Starting phenix.real_space_refine on Thu Jul 2 08:38:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m34_63598/07_2026/9m34_63598.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m34_63598/07_2026/9m34_63598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m34_63598/07_2026/9m34_63598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m34_63598/07_2026/9m34_63598.map" model { file = "/net/cci-nas-00/data/ceres_data/9m34_63598/07_2026/9m34_63598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m34_63598/07_2026/9m34_63598.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 6 Type Number sf(0) Gaussians P 67 5.49 5 Mg 1 5.21 5 S 21 5.16 5 C 4673 2.51 5 N 1309 2.21 5 O 1610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7681 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6236 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 750, 6226 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 19, 'TRANS': 730} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 750, 6226 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 19, 'TRANS': 730} Chain breaks: 3 bond proxies already assigned to first conformer: 6351 Chain: "B" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1042 Classifications: {'RNA': 49} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p_pur': 23, 'rna3p_pyr': 18} Link IDs: {'rna2p': 8, 'rna3p': 40} Chain: "C" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 402 Classifications: {'RNA': 19} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 575 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 575 " occ=0.50 Time building chain proxies: 2.83, per 1000 atoms: 0.37 Number of scatterers: 7681 At special positions: 0 Unit cell: (93.195, 95.76, 110.295, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 67 15.00 Mg 1 11.99 O 1610 8.00 N 1309 7.00 C 4673 6.00 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=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 419.3 milliseconds 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1456 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 1 sheets defined 74.5% alpha, 0.3% beta 11 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 113 through 143 removed outlier: 4.456A pdb=" N GLN A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.984A pdb=" N LEU A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG A 170 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 186 through 191 removed outlier: 3.510A pdb=" N TYR A 190 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 191 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 222 Processing helix chain 'A' and resid 247 through 273 removed outlier: 3.740A pdb=" N LYS A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 284 removed outlier: 4.124A pdb=" N ILE A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 298 removed outlier: 3.516A pdb=" N VAL A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 322 through 329 removed outlier: 4.153A pdb=" N SER A 327 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE A 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.828A pdb=" N SER A 335 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 356 removed outlier: 5.168A pdb=" N LEU A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 Processing helix chain 'A' and resid 371 through 399 removed outlier: 6.557A pdb=" N ALA A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.625A pdb=" N LYS A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 removed outlier: 3.865A pdb=" N GLU A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 473 Processing helix chain 'A' and resid 480 through 485 removed outlier: 4.477A pdb=" N ASP A 485 " --> pdb=" O PRO A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 504 Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 582 through 590 removed outlier: 4.158A pdb=" N THR A 586 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ARG A 587 " --> pdb=" O HIS A 584 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR A 588 " --> pdb=" O LYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 removed outlier: 3.576A pdb=" N VAL A 596 " --> pdb=" O ASN A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.695A pdb=" N ILE A 608 " --> pdb=" O PRO A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 639 removed outlier: 3.804A pdb=" N SER A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 648 removed outlier: 3.938A pdb=" N ASP A 647 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL A 648 " --> pdb=" O PHE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 712 removed outlier: 3.510A pdb=" N TYR A 679 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 680 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 686 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 709 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 710 " --> pdb=" O ARG A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 733 removed outlier: 3.640A pdb=" N THR A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 733 " --> pdb=" O THR A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 751 through 761 removed outlier: 3.852A pdb=" N GLN A 761 " --> pdb=" O LYS A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 778 Processing helix chain 'A' and resid 778 through 783 removed outlier: 4.054A pdb=" N ARG A 782 " --> pdb=" O ILE A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 813 Processing helix chain 'A' and resid 822 through 834 removed outlier: 3.680A pdb=" N TYR A 826 " --> pdb=" O LYS A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 844 Processing helix chain 'A' and resid 845 through 849 Processing helix chain 'A' and resid 851 through 860 Processing helix chain 'A' and resid 860 through 865 removed outlier: 4.214A pdb=" N ASP A 865 " --> pdb=" O ASN A 861 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 197 353 hydrogen bonds defined for protein. 1015 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2141 1.34 - 1.46: 1730 1.46 - 1.57: 3951 1.57 - 1.69: 133 1.69 - 1.81: 34 Bond restraints: 7989 Sorted by residual: bond pdb=" CG PRO A 285 " pdb=" CD PRO A 285 " ideal model delta sigma weight residual 1.503 1.408 0.095 3.40e-02 8.65e+02 7.76e+00 bond pdb=" CB PRO A 285 " pdb=" CG PRO A 285 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.45e+00 bond pdb=" CB PRO A 622 " pdb=" CG PRO A 622 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.30e+00 bond pdb=" CA VAL A 590 " pdb=" C VAL A 590 " ideal model delta sigma weight residual 1.520 1.534 -0.014 1.23e-02 6.61e+03 1.29e+00 bond pdb=" CB LYS A 313 " pdb=" CG LYS A 313 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 ... (remaining 7984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 10972 1.92 - 3.84: 120 3.84 - 5.76: 14 5.76 - 7.68: 2 7.68 - 9.60: 4 Bond angle restraints: 11112 Sorted by residual: angle pdb=" N PRO A 285 " pdb=" CD PRO A 285 " pdb=" CG PRO A 285 " ideal model delta sigma weight residual 103.20 94.39 8.81 1.50e+00 4.44e-01 3.45e+01 angle pdb=" CA PRO A 285 " pdb=" N PRO A 285 " pdb=" CD PRO A 285 " ideal model delta sigma weight residual 112.00 103.79 8.21 1.40e+00 5.10e-01 3.44e+01 angle pdb=" N VAL A 568 " pdb=" CA VAL A 568 " pdb=" C VAL A 568 " ideal model delta sigma weight residual 112.12 108.27 3.85 8.40e-01 1.42e+00 2.11e+01 angle pdb=" N VAL A 275 " pdb=" CA VAL A 275 " pdb=" C VAL A 275 " ideal model delta sigma weight residual 111.90 108.93 2.97 8.10e-01 1.52e+00 1.35e+01 angle pdb=" N ILE A 788 " pdb=" CA ILE A 788 " pdb=" C ILE A 788 " ideal model delta sigma weight residual 112.83 109.47 3.36 9.90e-01 1.02e+00 1.15e+01 ... (remaining 11107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.20: 4213 18.20 - 36.40: 456 36.40 - 54.60: 111 54.60 - 72.80: 60 72.80 - 91.00: 32 Dihedral angle restraints: 4872 sinusoidal: 2621 harmonic: 2251 Sorted by residual: dihedral pdb=" CA LYS A 303 " pdb=" C LYS A 303 " pdb=" N SER A 304 " pdb=" CA SER A 304 " ideal model delta harmonic sigma weight residual 180.00 155.43 24.57 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA LEU A 325 " pdb=" C LEU A 325 " pdb=" N LYS A 326 " pdb=" CA LYS A 326 " ideal model delta harmonic sigma weight residual 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA LYS A 302 " pdb=" C LYS A 302 " pdb=" N LYS A 303 " pdb=" CA LYS A 303 " ideal model delta harmonic sigma weight residual -180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 4869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 900 0.030 - 0.059: 267 0.059 - 0.089: 80 0.089 - 0.119: 30 0.119 - 0.148: 6 Chirality restraints: 1283 Sorted by residual: chirality pdb=" CB ILE A 603 " pdb=" CA ILE A 603 " pdb=" CG1 ILE A 603 " pdb=" CG2 ILE A 603 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE A 603 " pdb=" N ILE A 603 " pdb=" C ILE A 603 " pdb=" CB ILE A 603 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA PHE A 701 " pdb=" N PHE A 701 " pdb=" C PHE A 701 " pdb=" CB PHE A 701 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1280 not shown) Planarity restraints: 1157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 621 " -0.071 5.00e-02 4.00e+02 1.06e-01 1.80e+01 pdb=" N PRO A 622 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO A 622 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 622 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 284 " 0.055 5.00e-02 4.00e+02 7.90e-02 9.97e+00 pdb=" N PRO A 285 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 480 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO A 481 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 481 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 481 " -0.030 5.00e-02 4.00e+02 ... (remaining 1154 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 123 2.66 - 3.22: 7073 3.22 - 3.78: 11930 3.78 - 4.34: 15851 4.34 - 4.90: 24658 Nonbonded interactions: 59635 Sorted by model distance: nonbonded pdb=" OH TYR A 190 " pdb=" OD2 ASP A 522 " model vdw 2.101 3.040 nonbonded pdb=" O LEU A 270 " pdb=" OG1 THR A 274 " model vdw 2.138 3.040 nonbonded pdb=" NH2 ARG A 294 " pdb=" OD1 ASP A 422 " model vdw 2.164 3.120 nonbonded pdb=" N HIS A 795 " pdb=" OE2 GLU A 799 " model vdw 2.250 3.120 nonbonded pdb=" O ASN A 582 " pdb=" OG1 THR A 586 " model vdw 2.263 3.040 ... (remaining 59630 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=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.940 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 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 : 0.003 0.095 7989 Z= 0.142 Angle : 0.549 9.599 11112 Z= 0.332 Chirality : 0.034 0.148 1283 Planarity : 0.005 0.106 1157 Dihedral : 17.668 91.000 3416 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.15 % Allowed : 0.29 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.31), residues: 745 helix: 1.03 (0.24), residues: 485 sheet: None (None), residues: 0 loop : -1.52 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 696 TYR 0.016 0.001 TYR A 296 PHE 0.023 0.001 PHE A 701 TRP 0.019 0.002 TRP A 258 HIS 0.006 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 7989) covalent geometry : angle 0.54891 / 0.33 (11112) hydrogen bonds : bond 0.20725 / 13.77 ( 378) hydrogen bonds : angle 5.98426 / 4.17 ( 1065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.246 Fit side-chains REVERT: A 102 MET cc_start: 0.6906 (ttt) cc_final: 0.6674 (ttt) REVERT: A 122 LEU cc_start: 0.7926 (mm) cc_final: 0.7639 (mt) REVERT: A 140 ASP cc_start: 0.7114 (t70) cc_final: 0.6835 (t0) REVERT: A 186 LYS cc_start: 0.8319 (tttt) cc_final: 0.8062 (ptmt) REVERT: A 201 ARG cc_start: 0.7680 (mmm-85) cc_final: 0.7248 (ttm170) REVERT: A 316 ARG cc_start: 0.7439 (ptm160) cc_final: 0.6975 (ptt180) REVERT: A 319 MET cc_start: 0.7892 (mtm) cc_final: 0.7571 (mtm) REVERT: A 381 LYS cc_start: 0.8822 (pttm) cc_final: 0.8485 (pttm) REVERT: A 493 ARG cc_start: 0.6799 (ttm-80) cc_final: 0.6589 (mtt-85) REVERT: A 522 ASP cc_start: 0.7312 (m-30) cc_final: 0.6975 (m-30) REVERT: A 811 LYS cc_start: 0.8065 (tptp) cc_final: 0.7581 (tptp) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.0977 time to fit residues: 17.2773 Evaluate side-chains 124 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.0040 overall best weight: 0.3170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 458 ASN A 491 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.201206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.148576 restraints weight = 25173.702| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 4.34 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3845 r_free = 0.3845 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3840 r_free = 0.3840 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (20 function evaluations) r_final: 0.3840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7989 Z= 0.153 Angle : 0.603 9.718 11112 Z= 0.337 Chirality : 0.038 0.175 1283 Planarity : 0.005 0.072 1157 Dihedral : 17.541 90.945 1855 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.44 % Allowed : 7.84 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.31), residues: 745 helix: 1.05 (0.23), residues: 495 sheet: None (None), residues: 0 loop : -1.53 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 294 TYR 0.025 0.002 TYR A 341 PHE 0.027 0.002 PHE A 344 TRP 0.015 0.002 TRP A 258 HIS 0.003 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 ( 7989) covalent geometry : angle 0.60287 / 0.34 (11112) hydrogen bonds : bond 0.07840 / 5.86 ( 378) hydrogen bonds : angle 4.26296 / 2.93 ( 1065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 0.240 Fit side-chains REVERT: A 102 MET cc_start: 0.7053 (ttt) cc_final: 0.6818 (ttt) REVERT: A 122 LEU cc_start: 0.7816 (mm) cc_final: 0.7586 (mt) REVERT: A 123 ASP cc_start: 0.7445 (t70) cc_final: 0.7105 (t0) REVERT: A 140 ASP cc_start: 0.7237 (t70) cc_final: 0.6910 (t0) REVERT: A 201 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.7145 (ttm170) REVERT: A 242 LEU cc_start: 0.8123 (mt) cc_final: 0.7888 (mp) REVERT: A 300 LEU cc_start: 0.7689 (pp) cc_final: 0.7389 (pt) REVERT: A 316 ARG cc_start: 0.7540 (ptm160) cc_final: 0.7141 (ptt180) REVERT: A 319 MET cc_start: 0.7584 (mtm) cc_final: 0.7306 (mtm) REVERT: A 381 LYS cc_start: 0.8835 (pttm) cc_final: 0.8488 (pttm) REVERT: A 396 LYS cc_start: 0.8565 (tttt) cc_final: 0.7910 (tptp) REVERT: A 493 ARG cc_start: 0.6977 (ttm-80) cc_final: 0.6690 (mtt-85) REVERT: A 522 ASP cc_start: 0.7631 (m-30) cc_final: 0.7331 (m-30) REVERT: A 839 ASP cc_start: 0.7892 (m-30) cc_final: 0.7624 (m-30) REVERT: A 842 LYS cc_start: 0.8072 (mttp) cc_final: 0.7843 (ttmm) REVERT: A 850 TYR cc_start: 0.7532 (p90) cc_final: 0.6961 (p90) outliers start: 3 outliers final: 1 residues processed: 142 average time/residue: 0.1035 time to fit residues: 18.8862 Evaluate side-chains 126 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 HIS A 491 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN ** A 820 GLN ** 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 = 0.4483 r_free = 0.4483 target = 0.198724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.146423 restraints weight = 26534.250| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 4.29 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3824 r_free = 0.3824 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3824 r_free = 0.3824 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7989 Z= 0.163 Angle : 0.571 9.586 11112 Z= 0.322 Chirality : 0.039 0.180 1283 Planarity : 0.005 0.062 1157 Dihedral : 17.582 88.345 1855 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.29 % Allowed : 10.30 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.31), residues: 745 helix: 0.94 (0.23), residues: 495 sheet: None (None), residues: 0 loop : -1.42 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 543 TYR 0.022 0.002 TYR A 351 PHE 0.028 0.002 PHE A 269 TRP 0.018 0.002 TRP A 258 HIS 0.005 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 7989) covalent geometry : angle 0.57051 / 0.32 (11112) hydrogen bonds : bond 0.07709 / 5.74 ( 378) hydrogen bonds : angle 4.26330 / 2.93 ( 1065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7151 (ttt) cc_final: 0.6928 (ttt) REVERT: A 122 LEU cc_start: 0.7908 (mm) cc_final: 0.7660 (mt) REVERT: A 140 ASP cc_start: 0.7343 (t70) cc_final: 0.7047 (t0) REVERT: A 201 ARG cc_start: 0.7655 (mmm-85) cc_final: 0.7059 (ttm170) REVERT: A 242 LEU cc_start: 0.8168 (mt) cc_final: 0.7932 (mp) REVERT: A 300 LEU cc_start: 0.7683 (pp) cc_final: 0.7412 (pt) REVERT: A 313 LYS cc_start: 0.8162 (tppt) cc_final: 0.7419 (tppt) REVERT: A 316 ARG cc_start: 0.7672 (ptm160) cc_final: 0.7186 (ttt180) REVERT: A 319 MET cc_start: 0.7704 (mtm) cc_final: 0.7427 (mtm) REVERT: A 396 LYS cc_start: 0.8198 (tttt) cc_final: 0.7883 (tptp) REVERT: A 493 ARG cc_start: 0.7021 (ttm-80) cc_final: 0.6702 (mtt-85) REVERT: A 522 ASP cc_start: 0.7607 (m-30) cc_final: 0.7279 (m-30) REVERT: A 850 TYR cc_start: 0.7646 (p90) cc_final: 0.7069 (p90) outliers start: 2 outliers final: 1 residues processed: 133 average time/residue: 0.1078 time to fit residues: 18.1625 Evaluate side-chains 131 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 ASN A 458 ASN A 491 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 ASN ** A 820 GLN ** 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 = 0.4471 r_free = 0.4471 target = 0.196054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.143455 restraints weight = 30776.793| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 4.86 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7989 Z= 0.182 Angle : 0.571 10.225 11112 Z= 0.322 Chirality : 0.039 0.181 1283 Planarity : 0.005 0.055 1157 Dihedral : 17.587 86.366 1855 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.31 % Allowed : 10.89 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.31), residues: 745 helix: 0.93 (0.24), residues: 497 sheet: None (None), residues: 0 loop : -1.32 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 202 TYR 0.018 0.002 TYR A 341 PHE 0.024 0.002 PHE A 269 TRP 0.020 0.002 TRP A 258 HIS 0.029 0.002 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 7989) covalent geometry : angle 0.57139 / 0.32 (11112) hydrogen bonds : bond 0.07471 / 5.47 ( 378) hydrogen bonds : angle 4.26069 / 2.91 ( 1065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7356 (t70) cc_final: 0.7061 (t0) REVERT: A 201 ARG cc_start: 0.7611 (mmm-85) cc_final: 0.7310 (ttm170) REVERT: A 242 LEU cc_start: 0.8184 (mt) cc_final: 0.7941 (mp) REVERT: A 243 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7270 (mm-30) REVERT: A 313 LYS cc_start: 0.8243 (tppt) cc_final: 0.7646 (tppt) REVERT: A 316 ARG cc_start: 0.7645 (ptm160) cc_final: 0.7090 (ttt180) REVERT: A 317 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7557 (mm-30) REVERT: A 319 MET cc_start: 0.7779 (mtm) cc_final: 0.7536 (mtm) REVERT: A 396 LYS cc_start: 0.8241 (tttt) cc_final: 0.7899 (tptp) REVERT: A 493 ARG cc_start: 0.7054 (ttm-80) cc_final: 0.6720 (mtt-85) REVERT: A 522 ASP cc_start: 0.7607 (m-30) cc_final: 0.7339 (m-30) REVERT: A 612 PHE cc_start: 0.8000 (t80) cc_final: 0.7758 (t80) REVERT: A 850 TYR cc_start: 0.7643 (p90) cc_final: 0.7093 (p90) outliers start: 9 outliers final: 7 residues processed: 136 average time/residue: 0.1180 time to fit residues: 20.4606 Evaluate side-chains 135 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 759 ASN Chi-restraints excluded: chain A residue 780 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 38 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 HIS A 491 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN A 759 ASN ** A 820 GLN ** 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 = 0.4476 r_free = 0.4476 target = 0.197883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.145372 restraints weight = 24845.715| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 4.28 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3808 r_free = 0.3808 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3808 r_free = 0.3808 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7989 Z= 0.149 Angle : 0.542 6.441 11112 Z= 0.308 Chirality : 0.037 0.184 1283 Planarity : 0.005 0.054 1157 Dihedral : 17.566 85.139 1855 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.31 % Allowed : 12.34 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.31), residues: 745 helix: 0.94 (0.24), residues: 497 sheet: None (None), residues: 0 loop : -1.29 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 561 TYR 0.014 0.001 TYR A 351 PHE 0.024 0.002 PHE A 269 TRP 0.018 0.002 TRP A 258 HIS 0.004 0.001 HIS A 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 7989) covalent geometry : angle 0.54210 / 0.31 (11112) hydrogen bonds : bond 0.07060 / 5.16 ( 378) hydrogen bonds : angle 4.20957 / 2.87 ( 1065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7807 (tttm) cc_final: 0.7261 (ttmm) REVERT: A 140 ASP cc_start: 0.7346 (t70) cc_final: 0.7057 (t0) REVERT: A 201 ARG cc_start: 0.7560 (mmm-85) cc_final: 0.7296 (ttm170) REVERT: A 242 LEU cc_start: 0.8164 (mt) cc_final: 0.7897 (mp) REVERT: A 243 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7298 (mm-30) REVERT: A 313 LYS cc_start: 0.8252 (tppt) cc_final: 0.7858 (tppt) REVERT: A 316 ARG cc_start: 0.7694 (ptm160) cc_final: 0.7274 (ptt90) REVERT: A 319 MET cc_start: 0.7753 (mtm) cc_final: 0.7493 (mtm) REVERT: A 396 LYS cc_start: 0.8184 (tttt) cc_final: 0.7889 (tptp) REVERT: A 493 ARG cc_start: 0.6919 (ttm-80) cc_final: 0.6635 (mtt-85) REVERT: A 522 ASP cc_start: 0.7577 (m-30) cc_final: 0.7279 (m-30) REVERT: A 612 PHE cc_start: 0.8064 (t80) cc_final: 0.7808 (t80) REVERT: A 629 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7726 (mm-40) REVERT: A 842 LYS cc_start: 0.8361 (ttmt) cc_final: 0.7907 (ttmm) REVERT: A 850 TYR cc_start: 0.7727 (p90) cc_final: 0.7090 (p90) outliers start: 9 outliers final: 7 residues processed: 134 average time/residue: 0.1142 time to fit residues: 19.4147 Evaluate side-chains 136 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 759 ASN Chi-restraints excluded: chain A residue 780 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 50.0000 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 HIS A 491 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN ** A 820 GLN ** 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 = 0.4469 r_free = 0.4469 target = 0.195789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.143857 restraints weight = 26529.372| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 4.29 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7989 Z= 0.165 Angle : 0.560 7.772 11112 Z= 0.316 Chirality : 0.037 0.187 1283 Planarity : 0.005 0.051 1157 Dihedral : 17.570 84.158 1855 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.45 % Allowed : 12.77 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.31), residues: 745 helix: 0.88 (0.24), residues: 497 sheet: None (None), residues: 0 loop : -1.27 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 202 TYR 0.014 0.002 TYR A 341 PHE 0.024 0.002 PHE A 269 TRP 0.018 0.002 TRP A 258 HIS 0.007 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 7989) covalent geometry : angle 0.55967 / 0.32 (11112) hydrogen bonds : bond 0.06978 / 5.06 ( 378) hydrogen bonds : angle 4.30222 / 2.93 ( 1065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7784 (tttm) cc_final: 0.7215 (ttmm) REVERT: A 140 ASP cc_start: 0.7306 (t70) cc_final: 0.7021 (t0) REVERT: A 201 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.7339 (ttm170) REVERT: A 242 LEU cc_start: 0.8208 (mt) cc_final: 0.7969 (mp) REVERT: A 243 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7172 (mm-30) REVERT: A 313 LYS cc_start: 0.8309 (tppt) cc_final: 0.7867 (tppt) REVERT: A 319 MET cc_start: 0.7711 (mtm) cc_final: 0.7473 (mtm) REVERT: A 396 LYS cc_start: 0.8185 (tttt) cc_final: 0.7877 (tptp) REVERT: A 493 ARG cc_start: 0.6968 (ttm-80) cc_final: 0.6677 (mtt-85) REVERT: A 522 ASP cc_start: 0.7597 (m-30) cc_final: 0.7304 (m-30) REVERT: A 597 LYS cc_start: 0.7640 (mttp) cc_final: 0.7279 (mmtt) REVERT: A 612 PHE cc_start: 0.8084 (t80) cc_final: 0.7846 (t80) REVERT: A 629 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7781 (mm-40) REVERT: A 842 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7888 (ttmm) REVERT: A 850 TYR cc_start: 0.7694 (p90) cc_final: 0.7138 (p90) outliers start: 10 outliers final: 7 residues processed: 133 average time/residue: 0.1036 time to fit residues: 17.6088 Evaluate side-chains 135 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 780 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 32 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 ASN ** A 820 GLN ** 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 = 0.4465 r_free = 0.4465 target = 0.195362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.141314 restraints weight = 29644.594| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 4.80 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7989 Z= 0.167 Angle : 0.561 8.065 11112 Z= 0.316 Chirality : 0.038 0.187 1283 Planarity : 0.005 0.050 1157 Dihedral : 17.579 83.353 1855 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.31 % Allowed : 13.50 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.31), residues: 745 helix: 0.85 (0.24), residues: 497 sheet: None (None), residues: 0 loop : -1.26 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 202 TYR 0.014 0.002 TYR A 341 PHE 0.024 0.002 PHE A 269 TRP 0.019 0.002 TRP A 258 HIS 0.017 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 7989) covalent geometry : angle 0.56149 / 0.32 (11112) hydrogen bonds : bond 0.06851 / 4.92 ( 378) hydrogen bonds : angle 4.30217 / 2.92 ( 1065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7804 (tttm) cc_final: 0.7047 (ttpt) REVERT: A 140 ASP cc_start: 0.7380 (t70) cc_final: 0.7100 (t0) REVERT: A 201 ARG cc_start: 0.7552 (mmm-85) cc_final: 0.7007 (ttm170) REVERT: A 242 LEU cc_start: 0.8162 (mt) cc_final: 0.7929 (mp) REVERT: A 243 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7237 (mm-30) REVERT: A 313 LYS cc_start: 0.8347 (tppt) cc_final: 0.7918 (tppt) REVERT: A 316 ARG cc_start: 0.7746 (ptm160) cc_final: 0.7528 (ptm160) REVERT: A 317 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7682 (mm-30) REVERT: A 319 MET cc_start: 0.7839 (mtm) cc_final: 0.7574 (mtm) REVERT: A 396 LYS cc_start: 0.8253 (tttt) cc_final: 0.7928 (tptp) REVERT: A 493 ARG cc_start: 0.6991 (ttm-80) cc_final: 0.6705 (mtt-85) REVERT: A 497 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6781 (mm-30) REVERT: A 522 ASP cc_start: 0.7660 (m-30) cc_final: 0.7329 (m-30) REVERT: A 612 PHE cc_start: 0.8106 (t80) cc_final: 0.7893 (t80) REVERT: A 629 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7839 (mm-40) REVERT: A 850 TYR cc_start: 0.7738 (p90) cc_final: 0.7134 (p90) outliers start: 9 outliers final: 9 residues processed: 134 average time/residue: 0.1132 time to fit residues: 19.4068 Evaluate side-chains 138 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 759 ASN Chi-restraints excluded: chain A residue 780 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 55 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 75 optimal weight: 70.0000 chunk 72 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 GLN ** 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 = 0.4478 r_free = 0.4478 target = 0.197883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.144612 restraints weight = 22056.199| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 4.23 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7989 Z= 0.141 Angle : 0.548 8.302 11112 Z= 0.308 Chirality : 0.037 0.184 1283 Planarity : 0.004 0.050 1157 Dihedral : 17.580 82.449 1855 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.02 % Allowed : 14.22 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.31), residues: 745 helix: 0.89 (0.24), residues: 496 sheet: None (None), residues: 0 loop : -1.30 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 202 TYR 0.015 0.002 TYR A 296 PHE 0.024 0.001 PHE A 269 TRP 0.016 0.002 TRP A 258 HIS 0.012 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 7989) covalent geometry : angle 0.54762 / 0.31 (11112) hydrogen bonds : bond 0.06474 / 4.65 ( 378) hydrogen bonds : angle 4.23241 / 2.87 ( 1065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7252 (t70) cc_final: 0.6975 (t0) REVERT: A 201 ARG cc_start: 0.7486 (mmm-85) cc_final: 0.7260 (ttm170) REVERT: A 242 LEU cc_start: 0.8194 (mt) cc_final: 0.7958 (mp) REVERT: A 243 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7207 (mm-30) REVERT: A 248 ASP cc_start: 0.7369 (m-30) cc_final: 0.7169 (m-30) REVERT: A 313 LYS cc_start: 0.8362 (tppt) cc_final: 0.7914 (tppt) REVERT: A 319 MET cc_start: 0.7875 (mtm) cc_final: 0.7595 (mtm) REVERT: A 343 LEU cc_start: 0.8519 (mm) cc_final: 0.8234 (mm) REVERT: A 396 LYS cc_start: 0.8248 (tttt) cc_final: 0.7912 (tptp) REVERT: A 493 ARG cc_start: 0.6898 (ttm-80) cc_final: 0.6600 (mtt-85) REVERT: A 522 ASP cc_start: 0.7582 (m-30) cc_final: 0.7234 (m-30) REVERT: A 540 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7978 (mt-10) REVERT: A 850 TYR cc_start: 0.7769 (p90) cc_final: 0.7109 (p90) outliers start: 7 outliers final: 6 residues processed: 135 average time/residue: 0.1121 time to fit residues: 19.1857 Evaluate side-chains 138 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 780 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 59 optimal weight: 0.6980 chunk 75 optimal weight: 70.0000 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 77 optimal weight: 40.0000 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 278 HIS A 282 HIS A 491 ASN A 558 GLN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 ASN ** A 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.194460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.142498 restraints weight = 19424.321| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.51 r_work: 0.3560 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7989 Z= 0.195 Angle : 0.596 9.505 11112 Z= 0.333 Chirality : 0.039 0.187 1283 Planarity : 0.005 0.062 1157 Dihedral : 17.636 82.317 1855 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.02 % Allowed : 15.09 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.31), residues: 745 helix: 0.75 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -1.28 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 294 TYR 0.018 0.002 TYR A 679 PHE 0.058 0.002 PHE A 612 TRP 0.023 0.003 TRP A 258 HIS 0.009 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 ( 7989) covalent geometry : angle 0.59564 / 0.33 (11112) hydrogen bonds : bond 0.07012 / 4.92 ( 378) hydrogen bonds : angle 4.37958 / 2.98 ( 1065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8159 (t70) cc_final: 0.7875 (t0) REVERT: A 201 ARG cc_start: 0.8167 (mmm-85) cc_final: 0.7541 (ttm170) REVERT: A 241 GLN cc_start: 0.8123 (mt0) cc_final: 0.7860 (mt0) REVERT: A 242 LEU cc_start: 0.8265 (mt) cc_final: 0.8016 (mp) REVERT: A 313 LYS cc_start: 0.8553 (tppt) cc_final: 0.8017 (tppt) REVERT: A 317 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7658 (mm-30) REVERT: A 319 MET cc_start: 0.8272 (mtm) cc_final: 0.7965 (mtm) REVERT: A 343 LEU cc_start: 0.8534 (mm) cc_final: 0.8235 (mm) REVERT: A 396 LYS cc_start: 0.8411 (tttt) cc_final: 0.8069 (tptp) REVERT: A 493 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7492 (mtt-85) REVERT: A 519 MET cc_start: 0.7224 (mmt) cc_final: 0.5931 (mmt) REVERT: A 522 ASP cc_start: 0.7957 (m-30) cc_final: 0.7583 (m-30) REVERT: A 612 PHE cc_start: 0.8376 (t80) cc_final: 0.8117 (t80) REVERT: A 850 TYR cc_start: 0.8063 (p90) cc_final: 0.7397 (p90) outliers start: 7 outliers final: 7 residues processed: 132 average time/residue: 0.1091 time to fit residues: 18.2858 Evaluate side-chains 137 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 759 ASN Chi-restraints excluded: chain A residue 780 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 16 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.0060 chunk 40 optimal weight: 0.6980 chunk 41 optimal weight: 0.0570 chunk 52 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 overall best weight: 0.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 GLN ** 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 = 0.4460 r_free = 0.4460 target = 0.194937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.141221 restraints weight = 30741.782| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 4.86 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (14 function evaluations) r_final: 0.3757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 7989 Z= 0.316 Angle : 1.212 59.190 11112 Z= 0.792 Chirality : 0.042 0.647 1283 Planarity : 0.006 0.091 1157 Dihedral : 17.653 82.333 1855 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.73 % Allowed : 15.53 % Favored : 83.74 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.31), residues: 745 helix: 0.73 (0.24), residues: 496 sheet: None (None), residues: 0 loop : -1.27 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 294 TYR 0.024 0.002 TYR A 580 PHE 0.056 0.002 PHE A 612 TRP 0.023 0.002 TRP A 258 HIS 0.135 0.005 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.32 ( 7989) covalent geometry : angle 1.21231 / 0.79 (11112) hydrogen bonds : bond 0.06939 / 4.89 ( 378) hydrogen bonds : angle 4.43689 / 3.03 ( 1065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7395 (t70) cc_final: 0.7130 (t0) REVERT: A 201 ARG cc_start: 0.7571 (mmm-85) cc_final: 0.7040 (ttm170) REVERT: A 241 GLN cc_start: 0.7824 (mt0) cc_final: 0.7568 (mt0) REVERT: A 242 LEU cc_start: 0.8181 (mt) cc_final: 0.7955 (mp) REVERT: A 313 LYS cc_start: 0.8392 (tppt) cc_final: 0.7890 (tppt) REVERT: A 317 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7518 (mm-30) REVERT: A 319 MET cc_start: 0.7934 (mtm) cc_final: 0.7660 (mtm) REVERT: A 343 LEU cc_start: 0.8543 (mm) cc_final: 0.8259 (mm) REVERT: A 396 LYS cc_start: 0.8297 (tttt) cc_final: 0.8011 (tptp) REVERT: A 493 ARG cc_start: 0.6995 (ttm-80) cc_final: 0.6662 (mtt-85) REVERT: A 519 MET cc_start: 0.6885 (mmt) cc_final: 0.5612 (mmt) REVERT: A 522 ASP cc_start: 0.7655 (m-30) cc_final: 0.7310 (m-30) REVERT: A 850 TYR cc_start: 0.7707 (p90) cc_final: 0.7071 (p90) outliers start: 5 outliers final: 5 residues processed: 129 average time/residue: 0.1061 time to fit residues: 17.3929 Evaluate side-chains 133 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 780 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 50.0000 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 8 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 GLN ** 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 = 0.4459 r_free = 0.4459 target = 0.194911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.142473 restraints weight = 28284.172| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 4.47 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 7989 Z= 0.316 Angle : 1.212 59.190 11112 Z= 0.792 Chirality : 0.042 0.647 1283 Planarity : 0.006 0.091 1157 Dihedral : 17.653 82.333 1855 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.73 % Allowed : 15.67 % Favored : 83.60 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.31), residues: 745 helix: 0.73 (0.24), residues: 496 sheet: None (None), residues: 0 loop : -1.27 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 294 TYR 0.024 0.002 TYR A 580 PHE 0.056 0.002 PHE A 612 TRP 0.023 0.002 TRP A 258 HIS 0.135 0.005 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.32 ( 7989) covalent geometry : angle 1.21231 / 0.79 (11112) hydrogen bonds : bond 0.06939 / 4.89 ( 378) hydrogen bonds : angle 4.43689 / 3.03 ( 1065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1724.14 seconds wall clock time: 30 minutes 20.96 seconds (1820.96 seconds total)