Starting phenix.real_space_refine on Wed Apr 30 22:18:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yas_39106/04_2025/8yas_39106.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yas_39106/04_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_39106/04_2025/8yas_39106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yas_39106/04_2025/8yas_39106.map" model { file = "/net/cci-nas-00/data/ceres_data/8yas_39106/04_2025/8yas_39106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yas_39106/04_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-5669/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: 8.40, per 1000 atoms: 0.85 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: 2.82 Conformation dependent library (CDL) restraints added in 1.3 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: 1.05 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: 4.60 Time building geometry restraints manager: 3.31 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: 94.020 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.090 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.130 ------------------------------------------------------------------------------- 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 : 1.071 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: 0.2587 time to fit residues: 141.5493 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 : 1.142 ------------------------------------------------------------------------------- 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 = 0.142984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.112719 restraints weight = 24401.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.115508 restraints weight = 14778.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.116917 restraints weight = 8933.198| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- 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 : 1.190 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: 0.7507 (pt0) REVERT: A 30 ARG cc_start: 0.1416 (OUTLIER) cc_final: 0.0638 (ppt170) REVERT: A 87 MET cc_start: 0.8485 (mmm) cc_final: 0.8259 (mmp) REVERT: A 305 ASP cc_start: 0.8597 (m-30) cc_final: 0.8036 (m-30) REVERT: A 365 GLU cc_start: 0.7864 (tt0) cc_final: 0.7592 (tm-30) REVERT: A 367 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8393 (tt) REVERT: A 380 GLU cc_start: 0.8511 (mp0) cc_final: 0.8078 (mp0) REVERT: A 411 MET cc_start: 0.7975 (mtp) cc_final: 0.7658 (mtp) REVERT: A 600 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7637 (t0) REVERT: A 725 MET cc_start: 0.8599 (ptm) cc_final: 0.7956 (ptm) REVERT: A 759 MET cc_start: 0.8540 (mmm) cc_final: 0.8217 (mmm) REVERT: A 763 MET cc_start: 0.8463 (tmm) cc_final: 0.7931 (tmm) REVERT: Y 24 MET cc_start: 0.8037 (mmp) cc_final: 0.7248 (mmp) REVERT: Y 164 MET cc_start: 0.8699 (ptp) cc_final: 0.8441 (ptp) REVERT: Y 217 LEU cc_start: 0.9094 (mt) cc_final: 0.8551 (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: 0.8006 (tp40) cc_final: 0.7729 (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: 0.2161 time to fit residues: 87.0284 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 : 1.198 ------------------------------------------------------------------------------- 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: 0.9990 chunk 70 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 114 optimal weight: 0.3980 chunk 56 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 HIS ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.131085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.101094 restraints weight = 24229.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.102984 restraints weight = 14307.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.104476 restraints weight = 9986.042| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 10065 Z= 0.190 Angle : 0.728 8.651 13594 Z= 0.381 Chirality : 0.045 0.168 1555 Planarity : 0.005 0.068 1740 Dihedral : 6.593 108.384 1368 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.81 % Allowed : 21.58 % Favored : 73.61 % 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: -0.12 (0.23), residues: 1235 helix: 0.78 (0.18), residues: 792 sheet: -0.84 (0.57), residues: 79 loop : -1.75 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 652 HIS 0.005 0.001 HIS A 93 PHE 0.029 0.002 PHE E 43 TYR 0.022 0.002 TYR A 385 ARG 0.006 0.001 ARG Y 29 Details of bonding type rmsd hydrogen bonds : bond 0.06151 ( 630) hydrogen bonds : angle 4.62196 ( 1860) covalent geometry : bond 0.00420 (10064) covalent geometry : angle 0.72772 (13594) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7905 (pt0) cc_final: 0.7614 (pt0) REVERT: A 70 ARG cc_start: 0.7423 (mmm160) cc_final: 0.7068 (ttt180) REVERT: A 189 MET cc_start: 0.8266 (ttm) cc_final: 0.7917 (mtp) REVERT: A 213 LEU cc_start: 0.9331 (mp) cc_final: 0.9109 (tp) REVERT: A 305 ASP cc_start: 0.8549 (m-30) cc_final: 0.7819 (m-30) REVERT: A 363 MET cc_start: 0.8840 (ttm) cc_final: 0.8475 (ttm) REVERT: A 365 GLU cc_start: 0.8179 (tt0) cc_final: 0.7877 (tm-30) REVERT: A 411 MET cc_start: 0.8150 (mtp) cc_final: 0.7888 (mtp) REVERT: A 559 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6853 (m-30) REVERT: A 666 LEU cc_start: 0.7837 (tp) cc_final: 0.7490 (tp) REVERT: A 689 MET cc_start: 0.6927 (tpt) cc_final: 0.6648 (tpt) REVERT: A 725 MET cc_start: 0.8510 (ptm) cc_final: 0.8154 (ptm) REVERT: A 759 MET cc_start: 0.8700 (mmm) cc_final: 0.8416 (mmm) REVERT: A 763 MET cc_start: 0.8690 (tmm) cc_final: 0.8169 (tmm) REVERT: Y 164 MET cc_start: 0.8720 (ptp) cc_final: 0.8262 (ptp) REVERT: Y 184 PHE cc_start: 0.9392 (t80) cc_final: 0.9175 (t80) REVERT: Y 217 LEU cc_start: 0.9137 (mt) cc_final: 0.8681 (tp) REVERT: Y 218 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8320 (mm) REVERT: Y 233 TYR cc_start: 0.8467 (t80) cc_final: 0.8039 (t80) REVERT: E 24 LYS cc_start: 0.9333 (mmtt) cc_final: 0.9072 (ttpp) outliers start: 51 outliers final: 30 residues processed: 262 average time/residue: 0.2067 time to fit residues: 79.7207 Evaluate side-chains 242 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 223 ILE 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 448 LEU 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 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: 2.9990 chunk 80 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 117 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 93 HIS A 202 HIS ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 133 ASN ** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.130365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.100315 restraints weight = 24177.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.101686 restraints weight = 14344.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.103179 restraints weight = 9734.484| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10065 Z= 0.171 Angle : 0.697 9.564 13594 Z= 0.363 Chirality : 0.044 0.160 1555 Planarity : 0.005 0.062 1740 Dihedral : 6.291 105.447 1368 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 6.13 % Allowed : 21.11 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1235 helix: 1.15 (0.18), residues: 785 sheet: -0.94 (0.53), residues: 96 loop : -1.66 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 20 HIS 0.005 0.001 HIS A 283 PHE 0.024 0.001 PHE E 7 TYR 0.015 0.001 TYR A 599 ARG 0.006 0.001 ARG A 750 Details of bonding type rmsd hydrogen bonds : bond 0.05816 ( 630) hydrogen bonds : angle 4.43377 ( 1860) covalent geometry : bond 0.00372 (10064) covalent geometry : angle 0.69654 (13594) Misc. bond : bond 0.00010 ( 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 286 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 221 time to evaluate : 1.215 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 42 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6837 (ptpt) REVERT: A 70 ARG cc_start: 0.7795 (mmm160) cc_final: 0.7346 (ttt180) REVERT: A 305 ASP cc_start: 0.8440 (m-30) cc_final: 0.7758 (m-30) REVERT: A 324 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7181 (ttp) REVERT: A 327 ARG cc_start: 0.5827 (mmm160) cc_final: 0.3537 (tpt170) REVERT: A 380 GLU cc_start: 0.8729 (mp0) cc_final: 0.8411 (mp0) REVERT: A 411 MET cc_start: 0.8242 (mtp) cc_final: 0.7956 (mtp) REVERT: A 559 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: A 586 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8167 (mm-30) REVERT: A 600 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7630 (t0) REVERT: A 630 MET cc_start: 0.7981 (mmt) cc_final: 0.7684 (mmt) REVERT: A 684 MET cc_start: 0.7879 (mtt) cc_final: 0.7653 (mtt) REVERT: A 725 MET cc_start: 0.8352 (ptm) cc_final: 0.8147 (ptm) REVERT: A 759 MET cc_start: 0.8718 (mmm) cc_final: 0.8429 (mmm) REVERT: A 763 MET cc_start: 0.8835 (tmm) cc_final: 0.7860 (tmm) REVERT: Y 24 MET cc_start: 0.8103 (mmm) cc_final: 0.7659 (mmm) REVERT: Y 30 ILE cc_start: 0.8920 (tp) cc_final: 0.8667 (pt) REVERT: Y 217 LEU cc_start: 0.9048 (mt) cc_final: 0.8602 (tt) REVERT: Y 233 TYR cc_start: 0.8469 (t80) cc_final: 0.8118 (t80) REVERT: E 9 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8786 (mttt) REVERT: E 13 ARG cc_start: 0.8402 (ttm110) cc_final: 0.8182 (ttp-110) REVERT: E 14 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8693 (mm-30) REVERT: E 17 LYS cc_start: 0.9297 (mtmm) cc_final: 0.8905 (mppt) REVERT: E 23 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7900 (mpt180) REVERT: E 24 LYS cc_start: 0.9336 (mmtt) cc_final: 0.9078 (ttpp) outliers start: 65 outliers final: 31 residues processed: 257 average time/residue: 0.2122 time to fit residues: 77.9819 Evaluate side-chains 239 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 42 LYS 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 131 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 491 THR 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 749 LEU Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Y residue 128 MET Chi-restraints excluded: chain Y residue 156 LEU Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 181 ILE Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 378 ILE Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 23 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN Y 66 ASN 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 = 0.3890 r_free = 0.3890 target = 0.127590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.098087 restraints weight = 24180.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099262 restraints weight = 14857.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.100664 restraints weight = 10280.354| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.6854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10065 Z= 0.158 Angle : 0.675 8.509 13594 Z= 0.352 Chirality : 0.043 0.184 1555 Planarity : 0.004 0.061 1740 Dihedral : 6.027 101.229 1368 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.34 % Allowed : 25.07 % Favored : 70.59 % 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: 0.63 (0.24), residues: 1235 helix: 1.43 (0.18), residues: 784 sheet: -0.67 (0.55), residues: 94 loop : -1.54 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 299 HIS 0.004 0.001 HIS A 283 PHE 0.028 0.001 PHE Y 184 TYR 0.015 0.001 TYR A 743 ARG 0.005 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.05699 ( 630) hydrogen bonds : angle 4.29597 ( 1860) covalent geometry : bond 0.00341 (10064) covalent geometry : angle 0.67488 (13594) Misc. bond : bond 0.00009 ( 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 260 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8278 (pt0) cc_final: 0.8046 (pt0) REVERT: A 146 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 173 THR cc_start: 0.9314 (m) cc_final: 0.8972 (p) REVERT: A 305 ASP cc_start: 0.8384 (m-30) cc_final: 0.7705 (m-30) REVERT: A 324 MET cc_start: 0.7792 (mtp) cc_final: 0.7213 (ttp) REVERT: A 327 ARG cc_start: 0.5913 (mmm160) cc_final: 0.3687 (tpt170) REVERT: A 380 GLU cc_start: 0.8800 (mp0) cc_final: 0.8507 (mp0) REVERT: A 411 MET cc_start: 0.8309 (mtp) cc_final: 0.8009 (mtp) REVERT: A 443 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7651 (tm-30) REVERT: A 586 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8308 (mm-30) REVERT: A 600 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7582 (t0) REVERT: A 630 MET cc_start: 0.8135 (mmt) cc_final: 0.7821 (mmt) REVERT: A 763 MET cc_start: 0.8897 (tmm) cc_final: 0.8357 (tmm) REVERT: Y 24 MET cc_start: 0.8251 (mmm) cc_final: 0.7870 (mmm) REVERT: Y 30 ILE cc_start: 0.8875 (tp) cc_final: 0.8649 (pt) REVERT: Y 164 MET cc_start: 0.8790 (ptp) cc_final: 0.8341 (ptp) REVERT: Y 217 LEU cc_start: 0.9023 (mt) cc_final: 0.8617 (tt) REVERT: Y 218 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8385 (mm) REVERT: Y 233 TYR cc_start: 0.8402 (t80) cc_final: 0.7991 (t80) REVERT: Y 391 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8303 (tt) REVERT: E 9 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8706 (mmtp) REVERT: E 23 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7926 (mpt180) REVERT: E 24 LYS cc_start: 0.9239 (mmtt) cc_final: 0.8981 (ttpp) outliers start: 46 outliers final: 33 residues processed: 239 average time/residue: 0.1973 time to fit residues: 68.5780 Evaluate side-chains 240 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 223 ILE 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 491 THR 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 749 LEU Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain Y residue 36 VAL 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 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 391 LEU Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 23 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.0570 chunk 89 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.126413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.097079 restraints weight = 24189.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.098217 restraints weight = 13858.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.099327 restraints weight = 10356.762| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.7343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10065 Z= 0.154 Angle : 0.683 11.434 13594 Z= 0.350 Chirality : 0.043 0.329 1555 Planarity : 0.004 0.060 1740 Dihedral : 5.920 99.141 1368 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.62 % Allowed : 26.11 % Favored : 69.27 % 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: 1.61 (0.18), residues: 777 sheet: -0.49 (0.59), residues: 83 loop : -1.34 (0.32), residues: 375 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 0.031 0.001 PHE Y 184 TYR 0.012 0.001 TYR A 250 ARG 0.013 0.001 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.05512 ( 630) hydrogen bonds : angle 4.27793 ( 1860) covalent geometry : bond 0.00327 (10064) covalent geometry : angle 0.68293 (13594) Misc. bond : bond 0.00010 ( 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 267 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.9510 (t) cc_final: 0.9155 (m) REVERT: A 146 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7521 (tm-30) REVERT: A 173 THR cc_start: 0.9251 (m) cc_final: 0.8879 (p) REVERT: A 305 ASP cc_start: 0.8341 (m-30) cc_final: 0.7664 (m-30) REVERT: A 324 MET cc_start: 0.7825 (mtp) cc_final: 0.7355 (ttt) REVERT: A 327 ARG cc_start: 0.5830 (mmm160) cc_final: 0.3532 (tpt170) REVERT: A 380 GLU cc_start: 0.8760 (mp0) cc_final: 0.8496 (mp0) REVERT: A 443 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7620 (tm-30) REVERT: A 555 MET cc_start: 0.8510 (mmt) cc_final: 0.7787 (mpp) REVERT: A 561 PHE cc_start: 0.7970 (m-80) cc_final: 0.7555 (m-80) REVERT: A 586 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8333 (mm-30) REVERT: A 600 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7496 (t0) REVERT: A 630 MET cc_start: 0.8348 (mmt) cc_final: 0.7994 (mmt) REVERT: A 632 LYS cc_start: 0.8785 (ptpp) cc_final: 0.8278 (mtmm) REVERT: A 689 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7374 (mmt) REVERT: A 763 MET cc_start: 0.8933 (tmm) cc_final: 0.8388 (tmm) REVERT: Y 8 PHE cc_start: 0.8340 (m-10) cc_final: 0.7806 (m-10) REVERT: Y 24 MET cc_start: 0.8218 (mmm) cc_final: 0.7843 (mmm) REVERT: Y 30 ILE cc_start: 0.8830 (tp) cc_final: 0.8603 (pt) REVERT: Y 164 MET cc_start: 0.8743 (ptp) cc_final: 0.8290 (ptp) REVERT: Y 217 LEU cc_start: 0.9013 (mt) cc_final: 0.8655 (tt) REVERT: Y 218 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8340 (pp) REVERT: Y 233 TYR cc_start: 0.8416 (t80) cc_final: 0.8000 (t80) REVERT: Y 410 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8676 (mm) REVERT: Y 417 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7855 (mt-10) REVERT: E 9 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8633 (mmtp) REVERT: E 23 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7986 (mpt180) REVERT: E 24 LYS cc_start: 0.9224 (mmtt) cc_final: 0.8897 (ttpp) outliers start: 49 outliers final: 27 residues processed: 243 average time/residue: 0.1983 time to fit residues: 69.6831 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 : 1.081 ------------------------------------------------------------------------------- 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 223 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 491 THR 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 689 MET 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 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 370 VAL Chi-restraints excluded: chain Y residue 383 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 410 LEU Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 23 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 117 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 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 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.123644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.095667 restraints weight = 23899.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.096829 restraints weight = 13347.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.097853 restraints weight = 9834.097| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.7696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10065 Z= 0.155 Angle : 0.697 12.264 13594 Z= 0.355 Chirality : 0.044 0.225 1555 Planarity : 0.005 0.057 1740 Dihedral : 5.865 95.836 1368 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.52 % Allowed : 28.37 % 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: 0.91 (0.24), residues: 1235 helix: 1.63 (0.18), residues: 774 sheet: -0.47 (0.59), residues: 83 loop : -1.30 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 299 HIS 0.003 0.001 HIS A 297 PHE 0.037 0.001 PHE Y 184 TYR 0.019 0.001 TYR A 385 ARG 0.013 0.001 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.05524 ( 630) hydrogen bonds : angle 4.28200 ( 1860) covalent geometry : bond 0.00340 (10064) covalent geometry : angle 0.69662 (13594) Misc. bond : bond 0.00008 ( 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 261 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.9468 (t) cc_final: 0.9127 (m) REVERT: A 146 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 173 THR cc_start: 0.9315 (m) cc_final: 0.8930 (p) REVERT: A 305 ASP cc_start: 0.8283 (m-30) cc_final: 0.7608 (m-30) REVERT: A 324 MET cc_start: 0.7746 (mtp) cc_final: 0.7334 (ttt) REVERT: A 327 ARG cc_start: 0.5825 (mmm160) cc_final: 0.3484 (tpt170) REVERT: A 380 GLU cc_start: 0.8749 (mp0) cc_final: 0.8512 (mp0) REVERT: A 443 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7615 (tm-30) REVERT: A 555 MET cc_start: 0.8554 (mmt) cc_final: 0.7959 (mpp) REVERT: A 559 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7389 (m-30) REVERT: A 586 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8365 (mm-30) REVERT: A 600 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7539 (t0) REVERT: A 630 MET cc_start: 0.8604 (mmt) cc_final: 0.8207 (mmt) REVERT: A 666 LEU cc_start: 0.7726 (tp) cc_final: 0.7231 (tt) REVERT: A 689 MET cc_start: 0.8238 (tpp) cc_final: 0.7690 (mmt) REVERT: A 763 MET cc_start: 0.9020 (tmm) cc_final: 0.8465 (tmm) REVERT: A 774 PHE cc_start: 0.6580 (OUTLIER) cc_final: 0.6233 (t80) REVERT: Y 24 MET cc_start: 0.8410 (mmm) cc_final: 0.8071 (mmm) REVERT: Y 30 ILE cc_start: 0.8818 (tp) cc_final: 0.8610 (pt) REVERT: Y 164 MET cc_start: 0.8744 (ptp) cc_final: 0.8287 (ptp) REVERT: Y 217 LEU cc_start: 0.9009 (mt) cc_final: 0.8674 (tt) REVERT: Y 218 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8346 (pp) REVERT: Y 233 TYR cc_start: 0.8448 (t80) cc_final: 0.7992 (t80) REVERT: Y 391 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8336 (tt) REVERT: Y 417 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7843 (mt-10) REVERT: E 23 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7974 (mpt180) REVERT: E 24 LYS cc_start: 0.9218 (mmtt) cc_final: 0.8949 (ttpp) outliers start: 48 outliers final: 33 residues processed: 238 average time/residue: 0.1936 time to fit residues: 67.0448 Evaluate side-chains 240 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 333 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 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 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 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 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: 0.9990 chunk 108 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 65 optimal weight: 0.0370 chunk 32 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS ** Y 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.123434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.094659 restraints weight = 24424.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.095608 restraints weight = 13981.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.096590 restraints weight = 10386.508| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.8081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10065 Z= 0.151 Angle : 0.721 13.108 13594 Z= 0.359 Chirality : 0.045 0.275 1555 Planarity : 0.004 0.056 1740 Dihedral : 5.801 91.959 1368 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.05 % Allowed : 28.28 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1235 helix: 1.64 (0.18), residues: 774 sheet: -0.45 (0.56), residues: 93 loop : -1.30 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 299 HIS 0.003 0.001 HIS A 739 PHE 0.032 0.001 PHE E 39 TYR 0.021 0.001 TYR A 385 ARG 0.009 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.05474 ( 630) hydrogen bonds : angle 4.26041 ( 1860) covalent geometry : bond 0.00330 (10064) covalent geometry : angle 0.72118 (13594) Misc. bond : bond 0.00027 ( 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 257 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 214 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7939 (mmm) cc_final: 0.7665 (mmm) REVERT: A 127 VAL cc_start: 0.9471 (t) cc_final: 0.9131 (m) REVERT: A 173 THR cc_start: 0.9295 (m) cc_final: 0.8920 (p) REVERT: A 305 ASP cc_start: 0.8304 (m-30) cc_final: 0.7606 (m-30) REVERT: A 324 MET cc_start: 0.7725 (mtp) cc_final: 0.7330 (ttt) REVERT: A 327 ARG cc_start: 0.5786 (mmm160) cc_final: 0.3728 (tpt170) REVERT: A 380 GLU cc_start: 0.8710 (mp0) cc_final: 0.8403 (mp0) REVERT: A 443 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7587 (tm-30) REVERT: A 546 MET cc_start: 0.8350 (ttm) cc_final: 0.8046 (ttm) REVERT: A 555 MET cc_start: 0.8604 (mmt) cc_final: 0.7974 (mpp) REVERT: A 586 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8414 (mm-30) REVERT: A 600 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7509 (t0) REVERT: A 630 MET cc_start: 0.8499 (mmt) cc_final: 0.8127 (mmt) REVERT: A 666 LEU cc_start: 0.7768 (tp) cc_final: 0.7375 (tp) REVERT: A 689 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7840 (mmt) REVERT: A 763 MET cc_start: 0.8941 (tmm) cc_final: 0.8370 (tmm) REVERT: A 769 ASP cc_start: 0.9090 (t0) cc_final: 0.8839 (t0) REVERT: A 774 PHE cc_start: 0.6561 (OUTLIER) cc_final: 0.6194 (t80) REVERT: Y 24 MET cc_start: 0.8389 (mmm) cc_final: 0.8043 (mmm) REVERT: Y 164 MET cc_start: 0.8627 (ptp) cc_final: 0.8195 (ptp) REVERT: Y 217 LEU cc_start: 0.9017 (mt) cc_final: 0.8630 (tt) REVERT: Y 218 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8218 (mm) REVERT: Y 233 TYR cc_start: 0.8380 (t80) cc_final: 0.7937 (t80) REVERT: Y 391 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8354 (tt) REVERT: Y 417 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7846 (mt-10) REVERT: E 23 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7988 (mpt180) REVERT: E 24 LYS cc_start: 0.9216 (mmtt) cc_final: 0.8875 (ttpp) outliers start: 43 outliers final: 33 residues processed: 234 average time/residue: 0.2271 time to fit residues: 77.0705 Evaluate side-chains 239 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 1.661 ------------------------------------------------------------------------------- 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 333 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 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 623 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 774 PHE Chi-restraints excluded: chain Y residue 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 278 VAL Chi-restraints excluded: chain Y residue 370 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 400 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 53 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 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 198 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS ** 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 = 0.3798 r_free = 0.3798 target = 0.120881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.093322 restraints weight = 23691.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.094291 restraints weight = 13584.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.095398 restraints weight = 9883.488| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.8376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10065 Z= 0.160 Angle : 0.726 11.041 13594 Z= 0.363 Chirality : 0.044 0.202 1555 Planarity : 0.004 0.057 1740 Dihedral : 5.785 88.413 1368 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.68 % Allowed : 28.84 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.96 (0.24), residues: 1235 helix: 1.68 (0.18), residues: 772 sheet: -0.51 (0.55), residues: 93 loop : -1.29 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 299 HIS 0.014 0.001 HIS A 739 PHE 0.030 0.002 PHE E 43 TYR 0.024 0.001 TYR A 665 ARG 0.009 0.001 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.05575 ( 630) hydrogen bonds : angle 4.26324 ( 1860) covalent geometry : bond 0.00350 (10064) covalent geometry : angle 0.72606 (13594) Misc. bond : bond 0.00015 ( 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 240 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.9443 (t) cc_final: 0.9091 (m) REVERT: A 173 THR cc_start: 0.9326 (m) cc_final: 0.8934 (p) REVERT: A 183 ASP cc_start: 0.8808 (t70) cc_final: 0.8456 (t70) REVERT: A 305 ASP cc_start: 0.8305 (m-30) cc_final: 0.7615 (m-30) REVERT: A 324 MET cc_start: 0.7767 (mtp) cc_final: 0.7374 (ttt) REVERT: A 327 ARG cc_start: 0.5816 (mmm160) cc_final: 0.3771 (tpt170) REVERT: A 380 GLU cc_start: 0.8744 (mp0) cc_final: 0.8309 (mp0) REVERT: A 443 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7572 (tm-30) REVERT: A 586 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8437 (mm-30) REVERT: A 600 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7505 (t0) REVERT: A 630 MET cc_start: 0.8684 (mmt) cc_final: 0.8350 (mmt) REVERT: A 632 LYS cc_start: 0.8815 (pttm) cc_final: 0.8504 (mtmm) REVERT: A 666 LEU cc_start: 0.7782 (tp) cc_final: 0.7400 (tp) REVERT: A 685 LEU cc_start: 0.8584 (mm) cc_final: 0.8158 (pp) REVERT: A 759 MET cc_start: 0.8843 (mtt) cc_final: 0.8523 (mmm) REVERT: A 763 MET cc_start: 0.8795 (tmm) cc_final: 0.8221 (tmm) REVERT: A 769 ASP cc_start: 0.9069 (t0) cc_final: 0.8806 (t0) REVERT: A 774 PHE cc_start: 0.6628 (OUTLIER) cc_final: 0.6304 (t80) REVERT: Y 24 MET cc_start: 0.8426 (mmm) cc_final: 0.8095 (mmm) REVERT: Y 164 MET cc_start: 0.8590 (ptp) cc_final: 0.8190 (ptp) REVERT: Y 217 LEU cc_start: 0.9001 (mt) cc_final: 0.8652 (tt) REVERT: Y 218 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8219 (mm) REVERT: Y 233 TYR cc_start: 0.8408 (t80) cc_final: 0.7934 (t80) REVERT: Y 391 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8360 (tt) REVERT: Y 417 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7851 (mt-10) REVERT: E 23 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8012 (mpt180) REVERT: E 24 LYS cc_start: 0.9202 (mmtt) cc_final: 0.8906 (ttpp) outliers start: 39 outliers final: 29 residues processed: 219 average time/residue: 0.2295 time to fit residues: 74.2064 Evaluate side-chains 225 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 363 MET Chi-restraints excluded: chain A residue 389 VAL 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 689 MET Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 774 PHE Chi-restraints excluded: chain Y residue 128 MET Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 218 LEU Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 370 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 400 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 19 optimal weight: 0.5980 chunk 46 optimal weight: 0.0270 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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** Y 308 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.121358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.094430 restraints weight = 23543.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.095023 restraints weight = 13120.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.096206 restraints weight = 9753.130| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.8555 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= 0.148 Angle : 0.751 13.246 13594 Z= 0.369 Chirality : 0.044 0.284 1555 Planarity : 0.004 0.055 1740 Dihedral : 5.733 88.155 1368 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.83 % Allowed : 29.59 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1235 helix: 1.71 (0.18), residues: 767 sheet: -0.35 (0.56), residues: 93 loop : -1.29 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP Y 98 HIS 0.004 0.001 HIS A 739 PHE 0.037 0.001 PHE E 39 TYR 0.034 0.001 TYR A 743 ARG 0.009 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.05356 ( 630) hydrogen bonds : angle 4.22253 ( 1860) covalent geometry : bond 0.00322 (10064) covalent geometry : angle 0.75104 (13594) Misc. bond : bond 0.00014 ( 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 235 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.9421 (t) cc_final: 0.9068 (m) REVERT: A 173 THR cc_start: 0.9332 (m) cc_final: 0.8954 (p) REVERT: A 183 ASP cc_start: 0.8811 (t70) cc_final: 0.8420 (t70) REVERT: A 305 ASP cc_start: 0.8227 (m-30) cc_final: 0.7550 (m-30) REVERT: A 324 MET cc_start: 0.7773 (mtp) cc_final: 0.7323 (ttt) REVERT: A 327 ARG cc_start: 0.5779 (mmm160) cc_final: 0.3605 (tpt170) REVERT: A 380 GLU cc_start: 0.8716 (mp0) cc_final: 0.8293 (mp0) REVERT: A 443 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 541 MET cc_start: 0.8643 (tpp) cc_final: 0.8359 (tpp) REVERT: A 586 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8439 (mm-30) REVERT: A 600 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7454 (t0) REVERT: A 630 MET cc_start: 0.8623 (mmt) cc_final: 0.8301 (mmt) REVERT: A 685 LEU cc_start: 0.8625 (mm) cc_final: 0.8214 (pp) REVERT: A 689 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7980 (tpp) REVERT: A 763 MET cc_start: 0.8839 (tmm) cc_final: 0.8246 (tmm) REVERT: A 774 PHE cc_start: 0.6521 (OUTLIER) cc_final: 0.6206 (t80) REVERT: A 776 MET cc_start: 0.8180 (tpp) cc_final: 0.7840 (tpp) REVERT: Y 24 MET cc_start: 0.8447 (mmm) cc_final: 0.8101 (mmm) REVERT: Y 217 LEU cc_start: 0.8973 (mt) cc_final: 0.8608 (tt) REVERT: Y 218 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8271 (mm) REVERT: Y 233 TYR cc_start: 0.8387 (t80) cc_final: 0.7897 (t80) REVERT: Y 391 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8338 (tt) REVERT: Y 417 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7857 (mt-10) REVERT: E 24 LYS cc_start: 0.9185 (mmtt) cc_final: 0.8962 (ttpp) REVERT: E 25 GLU cc_start: 0.9025 (pm20) cc_final: 0.8637 (pm20) outliers start: 30 outliers final: 24 residues processed: 220 average time/residue: 0.2125 time to fit residues: 68.3600 Evaluate side-chains 223 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 363 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 689 MET 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 128 MET 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 385 PHE Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 400 THR Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain E residue 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 0.0060 chunk 100 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 117 optimal weight: 0.0170 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.5434 ------------------------------------------------------------------------------- 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 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 = 0.3808 r_free = 0.3808 target = 0.121610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.093735 restraints weight = 24452.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.094409 restraints weight = 14077.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.095790 restraints weight = 10160.700| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.8755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10065 Z= 0.149 Angle : 0.743 12.951 13594 Z= 0.368 Chirality : 0.043 0.177 1555 Planarity : 0.004 0.057 1740 Dihedral : 5.704 91.331 1368 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.83 % Allowed : 29.69 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.24), residues: 1235 helix: 1.73 (0.18), residues: 768 sheet: -0.31 (0.56), residues: 93 loop : -1.28 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 98 HIS 0.003 0.001 HIS A 739 PHE 0.029 0.001 PHE E 43 TYR 0.033 0.001 TYR A 743 ARG 0.010 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.05298 ( 630) hydrogen bonds : angle 4.21493 ( 1860) covalent geometry : bond 0.00327 (10064) covalent geometry : angle 0.74259 (13594) Misc. bond : bond 0.00015 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3620.77 seconds wall clock time: 64 minutes 42.03 seconds (3882.03 seconds total)