVERT: A 630 MET cc_start: 0.8186 (mmt) cc_final: 0.7853 (mmt) REVERT: A 763 MET cc_start: 0.8898 (tmm) cc_final: 0.8352 (tmm) REVERT: Y 24 MET cc_start: 0.8616 (mmm) cc_final: 0.7993 (mmm) REVERT: Y 30 ILE cc_start: 0.8884 (tp) cc_final: 0.8683 (pt) REVERT: Y 164 MET cc_start: 0.8806 (ptp) cc_final: 0.8337 (ptp) REVERT: Y 217 LEU cc_start: 0.9024 (mt) cc_final: 0.8646 (tt) REVERT: Y 218 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8470 (pp) REVERT: Y 233 TYR cc_start: 0.8444 (t80) cc_final: 0.8011 (t80) REVERT: E 14 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8654 (mm-30) REVERT: E 17 LYS cc_start: 0.9244 (mtmm) cc_final: 0.8899 (mtmm) REVERT: E 23 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7902 (mpt180) REVERT: E 24 LYS cc_start: 0.9240 (mmtt) cc_final: 0.8997 (ttpp) outliers start: 47 outliers final: 31 residues processed: 247 average time/residue: 0.1992 time to fit residues: 70.0044 Evaluate side-chains 242 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 185 LEU Chi-restraints excluded: chain A residue 213 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 600 ASP 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 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 46 LEU 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 218 LEU Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 370 VAL Chi-restraints excluded: chain Y residue 378 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 0.0570 chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 chunk 89 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 133 ASN ** 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 = 0.3880 r_free = 0.3880 target = 0.126799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.098233 restraints weight = 24010.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.098853 restraints weight = 13680.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.099999 restraints weight = 10319.097| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.7282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10065 Z= 0.153 Angle : 0.696 11.752 13594 Z= 0.355 Chirality : 0.043 0.258 1555 Planarity : 0.004 0.060 1740 Dihedral : 5.965 99.348 1368 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.43 % Allowed : 26.96 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.24), residues: 1235 helix: 1.56 (0.18), residues: 779 sheet: -0.51 (0.56), residues: 94 loop : -1.55 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 20 HIS 0.003 0.001 HIS A 739 PHE 0.023 0.001 PHE Y 184 TYR 0.014 0.001 TYR A 385 ARG 0.004 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.05598 ( 630) hydrogen bonds : angle 4.27503 ( 1860) covalent geometry : bond 0.00330 (10064) covalent geometry : angle 0.69607 (13594) Misc. bond : bond 0.00007 ( 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 268 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 1.076 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: 0.9450 (t) cc_final: 0.9103 (m) REVERT: A 146 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7549 (tm-30) REVERT: A 173 THR cc_start: 0.9257 (m) cc_final: 0.8877 (p) REVERT: A 213 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8779 (tp) REVERT: A 305 ASP cc_start: 0.8318 (m-30) cc_final: 0.7695 (m-30) REVERT: A 380 GLU cc_start: 0.8803 (mp0) cc_final: 0.8560 (mp0) REVERT: A 443 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7640 (tm-30) REVERT: A 561 PHE cc_start: 0.7968 (m-80) cc_final: 0.7584 (m-80) REVERT: A 586 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8297 (mm-30) REVERT: A 600 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7564 (t0) REVERT: A 612 LYS cc_start: 0.9299 (tmmt) cc_final: 0.8986 (tmmt) REVERT: A 630 MET cc_start: 0.8114 (mmt) cc_final: 0.7878 (mmt) REVERT: A 666 LEU cc_start: 0.7669 (tp) cc_final: 0.7083 (tt) REVERT: A 763 MET cc_start: 0.8911 (tmm) cc_final: 0.8383 (tmm) REVERT: Y 24 MET cc_start: 0.8656 (mmm) cc_final: 0.8161 (mmm) REVERT: Y 30 ILE cc_start: 0.8840 (tp) cc_final: 0.8639 (pt) REVERT: Y 164 MET cc_start: 0.8766 (ptp) cc_final: 0.8329 (ptp) REVERT: Y 217 LEU cc_start: 0.9029 (mt) cc_final: 0.8665 (tt) REVERT: Y 218 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8408 (pp) REVERT: Y 233 TYR cc_start: 0.8432 (t80) cc_final: 0.8020 (t80) REVERT: Y 391 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8290 (tt) REVERT: E 14 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8734 (mm-30) REVERT: E 17 LYS cc_start: 0.9267 (mtmm) cc_final: 0.8944 (mtmm) REVERT: E 23 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7988 (mpt180) REVERT: E 24 LYS cc_start: 0.9232 (mmtt) cc_final: 0.8922 (ttpp) outliers start: 47 outliers final: 29 residues processed: 246 average time/residue: 0.1892 time to fit residues: 67.0662 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 : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 185 LEU Chi-restraints excluded: chain A residue 213 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 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 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 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 383 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 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 117 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.116853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.088502 restraints weight = 24002.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.089654 restraints weight = 14602.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.090634 restraints weight = 10274.049| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.8355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10065 Z= 0.234 Angle : 0.779 11.167 13594 Z= 0.406 Chirality : 0.046 0.187 1555 Planarity : 0.005 0.058 1740 Dihedral : 6.253 103.036 1368 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.66 % Allowed : 25.92 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1235 helix: 1.35 (0.18), residues: 764 sheet: -0.63 (0.54), residues: 89 loop : -1.68 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Y 299 HIS 0.006 0.001 HIS A 289 PHE 0.040 0.002 PHE Y 184 TYR 0.016 0.002 TYR A 385 ARG 0.009 0.001 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.06793 ( 630) hydrogen bonds : angle 4.62706 ( 1860) covalent geometry : bond 0.00518 (10064) covalent geometry : angle 0.77874 (13594) Misc. bond : bond 0.00049 ( 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 275 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 215 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7819 (mt0) REVERT: A 146 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7454 (tm-30) REVERT: A 173 THR cc_start: 0.9362 (m) cc_final: 0.8995 (p) REVERT: A 183 ASP cc_start: 0.8871 (t0) cc_final: 0.8664 (t70) REVERT: A 221 LEU cc_start: 0.9237 (mp) cc_final: 0.8925 (mt) REVERT: A 305 ASP cc_start: 0.8397 (m-30) cc_final: 0.7648 (m-30) REVERT: A 324 MET cc_start: 0.7830 (mtp) cc_final: 0.7588 (ttt) REVERT: A 327 ARG cc_start: 0.6419 (mmp-170) cc_final: 0.3781 (tpt170) REVERT: A 377 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8178 (mm-30) REVERT: A 380 GLU cc_start: 0.8760 (mp0) cc_final: 0.8501 (mp0) REVERT: A 443 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7601 (tm-30) REVERT: A 586 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8488 (mm-30) REVERT: A 600 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7432 (t0) REVERT: A 630 MET cc_start: 0.8824 (mmt) cc_final: 0.8486 (mmt) REVERT: A 666 LEU cc_start: 0.7818 (tp) cc_final: 0.7300 (tt) REVERT: A 689 MET cc_start: 0.8404 (tpp) cc_final: 0.8030 (tpt) REVERT: A 763 MET cc_start: 0.8862 (tmm) cc_final: 0.8258 (tmm) REVERT: A 769 ASP cc_start: 0.9120 (t0) cc_final: 0.8815 (t0) REVERT: A 774 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6811 (t80) REVERT: Y 13 ASP cc_start: 0.8858 (m-30) cc_final: 0.8616 (p0) REVERT: Y 24 MET cc_start: 0.8762 (mmm) cc_final: 0.8251 (mmm) REVERT: Y 30 ILE cc_start: 0.8862 (tp) cc_final: 0.8629 (pt) REVERT: Y 98 TRP cc_start: 0.8578 (m-10) cc_final: 0.8052 (m-10) REVERT: Y 164 MET cc_start: 0.8754 (ptp) cc_final: 0.8289 (ptp) REVERT: Y 217 LEU cc_start: 0.9105 (mt) cc_final: 0.8668 (tt) REVERT: Y 218 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8252 (mm) REVERT: Y 233 TYR cc_start: 0.8499 (t80) cc_final: 0.7971 (t80) REVERT: Y 413 MET cc_start: 0.8342 (tmm) cc_final: 0.8119 (tmm) REVERT: Y 419 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8393 (tm-30) REVERT: E 13 ARG cc_start: 0.8427 (ttp80) cc_final: 0.8086 (ttp-110) REVERT: E 14 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8522 (mm-30) REVERT: E 17 LYS cc_start: 0.9276 (mtmm) cc_final: 0.8818 (mppt) REVERT: E 23 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7958 (mpt180) REVERT: E 24 LYS cc_start: 0.9236 (mmtt) cc_final: 0.8960 (ttpp) outliers start: 60 outliers final: 38 residues processed: 250 average time/residue: 0.1971 time to fit residues: 70.8667 Evaluate side-chains 244 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 201 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 85 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 320 THR 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 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 642 TYR Chi-restraints excluded: chain A residue 712 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 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 36 VAL Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 55 VAL 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 220 VAL Chi-restraints excluded: chain Y residue 238 PHE Chi-restraints excluded: chain Y residue 370 VAL Chi-restraints excluded: chain Y residue 380 VAL 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 18 VAL Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 40 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 124 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 = 0.3750 r_free = 0.3750 target = 0.117188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.089800 restraints weight = 23878.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.090351 restraints weight = 14421.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.091600 restraints weight = 10278.211| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.8715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10065 Z= 0.176 Angle : 0.761 12.646 13594 Z= 0.379 Chirality : 0.045 0.215 1555 Planarity : 0.004 0.056 1740 Dihedral : 6.026 96.146 1368 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.86 % Allowed : 29.03 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.24), residues: 1235 helix: 1.59 (0.18), residues: 772 sheet: -0.67 (0.53), residues: 104 loop : -1.56 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 724 HIS 0.003 0.001 HIS A 762 PHE 0.036 0.002 PHE Y 184 TYR 0.023 0.002 TYR A 743 ARG 0.006 0.000 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.06187 ( 630) hydrogen bonds : angle 4.38808 ( 1860) covalent geometry : bond 0.00386 (10064) covalent geometry : angle 0.76147 (13594) Misc. bond : bond 0.00009 ( 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 252 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.8282 (mmm) cc_final: 0.7922 (mmm) REVERT: A 173 THR cc_start: 0.9339 (m) cc_final: 0.8952 (p) REVERT: A 305 ASP cc_start: 0.8368 (m-30) cc_final: 0.7637 (m-30) REVERT: A 324 MET cc_start: 0.7816 (mtp) cc_final: 0.7356 (ttt) REVERT: A 327 ARG cc_start: 0.6077 (mmp-170) cc_final: 0.3832 (tpt170) REVERT: A 380 GLU cc_start: 0.8719 (mp0) cc_final: 0.8390 (mp0) REVERT: A 433 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9106 (tt) REVERT: A 443 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7556 (tm-30) REVERT: A 600 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7422 (t0) REVERT: A 630 MET cc_start: 0.8891 (mmt) cc_final: 0.8486 (mmt) REVERT: A 685 LEU cc_start: 0.8631 (mm) cc_final: 0.8276 (pp) REVERT: A 689 MET cc_start: 0.8586 (tpp) cc_final: 0.8217 (mmt) REVERT: A 759 MET cc_start: 0.8883 (mtt) cc_final: 0.8570 (mmm) REVERT: A 763 MET cc_start: 0.8878 (tmm) cc_final: 0.8233 (tmm) REVERT: A 769 ASP cc_start: 0.9103 (t0) cc_final: 0.8810 (t0) REVERT: A 774 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6594 (t80) REVERT: Y 24 MET cc_start: 0.8827 (mmm) cc_final: 0.8472 (mmm) REVERT: Y 98 TRP cc_start: 0.8527 (m-10) cc_final: 0.8059 (m-10) REVERT: Y 164 MET cc_start: 0.8674 (ptp) cc_final: 0.8182 (ptp) REVERT: Y 217 LEU cc_start: 0.9015 (mt) cc_final: 0.8620 (tt) REVERT: Y 218 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8227 (mm) REVERT: Y 233 TYR cc_start: 0.8424 (t80) cc_final: 0.7930 (t80) REVERT: E 13 ARG cc_start: 0.8485 (ttp80) cc_final: 0.8240 (ttp-110) REVERT: E 14 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8500 (mm-30) REVERT: E 17 LYS cc_start: 0.9287 (mtmm) cc_final: 0.8874 (mppt) REVERT: E 24 LYS cc_start: 0.9222 (mmtt) cc_final: 0.8973 (ttpp) REVERT: E 25 GLU cc_start: 0.8941 (pm20) cc_final: 0.8687 (pm20) outliers start: 41 outliers final: 32 residues processed: 236 average time/residue: 0.1973 time to fit residues: 66.6948 Evaluate side-chains 225 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 223 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 491 THR 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 642 TYR Chi-restraints excluded: chain A residue 712 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 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 36 VAL 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 218 LEU Chi-restraints excluded: chain Y residue 238 PHE Chi-restraints excluded: chain Y residue 370 VAL Chi-restraints excluded: chain Y residue 380 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 400 THR Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain E residue 15 LEU 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 53 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 chunk 115 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** A 469 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 = 0.3760 r_free = 0.3760 target = 0.117911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.090892 restraints weight = 23885.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.091856 restraints weight = 14440.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.093036 restraints weight = 9961.128| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.8976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10065 Z= 0.162 Angle : 0.759 11.963 13594 Z= 0.378 Chirality : 0.044 0.176 1555 Planarity : 0.004 0.057 1740 Dihedral : 5.937 93.211 1368 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.20 % Allowed : 29.97 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.24), residues: 1235 helix: 1.66 (0.18), residues: 775 sheet: -0.62 (0.56), residues: 93 loop : -1.40 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 20 HIS 0.003 0.001 HIS A 93 PHE 0.030 0.002 PHE E 43 TYR 0.026 0.001 TYR A 743 ARG 0.006 0.000 ARG A 637 Details of bonding type rmsd hydrogen bonds : bond 0.05909 ( 630) hydrogen bonds : angle 4.31821 ( 1860) covalent geometry : bond 0.00352 (10064) covalent geometry : angle 0.75942 (13594) Misc. bond : bond 0.00006 ( 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 235 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 1.123 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 173 THR cc_start: 0.9340 (m) cc_final: 0.8962 (p) REVERT: A 183 ASP cc_start: 0.8849 (t70) cc_final: 0.8456 (t70) REVERT: A 305 ASP cc_start: 0.8332 (m-30) cc_final: 0.7618 (m-30) REVERT: A 324 MET cc_start: 0.7753 (mtp) cc_final: 0.7366 (ttt) REVERT: A 327 ARG cc_start: 0.6071 (mmp-170) cc_final: 0.3796 (tpt170) REVERT: A 343 LEU cc_start: 0.8889 (mm) cc_final: 0.8665 (mp) REVERT: A 380 GLU cc_start: 0.8686 (mp0) cc_final: 0.8369 (mp0) REVERT: A 433 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9092 (tt) REVERT: A 443 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7497 (tm-30) REVERT: A 600 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7368 (t0) REVERT: A 630 MET cc_start: 0.8714 (mmt) cc_final: 0.8290 (mmt) REVERT: A 689 MET cc_start: 0.8585 (tpp) cc_final: 0.8233 (mmt) REVERT: A 738 ILE cc_start: 0.8937 (tp) cc_final: 0.8658 (tp) REVERT: A 763 MET cc_start: 0.8914 (tmm) cc_final: 0.8227 (tmm) REVERT: A 769 ASP cc_start: 0.9135 (t0) cc_final: 0.8836 (t0) REVERT: A 774 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.6612 (t80) REVERT: Y 24 MET cc_start: 0.8898 (mmm) cc_final: 0.8450 (mmm) REVERT: Y 98 TRP cc_start: 0.8509 (m-10) cc_final: 0.8084 (m-10) REVERT: Y 164 MET cc_start: 0.8589 (ptp) cc_final: 0.8164 (ptp) REVERT: Y 184 PHE cc_start: 0.9025 (t80) cc_final: 0.8786 (t80) REVERT: Y 217 LEU cc_start: 0.9001 (mt) cc_final: 0.8628 (tt) REVERT: Y 218 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8290 (mm) REVERT: Y 233 TYR cc_start: 0.8450 (t80) cc_final: 0.7966 (t80) REVERT: Y 417 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7899 (mt-10) REVERT: Y 430 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7647 (mmmm) REVERT: E 10 GLU cc_start: 0.8616 (tt0) cc_final: 0.8409 (tt0) REVERT: E 24 LYS cc_start: 0.9222 (mmtt) cc_final: 0.8974 (ttpp) outliers start: 34 outliers final: 28 residues processed: 223 average time/residue: 0.1895 time to fit residues: 61.4082 Evaluate side-chains 223 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 232 LYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 545 LEU 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 642 TYR Chi-restraints excluded: chain A residue 712 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 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 46 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 218 LEU Chi-restraints excluded: chain Y residue 370 VAL Chi-restraints excluded: chain Y residue 380 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 400 THR Chi-restraints excluded: chain Y residue 421 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 19 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 103 optimal weight: 0.0980 chunk 97 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 0.0050 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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** Y 308 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.119251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.091820 restraints weight = 24703.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.092744 restraints weight = 15341.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.094020 restraints weight = 10753.761| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.9252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10065 Z= 0.153 Angle : 0.779 12.467 13594 Z= 0.384 Chirality : 0.045 0.246 1555 Planarity : 0.004 0.055 1740 Dihedral : 5.818 89.239 1368 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.20 % Allowed : 30.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1235 helix: 1.72 (0.18), residues: 774 sheet: -0.40 (0.57), residues: 93 loop : -1.38 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 652 HIS 0.003 0.001 HIS A 739 PHE 0.031 0.001 PHE Y 184 TYR 0.034 0.001 TYR A 743 ARG 0.012 0.001 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.05567 ( 630) hydrogen bonds : angle 4.22940 ( 1860) covalent geometry : bond 0.00332 (10064) covalent geometry : angle 0.77933 (13594) 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 237 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 THR cc_start: 0.9331 (m) cc_final: 0.8969 (p) REVERT: A 183 ASP cc_start: 0.8851 (t70) cc_final: 0.8412 (t70) REVERT: A 305 ASP cc_start: 0.8261 (m-30) cc_final: 0.7561 (m-30) REVERT: A 324 MET cc_start: 0.7698 (mtp) cc_final: 0.7427 (ttt) REVERT: A 327 ARG cc_start: 0.5937 (mmp-170) cc_final: 0.3727 (tpt170) REVERT: A 380 GLU cc_start: 0.8646 (mp0) cc_final: 0.8341 (mp0) REVERT: A 443 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7421 (tm-30) REVERT: A 600 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7420 (t0) REVERT: A 630 MET cc_start: 0.8702 (mmt) cc_final: 0.8352 (mmt) REVERT: A 632 LYS cc_start: 0.8939 (pttm) cc_final: 0.8632 (mtmm) REVERT: A 685 LEU cc_start: 0.8828 (mt) cc_final: 0.8452 (pp) REVERT: A 689 MET cc_start: 0.8724 (tpp) cc_final: 0.8367 (mmt) REVERT: A 738 ILE cc_start: 0.8874 (tp) cc_final: 0.8571 (tp) REVERT: A 763 MET cc_start: 0.8946 (tmm) cc_final: 0.8280 (tmm) REVERT: A 769 ASP cc_start: 0.9136 (t0) cc_final: 0.8881 (t0) REVERT: A 774 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.6405 (t80) REVERT: Y 24 MET cc_start: 0.8853 (mmm) cc_final: 0.8444 (mmm) REVERT: Y 164 MET cc_start: 0.8527 (ptp) cc_final: 0.8185 (tmm) REVERT: Y 184 PHE cc_start: 0.8980 (t80) cc_final: 0.8747 (t80) REVERT: Y 217 LEU cc_start: 0.9010 (mt) cc_final: 0.8630 (tt) REVERT: Y 218 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8257 (mm) REVERT: Y 233 TYR cc_start: 0.8426 (t80) cc_final: 0.7980 (t80) REVERT: Y 417 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7724 (mt-10) REVERT: Y 430 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7790 (mmmm) REVERT: E 17 LYS cc_start: 0.9277 (mtmm) cc_final: 0.8933 (mptt) REVERT: E 24 LYS cc_start: 0.9204 (mmtt) cc_final: 0.8937 (ttpp) outliers start: 34 outliers final: 25 residues processed: 221 average time/residue: 0.2025 time to fit residues: 64.8259 Evaluate side-chains 215 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 491 THR 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 642 TYR Chi-restraints excluded: chain A residue 712 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 A residue 767 ILE Chi-restraints excluded: chain A residue 774 PHE Chi-restraints excluded: chain Y residue 25 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 218 LEU Chi-restraints excluded: chain Y residue 380 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain E residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 1.9990 chunk 103 optimal weight: 0.0030 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 100 optimal weight: 0.0670 chunk 111 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 68 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 overall best weight: 0.4128 ------------------------------------------------------------------------------- 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** A 739 HIS Y 101 GLN ** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.118614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.092654 restraints weight = 23864.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.093520 restraints weight = 14222.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.094864 restraints weight = 9729.070| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.9409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10065 Z= 0.154 Angle : 0.785 12.100 13594 Z= 0.389 Chirality : 0.044 0.209 1555 Planarity : 0.005 0.065 1740 Dihedral : 5.775 88.160 1368 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.92 % Allowed : 30.73 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1235 helix: 1.76 (0.19), residues: 769 sheet: -0.03 (0.58), residues: 88 loop : -1.54 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP Y 98 HIS 0.003 0.001 HIS A 739 PHE 0.036 0.001 PHE Y 184 TYR 0.022 0.001 TYR A 665 ARG 0.020 0.001 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.05433 ( 630) hydrogen bonds : angle 4.19737 ( 1860) covalent geometry : bond 0.00331 (10064) covalent geometry : angle 0.78486 (13594) Misc. bond : bond 0.00001 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3284.42 seconds wall clock time: 58 minutes 17.33 seconds (3497.33 seconds total)