Starting phenix.real_space_refine on Wed Aug 5 01:02:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m34_63598/08_2026/9m34_63598.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m34_63598/08_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_63598/08_2026/9m34_63598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m34_63598/08_2026/9m34_63598.map" model { file = "/net/cci-nas-00/data/ceres_data/9m34_63598/08_2026/9m34_63598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m34_63598/08_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 2.22, per 1000 atoms: 0.29 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 391.0 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: 0.85 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: 1.14 Time building geometry restraints manager: 0.89 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: 10798 1.92 - 3.84: 293 3.84 - 5.76: 15 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=" O5' C B 3 " pdb=" C5' C B 3 " pdb=" C4' C B 3 " ideal model delta sigma weight residual 109.40 112.71 -3.31 8.00e-01 1.56e+00 1.71e+01 angle pdb=" O5' A B -2 " pdb=" C5' A B -2 " pdb=" C4' A B -2 " ideal model delta sigma weight residual 109.40 112.66 -3.26 8.00e-01 1.56e+00 1.66e+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: 846 0.030 - 0.061: 262 0.061 - 0.091: 80 0.091 - 0.121: 32 0.121 - 0.152: 63 Chirality restraints: 1283 Sorted by residual: chirality pdb=" C2' C B 2 " pdb=" C3' C B 2 " pdb=" O2' C B 2 " pdb=" C1' C B 2 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.75e-01 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=" C2' U C 27 " pdb=" C3' U C 27 " pdb=" O2' U C 27 " pdb=" C1' U C 27 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.79e-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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.860 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.790 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.040 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.430 ------------------------------------------------------------------------------- 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= 0.149 Angle : 0.629 9.599 11112 Z= 0.408 Chirality : 0.045 0.152 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 0.00331 / 0.15 ( 7989) covalent geometry : angle 0.62850 / 0.41 (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 : 0.272 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: 0.1191 time to fit residues: 21.0176 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 : 0.253 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.201296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.148767 restraints weight = 25154.661| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 4.30 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (12 function evaluations) r_final: 0.3848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7989 Z= 0.149 Angle : 0.618 9.806 11112 Z= 0.340 Chirality : 0.039 0.170 1283 Planarity : 0.005 0.074 1157 Dihedral : 17.452 87.965 1855 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.58 % Allowed : 7.55 % Favored : 91.87 % 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 : -1.55 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 294 TYR 0.026 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 0.00307 / 0.15 ( 7989) covalent geometry : angle 0.61807 / 0.34 (11112) hydrogen bonds : bond 0.08027 / 6.05 ( 378) hydrogen bonds : angle 4.26222 / 2.92 ( 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 146 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.251 Fit side-chains REVERT: A 102 MET cc_start: 0.7088 (ttt) cc_final: 0.6848 (ttt) REVERT: A 122 LEU cc_start: 0.7828 (mm) cc_final: 0.7595 (mt) REVERT: A 123 ASP cc_start: 0.7450 (t70) cc_final: 0.7113 (t0) REVERT: A 140 ASP cc_start: 0.7310 (t70) cc_final: 0.6982 (t0) REVERT: A 201 ARG cc_start: 0.7565 (mmm-85) cc_final: 0.7153 (ttm170) REVERT: A 242 LEU cc_start: 0.8130 (mt) cc_final: 0.7892 (mp) REVERT: A 300 LEU cc_start: 0.7678 (pp) cc_final: 0.7397 (pt) REVERT: A 316 ARG cc_start: 0.7548 (ptm160) cc_final: 0.7086 (ttt180) REVERT: A 319 MET cc_start: 0.7577 (mtm) cc_final: 0.7307 (mtm) REVERT: A 381 LYS cc_start: 0.8825 (pttm) cc_final: 0.8478 (pttm) REVERT: A 396 LYS cc_start: 0.8550 (tttt) cc_final: 0.7907 (tptp) REVERT: A 493 ARG cc_start: 0.6975 (ttm-80) cc_final: 0.6690 (mtt-85) REVERT: A 522 ASP cc_start: 0.7635 (m-30) cc_final: 0.7324 (m-30) REVERT: A 839 ASP cc_start: 0.7895 (m-30) cc_final: 0.7417 (m-30) REVERT: A 842 LYS cc_start: 0.8069 (mttp) cc_final: 0.7837 (ttmm) REVERT: A 850 TYR cc_start: 0.7547 (p90) cc_final: 0.6967 (p90) outliers start: 4 outliers final: 2 residues processed: 143 average time/residue: 0.1149 time to fit residues: 21.0958 Evaluate side-chains 128 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 HIS 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: 2.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 = 0.4471 r_free = 0.4471 target = 0.196110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.143962 restraints weight = 26419.540| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 4.37 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 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 = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (12 function evaluations) r_final: 0.3802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7989 Z= 0.182 Angle : 0.592 9.605 11112 Z= 0.332 Chirality : 0.040 0.169 1283 Planarity : 0.005 0.062 1157 Dihedral : 17.495 85.095 1855 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.44 % Allowed : 9.72 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.19 (0.31), residues: 745 helix: 0.90 (0.23), residues: 495 sheet: None (None), residues: 0 loop : -1.41 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 543 TYR 0.017 0.002 TYR A 341 PHE 0.028 0.002 PHE A 269 TRP 0.020 0.002 TRP A 258 HIS 0.005 0.001 HIS A 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 7989) covalent geometry : angle 0.59220 / 0.33 (11112) hydrogen bonds : bond 0.08117 / 6.03 ( 378) hydrogen bonds : angle 4.30830 / 2.96 ( 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: 3 poor density : 132 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7203 (ttt) cc_final: 0.6965 (ttt) REVERT: A 140 ASP cc_start: 0.7335 (t70) cc_final: 0.7028 (t0) REVERT: A 201 ARG cc_start: 0.7658 (mmm-85) cc_final: 0.7111 (ttm170) REVERT: A 242 LEU cc_start: 0.8180 (mt) cc_final: 0.7945 (mp) REVERT: A 319 MET cc_start: 0.7843 (mtm) cc_final: 0.7548 (mtm) REVERT: A 396 LYS cc_start: 0.8306 (tttt) cc_final: 0.7950 (tptp) REVERT: A 493 ARG cc_start: 0.7084 (ttm-80) cc_final: 0.6736 (mtt-85) REVERT: A 522 ASP cc_start: 0.7645 (m-30) cc_final: 0.7323 (m-30) REVERT: A 612 PHE cc_start: 0.8084 (t80) cc_final: 0.7857 (t80) REVERT: A 850 TYR cc_start: 0.7644 (p90) cc_final: 0.7067 (p90) outliers start: 3 outliers final: 2 residues processed: 133 average time/residue: 0.1184 time to fit residues: 20.1250 Evaluate side-chains 130 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 780 VAL 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: 0.5980 chunk 7 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 62 optimal weight: 0.0060 chunk 32 optimal weight: 0.8980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 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 = 0.4484 r_free = 0.4484 target = 0.198788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.145979 restraints weight = 30905.365| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 4.78 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7989 Z= 0.138 Angle : 0.553 6.446 11112 Z= 0.310 Chirality : 0.038 0.154 1283 Planarity : 0.005 0.056 1157 Dihedral : 17.487 82.003 1855 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.73 % Allowed : 11.61 % Favored : 87.66 % 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: 0.96 (0.24), residues: 495 sheet: None (None), residues: 0 loop : -1.37 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 202 TYR 0.017 0.001 TYR A 341 PHE 0.025 0.002 PHE A 269 TRP 0.016 0.002 TRP A 258 HIS 0.004 0.001 HIS A 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 7989) covalent geometry : angle 0.55309 / 0.31 (11112) hydrogen bonds : bond 0.07095 / 5.26 ( 378) hydrogen bonds : angle 4.13394 / 2.82 ( 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 138 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7135 (ttt) cc_final: 0.6927 (ttt) REVERT: A 140 ASP cc_start: 0.7329 (t70) cc_final: 0.7026 (t0) REVERT: A 183 ILE cc_start: 0.6956 (tt) cc_final: 0.6658 (tt) REVERT: A 201 ARG cc_start: 0.7588 (mmm-85) cc_final: 0.7301 (ttm170) REVERT: A 242 LEU cc_start: 0.8142 (mt) cc_final: 0.7922 (mp) REVERT: A 313 LYS cc_start: 0.8196 (tppt) cc_final: 0.7874 (tppt) REVERT: A 319 MET cc_start: 0.7672 (mtm) cc_final: 0.7407 (mtm) REVERT: A 396 LYS cc_start: 0.8156 (tttt) cc_final: 0.7826 (tptp) REVERT: A 493 ARG cc_start: 0.6981 (ttm-80) cc_final: 0.6672 (mtt-85) REVERT: A 522 ASP cc_start: 0.7625 (m-30) cc_final: 0.7342 (m-30) REVERT: A 612 PHE cc_start: 0.8008 (t80) cc_final: 0.7710 (t80) REVERT: A 629 GLN cc_start: 0.7775 (mm110) cc_final: 0.7570 (mm110) REVERT: A 850 TYR cc_start: 0.7613 (p90) cc_final: 0.7054 (p90) outliers start: 5 outliers final: 3 residues processed: 136 average time/residue: 0.1147 time to fit residues: 19.9933 Evaluate side-chains 135 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 665 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 15 optimal weight: 0.0970 chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 = 0.4480 r_free = 0.4480 target = 0.196779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.144924 restraints weight = 24956.404| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 4.26 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 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: 0.3819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2016 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= 0.142 Angle : 0.550 6.120 11112 Z= 0.306 Chirality : 0.038 0.151 1283 Planarity : 0.005 0.054 1157 Dihedral : 17.493 80.004 1855 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.87 % Allowed : 13.50 % Favored : 85.63 % 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: 0.30 (0.31), residues: 745 helix: 0.96 (0.24), residues: 495 sheet: None (None), residues: 0 loop : -1.31 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 294 TYR 0.022 0.002 TYR A 341 PHE 0.027 0.002 PHE A 269 TRP 0.017 0.002 TRP A 258 HIS 0.004 0.001 HIS A 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 7989) covalent geometry : angle 0.54952 / 0.31 (11112) hydrogen bonds : bond 0.06808 / 5.00 ( 378) hydrogen bonds : angle 4.09323 / 2.80 ( 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 136 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7324 (t70) cc_final: 0.7029 (t0) REVERT: A 201 ARG cc_start: 0.7617 (mmm-85) cc_final: 0.7343 (ttm170) REVERT: A 242 LEU cc_start: 0.8162 (mt) cc_final: 0.7912 (mp) REVERT: A 313 LYS cc_start: 0.8336 (tppt) cc_final: 0.7936 (tppt) REVERT: A 316 ARG cc_start: 0.7790 (ptm160) cc_final: 0.7079 (ptt180) REVERT: A 319 MET cc_start: 0.7804 (mtm) cc_final: 0.7536 (mtm) REVERT: A 343 LEU cc_start: 0.8530 (mm) cc_final: 0.8238 (mm) REVERT: A 396 LYS cc_start: 0.8244 (tttt) cc_final: 0.7881 (tptp) REVERT: A 522 ASP cc_start: 0.7591 (m-30) cc_final: 0.7270 (m-30) REVERT: A 612 PHE cc_start: 0.8093 (t80) cc_final: 0.7812 (t80) REVERT: A 850 TYR cc_start: 0.7734 (p90) cc_final: 0.7159 (p90) outliers start: 6 outliers final: 4 residues processed: 132 average time/residue: 0.1191 time to fit residues: 19.9893 Evaluate side-chains 136 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 48 optimal weight: 0.4980 chunk 52 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 77 optimal weight: 50.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN A 806 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 = 0.4472 r_free = 0.4472 target = 0.196040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.144379 restraints weight = 26645.682| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 4.39 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 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 = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2219 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= 0.165 Angle : 0.562 6.876 11112 Z= 0.314 Chirality : 0.038 0.147 1283 Planarity : 0.005 0.050 1157 Dihedral : 17.526 79.637 1855 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.16 % Allowed : 13.64 % 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: 0.31 (0.32), residues: 745 helix: 0.95 (0.24), residues: 495 sheet: None (None), residues: 0 loop : -1.26 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 493 TYR 0.020 0.002 TYR A 341 PHE 0.025 0.002 PHE A 269 TRP 0.019 0.002 TRP A 258 HIS 0.004 0.001 HIS A 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 7989) covalent geometry : angle 0.56176 / 0.31 (11112) hydrogen bonds : bond 0.06824 / 4.92 ( 378) hydrogen bonds : angle 4.15329 / 2.83 ( 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 145 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 91 MET cc_start: 0.4952 (OUTLIER) cc_final: 0.3939 (ppp) REVERT: A 97 LYS cc_start: 0.7791 (tttm) cc_final: 0.7051 (ttpt) REVERT: A 140 ASP cc_start: 0.7353 (t70) cc_final: 0.7065 (t0) REVERT: A 201 ARG cc_start: 0.7592 (mmm-85) cc_final: 0.7357 (ttm170) REVERT: A 242 LEU cc_start: 0.8191 (mt) cc_final: 0.7965 (mp) REVERT: A 313 LYS cc_start: 0.8329 (tppt) cc_final: 0.8043 (tppt) REVERT: A 316 ARG cc_start: 0.7771 (ptm160) cc_final: 0.7491 (ptm160) REVERT: A 319 MET cc_start: 0.7834 (mtm) cc_final: 0.7559 (mtm) REVERT: A 343 LEU cc_start: 0.8552 (mm) cc_final: 0.8261 (mm) REVERT: A 396 LYS cc_start: 0.8183 (tttt) cc_final: 0.7833 (tptp) REVERT: A 522 ASP cc_start: 0.7624 (m-30) cc_final: 0.7319 (m-30) REVERT: A 612 PHE cc_start: 0.8155 (t80) cc_final: 0.7762 (t80) REVERT: A 850 TYR cc_start: 0.7760 (p90) cc_final: 0.7125 (p90) outliers start: 8 outliers final: 5 residues processed: 138 average time/residue: 0.1250 time to fit residues: 21.8602 Evaluate side-chains 140 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 72 optimal weight: 0.0050 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 759 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 = 0.4465 r_free = 0.4465 target = 0.195505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141852 restraints weight = 29541.242| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 4.78 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3766 r_free = 0.3766 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3766 r_free = 0.3766 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7989 Z= 0.175 Angle : 0.568 7.097 11112 Z= 0.317 Chirality : 0.039 0.166 1283 Planarity : 0.005 0.049 1157 Dihedral : 17.562 79.690 1855 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.16 % Allowed : 13.93 % Favored : 84.91 % 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: 0.89 (0.23), residues: 495 sheet: None (None), residues: 0 loop : -1.27 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 493 TYR 0.018 0.002 TYR A 341 PHE 0.021 0.002 PHE A 269 TRP 0.019 0.002 TRP A 258 HIS 0.005 0.001 HIS A 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 7989) covalent geometry : angle 0.56754 / 0.32 (11112) hydrogen bonds : bond 0.06817 / 4.86 ( 378) hydrogen bonds : angle 4.20687 / 2.87 ( 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 139 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7414 (t70) cc_final: 0.7133 (t0) REVERT: A 201 ARG cc_start: 0.7552 (mmm-85) cc_final: 0.7018 (ttm170) REVERT: A 242 LEU cc_start: 0.8189 (mt) cc_final: 0.7967 (mp) REVERT: A 313 LYS cc_start: 0.8361 (tppt) cc_final: 0.8089 (tppt) REVERT: A 316 ARG cc_start: 0.7807 (ptm160) cc_final: 0.7602 (ptm160) REVERT: A 319 MET cc_start: 0.7912 (mtm) cc_final: 0.7633 (mtm) REVERT: A 326 LYS cc_start: 0.7301 (mmtt) cc_final: 0.7088 (mmtt) REVERT: A 343 LEU cc_start: 0.8527 (mm) cc_final: 0.8212 (mm) REVERT: A 396 LYS cc_start: 0.8229 (tttt) cc_final: 0.7909 (tptp) REVERT: A 497 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6780 (mm-30) REVERT: A 522 ASP cc_start: 0.7675 (m-30) cc_final: 0.7337 (m-30) REVERT: A 612 PHE cc_start: 0.8181 (t80) cc_final: 0.7806 (t80) REVERT: A 850 TYR cc_start: 0.7759 (p90) cc_final: 0.7123 (p90) outliers start: 8 outliers final: 6 residues processed: 133 average time/residue: 0.1041 time to fit residues: 17.6954 Evaluate side-chains 137 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 300 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 55 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 44 optimal weight: 0.0670 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 75 optimal weight: 60.0000 chunk 72 optimal weight: 0.0970 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN A 558 GLN ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4472 r_free = 0.4472 target = 0.196255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.143386 restraints weight = 22015.666| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 3.86 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7989 Z= 0.135 Angle : 0.556 7.842 11112 Z= 0.309 Chirality : 0.037 0.174 1283 Planarity : 0.004 0.049 1157 Dihedral : 17.586 79.800 1855 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.73 % Allowed : 14.22 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.31), residues: 745 helix: 0.97 (0.24), residues: 497 sheet: None (None), residues: 0 loop : -1.25 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 493 TYR 0.016 0.001 TYR A 341 PHE 0.022 0.001 PHE A 344 TRP 0.014 0.002 TRP A 258 HIS 0.008 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7989) covalent geometry : angle 0.55630 / 0.31 (11112) hydrogen bonds : bond 0.06168 / 4.40 ( 378) hydrogen bonds : angle 4.17932 / 2.84 ( 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 141 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.238 Fit side-chains REVERT: A 140 ASP cc_start: 0.7289 (t70) cc_final: 0.7000 (t0) REVERT: A 201 ARG cc_start: 0.7493 (mmm-85) cc_final: 0.7274 (ttm-80) REVERT: A 242 LEU cc_start: 0.8188 (mt) cc_final: 0.7975 (mp) REVERT: A 308 MET cc_start: 0.4070 (tpt) cc_final: 0.3868 (mmm) REVERT: A 313 LYS cc_start: 0.8407 (tppt) cc_final: 0.8126 (tppt) REVERT: A 316 ARG cc_start: 0.7963 (ptm160) cc_final: 0.7760 (ptm160) REVERT: A 319 MET cc_start: 0.8002 (mtm) cc_final: 0.7716 (mtm) REVERT: A 343 LEU cc_start: 0.8494 (mm) cc_final: 0.8149 (mm) REVERT: A 396 LYS cc_start: 0.8292 (tttt) cc_final: 0.7954 (tptp) REVERT: A 522 ASP cc_start: 0.7584 (m-30) cc_final: 0.7240 (m-30) REVERT: A 612 PHE cc_start: 0.8184 (t80) cc_final: 0.7828 (t80) REVERT: A 647 ASP cc_start: 0.7359 (t0) cc_final: 0.6947 (t0) REVERT: A 850 TYR cc_start: 0.7789 (p90) cc_final: 0.7181 (p90) outliers start: 5 outliers final: 5 residues processed: 137 average time/residue: 0.0910 time to fit residues: 15.9600 Evaluate side-chains 135 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 300 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 468 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 59 optimal weight: 0.8980 chunk 75 optimal weight: 60.0000 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 69 optimal weight: 0.0040 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 50.0000 chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 GLN ** 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 = 0.4460 r_free = 0.4460 target = 0.195222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.143254 restraints weight = 19451.577| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.62 r_work: 0.3572 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7989 Z= 0.161 Angle : 0.579 7.819 11112 Z= 0.320 Chirality : 0.038 0.169 1283 Planarity : 0.005 0.051 1157 Dihedral : 17.623 79.831 1855 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.02 % Allowed : 14.37 % Favored : 84.62 % 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: 0.28 (0.31), residues: 745 helix: 0.92 (0.23), residues: 497 sheet: None (None), residues: 0 loop : -1.26 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 493 TYR 0.016 0.001 TYR A 341 PHE 0.024 0.002 PHE A 269 TRP 0.019 0.002 TRP A 258 HIS 0.006 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 7989) covalent geometry : angle 0.57947 / 0.32 (11112) hydrogen bonds : bond 0.06396 / 4.52 ( 378) hydrogen bonds : angle 4.24583 / 2.89 ( 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 140 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8133 (t70) cc_final: 0.7829 (t0) REVERT: A 201 ARG cc_start: 0.8074 (mmm-85) cc_final: 0.7718 (ttm-80) REVERT: A 242 LEU cc_start: 0.8251 (mt) cc_final: 0.8017 (mp) REVERT: A 313 LYS cc_start: 0.8577 (tppt) cc_final: 0.8110 (tppt) REVERT: A 317 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7479 (mm-30) REVERT: A 319 MET cc_start: 0.8275 (mtm) cc_final: 0.7972 (mtm) REVERT: A 343 LEU cc_start: 0.8508 (mm) cc_final: 0.8148 (mm) REVERT: A 396 LYS cc_start: 0.8302 (tttt) cc_final: 0.7964 (tptp) REVERT: A 522 ASP cc_start: 0.7999 (m-30) cc_final: 0.7644 (m-30) REVERT: A 612 PHE cc_start: 0.8453 (t80) cc_final: 0.8161 (t80) REVERT: A 850 TYR cc_start: 0.8103 (p90) cc_final: 0.7516 (p90) outliers start: 7 outliers final: 5 residues processed: 134 average time/residue: 0.1070 time to fit residues: 18.2332 Evaluate side-chains 138 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 300 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 468 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 16 optimal weight: 0.7980 chunk 50 optimal weight: 0.0070 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 0.0870 chunk 40 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 chunk 52 optimal weight: 0.4980 chunk 72 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 overall best weight: 0.1376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 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 = 0.4498 r_free = 0.4498 target = 0.198509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.147465 restraints weight = 30606.391| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 4.73 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7989 Z= 0.116 Angle : 0.554 7.338 11112 Z= 0.301 Chirality : 0.036 0.165 1283 Planarity : 0.004 0.052 1157 Dihedral : 17.568 79.947 1855 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.44 % Allowed : 15.24 % Favored : 84.33 % 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: 0.35 (0.31), residues: 745 helix: 0.95 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.24 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 493 TYR 0.016 0.001 TYR A 844 PHE 0.023 0.001 PHE A 344 TRP 0.011 0.002 TRP A 752 HIS 0.003 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 7989) covalent geometry : angle 0.55414 / 0.30 (11112) hydrogen bonds : bond 0.05282 / 3.79 ( 378) hydrogen bonds : angle 4.05224 / 2.75 ( 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 134 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7283 (t70) cc_final: 0.6980 (t0) REVERT: A 182 TYR cc_start: 0.6661 (t80) cc_final: 0.6401 (t80) REVERT: A 242 LEU cc_start: 0.8041 (mt) cc_final: 0.7822 (mp) REVERT: A 264 ARG cc_start: 0.8377 (ttt180) cc_final: 0.8013 (ttt-90) REVERT: A 313 LYS cc_start: 0.8308 (tppt) cc_final: 0.7970 (tppt) REVERT: A 319 MET cc_start: 0.7901 (mtm) cc_final: 0.7618 (mtm) REVERT: A 343 LEU cc_start: 0.8427 (mm) cc_final: 0.8063 (mm) REVERT: A 396 LYS cc_start: 0.8170 (tttt) cc_final: 0.7848 (tptp) REVERT: A 504 SER cc_start: 0.8014 (m) cc_final: 0.7798 (m) REVERT: A 522 ASP cc_start: 0.7650 (m-30) cc_final: 0.7319 (m-30) REVERT: A 597 LYS cc_start: 0.7637 (mttp) cc_final: 0.7354 (mptt) REVERT: A 610 ARG cc_start: 0.7143 (mtp-110) cc_final: 0.6764 (mtp180) REVERT: A 612 PHE cc_start: 0.8169 (t80) cc_final: 0.7838 (t80) REVERT: A 850 TYR cc_start: 0.7711 (p90) cc_final: 0.7183 (p90) outliers start: 3 outliers final: 2 residues processed: 132 average time/residue: 0.0892 time to fit residues: 15.0160 Evaluate side-chains 127 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 336 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 10 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 50.0000 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 GLN ** 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 = 0.4475 r_free = 0.4475 target = 0.196903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.144186 restraints weight = 27967.301| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 4.60 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7989 Z= 0.146 Angle : 0.572 8.736 11112 Z= 0.312 Chirality : 0.038 0.169 1283 Planarity : 0.004 0.050 1157 Dihedral : 17.548 79.915 1855 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.58 % Allowed : 16.11 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.33 (0.32), residues: 745 helix: 0.96 (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 0.005 0.001 ARG A 543 TYR 0.019 0.001 TYR A 576 PHE 0.026 0.002 PHE A 269 TRP 0.020 0.002 TRP A 258 HIS 0.005 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 7989) covalent geometry : angle 0.57186 / 0.31 (11112) hydrogen bonds : bond 0.05879 / 4.14 ( 378) hydrogen bonds : angle 4.10412 / 2.79 ( 1065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1725.43 seconds wall clock time: 30 minutes 22.97 seconds (1822.97 seconds total)