Starting phenix.real_space_refine on Sat Aug 23 00:58:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e9f_9014/08_2025/6e9f_9014.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e9f_9014/08_2025/6e9f_9014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6e9f_9014/08_2025/6e9f_9014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e9f_9014/08_2025/6e9f_9014.map" model { file = "/net/cci-nas-00/data/ceres_data/6e9f_9014/08_2025/6e9f_9014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e9f_9014/08_2025/6e9f_9014.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 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 79 5.49 5 Mg 1 5.21 5 S 30 5.16 5 C 5245 2.51 5 N 1491 2.21 5 O 1899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8745 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 864, 7065 Classifications: {'peptide': 864} Link IDs: {'PTRANS': 13, 'TRANS': 850} Chain breaks: 5 Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1110 Classifications: {'RNA': 52} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 1, 'rna3p_pur': 24, 'rna3p_pyr': 21} Link IDs: {'rna2p': 7, 'rna3p': 44} Chain: "C" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 569 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 11, 'rna3p_pyr': 15} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.04, per 1000 atoms: 0.23 Number of scatterers: 8745 At special positions: 0 Unit cell: (106.65, 80.58, 97.17, 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 30 16.00 P 79 15.00 Mg 1 11.99 O 1899 8.00 N 1491 7.00 C 5245 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: 0.85 Conformation dependent library (CDL) restraints added in 268.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 57.5% alpha, 3.0% beta 23 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 159 through 168 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 183 through 188 removed outlier: 4.053A pdb=" N ASP A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 187 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.525A pdb=" N ASP A 243 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 280 through 298 removed outlier: 3.556A pdb=" N TYR A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.902A pdb=" N LEU A 313 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP A 314 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 315 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 316 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 removed outlier: 3.695A pdb=" N LYS A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.583A pdb=" N VAL A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.581A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 381 through 390 removed outlier: 4.531A pdb=" N GLU A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.729A pdb=" N ASP A 401 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER A 402 " --> pdb=" O GLU A 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 398 through 402' Processing helix chain 'A' and resid 403 through 422 removed outlier: 4.135A pdb=" N GLN A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.634A pdb=" N ALA A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 445 Processing helix chain 'A' and resid 446 through 467 removed outlier: 4.517A pdb=" N LYS A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU A 460 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N SER A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.852A pdb=" N PHE A 493 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 511 removed outlier: 3.513A pdb=" N THR A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.941A pdb=" N ASN A 520 " --> pdb=" O GLY A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.533A pdb=" N LYS A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 539 Processing helix chain 'A' and resid 558 through 571 removed outlier: 3.636A pdb=" N ALA A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 595 removed outlier: 3.693A pdb=" N LEU A 591 " --> pdb=" O TYR A 587 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 604 Processing helix chain 'A' and resid 605 through 614 Processing helix chain 'A' and resid 628 through 640 removed outlier: 3.686A pdb=" N ILE A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA A 634 " --> pdb=" O ARG A 630 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 647 removed outlier: 3.544A pdb=" N LYS A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.895A pdb=" N LYS A 654 " --> pdb=" O ASN A 651 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 655 " --> pdb=" O PRO A 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 651 through 655' Processing helix chain 'A' and resid 661 through 669 Processing helix chain 'A' and resid 673 through 682 removed outlier: 3.565A pdb=" N ARG A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 706 removed outlier: 3.602A pdb=" N ARG A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 701 " --> pdb=" O ARG A 697 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N MET A 704 " --> pdb=" O LYS A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 739 removed outlier: 4.406A pdb=" N LYS A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 758 removed outlier: 3.971A pdb=" N TYR A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 752 " --> pdb=" O MET A 748 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 777 removed outlier: 3.837A pdb=" N TYR A 762 " --> pdb=" O VAL A 758 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU A 770 " --> pdb=" O PHE A 766 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP A 772 " --> pdb=" O CYS A 768 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 797 Processing helix chain 'A' and resid 826 through 838 removed outlier: 3.790A pdb=" N ILE A 833 " --> pdb=" O TRP A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 853 removed outlier: 3.929A pdb=" N VAL A 845 " --> pdb=" O GLU A 841 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 890 removed outlier: 4.169A pdb=" N HIS A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 909 removed outlier: 4.097A pdb=" N PHE A 902 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 903 " --> pdb=" O THR A 899 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 904 " --> pdb=" O GLY A 900 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS A 909 " --> pdb=" O LYS A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.557A pdb=" N TYR A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 926 removed outlier: 3.600A pdb=" N PHE A 924 " --> pdb=" O CYS A 921 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR A 926 " --> pdb=" O PRO A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 934 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 82 removed outlier: 3.521A pdb=" N VAL A 89 " --> pdb=" O SER A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 95 removed outlier: 3.628A pdb=" N VAL A 95 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 114 removed outlier: 6.807A pdb=" N SER A 120 " --> pdb=" O ASN A 112 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL A 114 " --> pdb=" O GLY A 118 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 265 252 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2309 1.33 - 1.45: 2182 1.45 - 1.57: 4364 1.57 - 1.69: 156 1.69 - 1.81: 47 Bond restraints: 9058 Sorted by residual: bond pdb=" N LYS A 160 " pdb=" CA LYS A 160 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.04e-02 9.25e+03 8.19e+00 bond pdb=" N LEU A 159 " pdb=" CA LEU A 159 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.19e-02 7.06e+03 8.11e+00 bond pdb=" N LYS A 165 " pdb=" CA LYS A 165 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.23e+00 bond pdb=" N THR A 922 " pdb=" CA THR A 922 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.04e-02 9.25e+03 7.19e+00 bond pdb=" CB PRO A 923 " pdb=" CG PRO A 923 " ideal model delta sigma weight residual 1.492 1.368 0.124 5.00e-02 4.00e+02 6.19e+00 ... (remaining 9053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 12198 2.79 - 5.59: 326 5.59 - 8.38: 33 8.38 - 11.18: 12 11.18 - 13.97: 2 Bond angle restraints: 12571 Sorted by residual: angle pdb=" N CYS A 921 " pdb=" CA CYS A 921 " pdb=" C CYS A 921 " ideal model delta sigma weight residual 113.17 105.61 7.56 1.26e+00 6.30e-01 3.60e+01 angle pdb=" C THR A 922 " pdb=" N PRO A 923 " pdb=" CA PRO A 923 " ideal model delta sigma weight residual 119.84 112.63 7.21 1.25e+00 6.40e-01 3.33e+01 angle pdb=" N LEU A 111 " pdb=" CA LEU A 111 " pdb=" C LEU A 111 " ideal model delta sigma weight residual 109.24 118.32 -9.08 1.63e+00 3.76e-01 3.11e+01 angle pdb=" N VAL A 523 " pdb=" CA VAL A 523 " pdb=" C VAL A 523 " ideal model delta sigma weight residual 111.91 107.19 4.72 8.90e-01 1.26e+00 2.81e+01 angle pdb=" N ILE A 882 " pdb=" CA ILE A 882 " pdb=" C ILE A 882 " ideal model delta sigma weight residual 113.53 109.01 4.52 9.80e-01 1.04e+00 2.12e+01 ... (remaining 12566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.84: 5074 19.84 - 39.68: 334 39.68 - 59.51: 106 59.51 - 79.35: 54 79.35 - 99.19: 6 Dihedral angle restraints: 5574 sinusoidal: 3005 harmonic: 2569 Sorted by residual: dihedral pdb=" CA ILE A 494 " pdb=" C ILE A 494 " pdb=" N SER A 495 " pdb=" CA SER A 495 " ideal model delta harmonic sigma weight residual -180.00 -150.33 -29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA ILE A 94 " pdb=" C ILE A 94 " pdb=" N VAL A 95 " pdb=" CA VAL A 95 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA GLU A 518 " pdb=" C GLU A 518 " pdb=" N ILE A 519 " pdb=" CA ILE A 519 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 5571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1047 0.068 - 0.135: 328 0.135 - 0.203: 71 0.203 - 0.271: 9 0.271 - 0.338: 4 Chirality restraints: 1459 Sorted by residual: chirality pdb=" CB VAL A 523 " pdb=" CA VAL A 523 " pdb=" CG1 VAL A 523 " pdb=" CG2 VAL A 523 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA LYS A 273 " pdb=" N LYS A 273 " pdb=" C LYS A 273 " pdb=" CB LYS A 273 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB ILE A 484 " pdb=" CA ILE A 484 " pdb=" CG1 ILE A 484 " pdb=" CG2 ILE A 484 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1456 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 330 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO A 331 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B 38 " 0.032 2.00e-02 2.50e+03 1.70e-02 7.91e+00 pdb=" N9 A B 38 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A B 38 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A B 38 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A B 38 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B 38 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 38 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A B 38 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A B 38 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A B 38 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A B 38 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 916 " 0.023 2.00e-02 2.50e+03 2.06e-02 7.43e+00 pdb=" CG PHE A 916 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 916 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 916 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 916 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 916 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 916 " 0.002 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 72 2.48 - 3.08: 5891 3.08 - 3.69: 14370 3.69 - 4.29: 20924 4.29 - 4.90: 32380 Nonbonded interactions: 73637 Sorted by model distance: nonbonded pdb=" O4 U C 4 " pdb=" N3 U C 5 " model vdw 1.872 3.120 nonbonded pdb=" O2' A B 32 " pdb=" O5' C B 33 " model vdw 2.091 3.040 nonbonded pdb=" OP1 U B 23 " pdb="MG MG B 101 " model vdw 2.102 2.170 nonbonded pdb=" N1 G B 22 " pdb=" N6 A B 28 " model vdw 2.169 3.200 nonbonded pdb=" C4 U C 4 " pdb=" N3 U C 5 " model vdw 2.178 3.340 ... (remaining 73632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.730 Find NCS groups from input model: 0.030 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:1.390 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: 0.7904 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 : 0.011 0.124 9058 Z= 0.515 Angle : 1.131 13.972 12571 Z= 0.620 Chirality : 0.069 0.338 1459 Planarity : 0.006 0.077 1316 Dihedral : 16.250 99.187 3910 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.59 (0.20), residues: 852 helix: -4.18 (0.13), residues: 473 sheet: -4.08 (0.83), residues: 25 loop : -2.73 (0.27), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 930 TYR 0.028 0.004 TYR A 912 PHE 0.048 0.004 PHE A 916 TRP 0.019 0.004 TRP A 829 HIS 0.011 0.002 HIS A 885 Details of bonding type rmsd covalent geometry : bond 0.01138 ( 9058) covalent geometry : angle 1.13141 (12571) hydrogen bonds : bond 0.29594 ( 306) hydrogen bonds : angle 10.97877 ( 820) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.315 Fit side-chains REVERT: A 223 ASP cc_start: 0.8179 (t70) cc_final: 0.7925 (t0) REVERT: A 241 LYS cc_start: 0.7553 (tttp) cc_final: 0.7239 (tptp) REVERT: A 338 ARG cc_start: 0.7152 (mtm110) cc_final: 0.6853 (mmp80) REVERT: A 375 TYR cc_start: 0.7400 (m-10) cc_final: 0.7167 (m-10) REVERT: A 479 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7356 (ttpp) REVERT: A 541 ASP cc_start: 0.7579 (t0) cc_final: 0.7297 (t0) REVERT: A 768 CYS cc_start: 0.7385 (m) cc_final: 0.6968 (m) REVERT: A 888 ASN cc_start: 0.7821 (t0) cc_final: 0.7558 (m-40) REVERT: A 896 GLU cc_start: 0.6622 (pm20) cc_final: 0.6219 (tp30) REVERT: A 926 TYR cc_start: 0.7934 (p90) cc_final: 0.7694 (p90) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1398 time to fit residues: 40.5633 Evaluate side-chains 118 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.0170 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0370 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN A 885 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129574 restraints weight = 13332.076| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.02 r_work: 0.3390 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9058 Z= 0.125 Angle : 0.629 7.828 12571 Z= 0.332 Chirality : 0.040 0.162 1459 Planarity : 0.005 0.046 1316 Dihedral : 17.959 88.903 2131 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.84 % Allowed : 11.86 % Favored : 85.31 % 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 aren not related in a simple way. whole: -4.14 (0.24), residues: 852 helix: -2.86 (0.18), residues: 490 sheet: -3.88 (0.87), residues: 25 loop : -2.18 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 584 TYR 0.013 0.001 TYR A 645 PHE 0.016 0.002 PHE A 848 TRP 0.007 0.002 TRP A 309 HIS 0.004 0.001 HIS A 879 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9058) covalent geometry : angle 0.62938 (12571) hydrogen bonds : bond 0.04934 ( 306) hydrogen bonds : angle 4.89998 ( 820) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.301 Fit side-chains REVERT: A 167 PHE cc_start: 0.7345 (m-10) cc_final: 0.6906 (m-80) REVERT: A 223 ASP cc_start: 0.8652 (t70) cc_final: 0.8411 (t0) REVERT: A 241 LYS cc_start: 0.7638 (tttp) cc_final: 0.7225 (tptp) REVERT: A 261 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7381 (t0) REVERT: A 479 LYS cc_start: 0.8252 (mtpp) cc_final: 0.7513 (ttpp) REVERT: A 491 LYS cc_start: 0.8381 (ptpt) cc_final: 0.7934 (pttm) REVERT: A 538 GLU cc_start: 0.7801 (tp30) cc_final: 0.7531 (tp30) REVERT: A 541 ASP cc_start: 0.7848 (t0) cc_final: 0.7596 (t0) REVERT: A 579 ASP cc_start: 0.7109 (p0) cc_final: 0.6803 (p0) REVERT: A 602 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6897 (tm-30) REVERT: A 682 GLU cc_start: 0.8325 (tp30) cc_final: 0.8116 (tp30) REVERT: A 704 MET cc_start: 0.8225 (mtp) cc_final: 0.8014 (mtp) REVERT: A 768 CYS cc_start: 0.8522 (m) cc_final: 0.8191 (m) REVERT: A 832 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7159 (mt) REVERT: A 841 GLU cc_start: 0.8388 (pt0) cc_final: 0.8099 (pt0) REVERT: A 888 ASN cc_start: 0.8030 (t0) cc_final: 0.7375 (m-40) REVERT: A 896 GLU cc_start: 0.6749 (pm20) cc_final: 0.5974 (tp30) outliers start: 22 outliers final: 14 residues processed: 177 average time/residue: 0.1025 time to fit residues: 24.8255 Evaluate side-chains 147 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 80 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 346 ASN A 348 GLN A 481 ASN A 581 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115607 restraints weight = 13340.586| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.81 r_work: 0.3234 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9058 Z= 0.247 Angle : 0.690 7.404 12571 Z= 0.362 Chirality : 0.045 0.185 1459 Planarity : 0.004 0.036 1316 Dihedral : 17.751 91.022 2131 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.64 % Allowed : 14.82 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.32 (0.26), residues: 852 helix: -2.16 (0.21), residues: 497 sheet: -3.74 (0.84), residues: 25 loop : -1.86 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 330 TYR 0.029 0.002 TYR A 762 PHE 0.025 0.003 PHE A 916 TRP 0.013 0.002 TRP A 297 HIS 0.005 0.002 HIS A 879 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 9058) covalent geometry : angle 0.68998 (12571) hydrogen bonds : bond 0.04878 ( 306) hydrogen bonds : angle 4.44189 ( 820) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 241 LYS cc_start: 0.7941 (tttp) cc_final: 0.7353 (tptp) REVERT: A 479 LYS cc_start: 0.8780 (mtpp) cc_final: 0.8011 (ttpp) REVERT: A 538 GLU cc_start: 0.8071 (tp30) cc_final: 0.7813 (tp30) REVERT: A 602 GLU cc_start: 0.7205 (tm-30) cc_final: 0.7003 (tm-30) REVERT: A 645 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7766 (m-10) REVERT: A 682 GLU cc_start: 0.8589 (tp30) cc_final: 0.8252 (tp30) REVERT: A 832 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7405 (mt) REVERT: A 867 GLU cc_start: 0.7101 (mp0) cc_final: 0.6679 (mt-10) REVERT: A 888 ASN cc_start: 0.8219 (t0) cc_final: 0.7462 (m-40) REVERT: A 897 ARG cc_start: 0.7321 (ttp80) cc_final: 0.7031 (ttp80) outliers start: 36 outliers final: 21 residues processed: 151 average time/residue: 0.0992 time to fit residues: 20.7045 Evaluate side-chains 129 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 935 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 63 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 69 optimal weight: 0.2980 chunk 55 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 103 ASN A 346 ASN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.138411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.122533 restraints weight = 13230.088| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.80 r_work: 0.3318 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9058 Z= 0.111 Angle : 0.550 7.255 12571 Z= 0.286 Chirality : 0.038 0.151 1459 Planarity : 0.003 0.037 1316 Dihedral : 17.409 90.754 2131 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.99 % Allowed : 17.27 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.27), residues: 852 helix: -1.59 (0.22), residues: 503 sheet: -3.53 (0.93), residues: 24 loop : -1.59 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 404 TYR 0.014 0.001 TYR A 645 PHE 0.017 0.001 PHE A 848 TRP 0.009 0.001 TRP A 297 HIS 0.004 0.001 HIS A 879 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9058) covalent geometry : angle 0.55022 (12571) hydrogen bonds : bond 0.03949 ( 306) hydrogen bonds : angle 3.99402 ( 820) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 241 LYS cc_start: 0.8015 (tttp) cc_final: 0.7500 (tptp) REVERT: A 261 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7858 (t70) REVERT: A 397 ASP cc_start: 0.7794 (t0) cc_final: 0.7393 (t0) REVERT: A 479 LYS cc_start: 0.8867 (mtpp) cc_final: 0.8161 (ttpt) REVERT: A 488 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7343 (ttmm) REVERT: A 491 LYS cc_start: 0.8434 (pttt) cc_final: 0.8156 (pttm) REVERT: A 538 GLU cc_start: 0.7940 (tp30) cc_final: 0.7659 (tp30) REVERT: A 546 ASP cc_start: 0.7858 (t0) cc_final: 0.7603 (m-30) REVERT: A 608 MET cc_start: 0.8240 (ttm) cc_final: 0.8023 (ttp) REVERT: A 620 ASP cc_start: 0.7194 (p0) cc_final: 0.6961 (t70) REVERT: A 649 TYR cc_start: 0.8173 (t80) cc_final: 0.7902 (t80) REVERT: A 682 GLU cc_start: 0.8449 (tp30) cc_final: 0.8053 (tp30) REVERT: A 806 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7681 (tt) REVERT: A 832 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7110 (mt) REVERT: A 867 GLU cc_start: 0.6986 (mp0) cc_final: 0.6676 (mt-10) REVERT: A 888 ASN cc_start: 0.8059 (t0) cc_final: 0.7360 (m-40) REVERT: A 896 GLU cc_start: 0.6758 (pm20) cc_final: 0.6282 (tp30) outliers start: 31 outliers final: 17 residues processed: 155 average time/residue: 0.0968 time to fit residues: 20.7555 Evaluate side-chains 144 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 868 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 3 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 25 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 346 ASN A 581 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116383 restraints weight = 13268.312| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.81 r_work: 0.3235 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9058 Z= 0.185 Angle : 0.611 7.936 12571 Z= 0.317 Chirality : 0.041 0.171 1459 Planarity : 0.004 0.042 1316 Dihedral : 17.377 91.781 2131 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.15 % Allowed : 17.91 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.27), residues: 852 helix: -1.36 (0.23), residues: 496 sheet: -3.44 (0.78), residues: 34 loop : -1.44 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 404 TYR 0.016 0.002 TYR A 416 PHE 0.018 0.002 PHE A 167 TRP 0.014 0.002 TRP A 297 HIS 0.006 0.001 HIS A 879 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 9058) covalent geometry : angle 0.61111 (12571) hydrogen bonds : bond 0.04204 ( 306) hydrogen bonds : angle 3.92414 ( 820) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.312 Fit side-chains REVERT: A 241 LYS cc_start: 0.8126 (tttp) cc_final: 0.7460 (tptp) REVERT: A 315 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8129 (mp0) REVERT: A 397 ASP cc_start: 0.7910 (t0) cc_final: 0.7045 (t0) REVERT: A 399 GLU cc_start: 0.8021 (pm20) cc_final: 0.7296 (pm20) REVERT: A 449 LYS cc_start: 0.8119 (tptp) cc_final: 0.7680 (tppt) REVERT: A 454 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8478 (mp) REVERT: A 479 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8159 (tmmt) REVERT: A 538 GLU cc_start: 0.8076 (tp30) cc_final: 0.7831 (tp30) REVERT: A 546 ASP cc_start: 0.7944 (t0) cc_final: 0.7647 (m-30) REVERT: A 682 GLU cc_start: 0.8573 (tp30) cc_final: 0.8207 (tp30) REVERT: A 832 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7243 (mt) REVERT: A 841 GLU cc_start: 0.8388 (pt0) cc_final: 0.8110 (pt0) REVERT: A 867 GLU cc_start: 0.7042 (mp0) cc_final: 0.6695 (mt-10) REVERT: A 888 ASN cc_start: 0.8151 (t0) cc_final: 0.7381 (m110) REVERT: A 896 GLU cc_start: 0.6911 (pm20) cc_final: 0.6558 (tp30) outliers start: 40 outliers final: 24 residues processed: 157 average time/residue: 0.1047 time to fit residues: 22.4547 Evaluate side-chains 143 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 911 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 15 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121862 restraints weight = 13267.597| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.78 r_work: 0.3296 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9058 Z= 0.118 Angle : 0.554 8.070 12571 Z= 0.284 Chirality : 0.038 0.151 1459 Planarity : 0.004 0.047 1316 Dihedral : 17.225 91.665 2131 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.51 % Allowed : 19.33 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.28), residues: 852 helix: -1.10 (0.23), residues: 497 sheet: -3.28 (0.81), residues: 33 loop : -1.38 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 897 TYR 0.015 0.001 TYR A 416 PHE 0.016 0.002 PHE A 71 TRP 0.010 0.001 TRP A 297 HIS 0.004 0.001 HIS A 879 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9058) covalent geometry : angle 0.55356 (12571) hydrogen bonds : bond 0.03776 ( 306) hydrogen bonds : angle 3.74334 ( 820) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: A 230 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7573 (mt-10) REVERT: A 241 LYS cc_start: 0.8080 (tttp) cc_final: 0.7432 (tptp) REVERT: A 397 ASP cc_start: 0.7811 (t0) cc_final: 0.7249 (t70) REVERT: A 449 LYS cc_start: 0.7943 (tptp) cc_final: 0.7511 (tppt) REVERT: A 479 LYS cc_start: 0.8973 (mtpp) cc_final: 0.8208 (tmmt) REVERT: A 546 ASP cc_start: 0.7952 (t0) cc_final: 0.7672 (m-30) REVERT: A 587 TYR cc_start: 0.8469 (t80) cc_final: 0.8241 (t80) REVERT: A 682 GLU cc_start: 0.8539 (tp30) cc_final: 0.8197 (tp30) REVERT: A 832 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7169 (mt) REVERT: A 867 GLU cc_start: 0.6941 (mp0) cc_final: 0.6635 (mt-10) outliers start: 35 outliers final: 22 residues processed: 150 average time/residue: 0.0959 time to fit residues: 20.0676 Evaluate side-chains 141 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 911 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 346 ASN A 792 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.133252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117776 restraints weight = 13274.396| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.80 r_work: 0.3250 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9058 Z= 0.159 Angle : 0.594 8.223 12571 Z= 0.306 Chirality : 0.041 0.222 1459 Planarity : 0.004 0.064 1316 Dihedral : 17.215 92.057 2131 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.74 % Allowed : 20.49 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.28), residues: 852 helix: -0.98 (0.23), residues: 496 sheet: -3.34 (0.95), residues: 24 loop : -1.25 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 255 TYR 0.015 0.002 TYR A 416 PHE 0.017 0.002 PHE A 71 TRP 0.012 0.002 TRP A 297 HIS 0.005 0.001 HIS A 879 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9058) covalent geometry : angle 0.59367 (12571) hydrogen bonds : bond 0.03905 ( 306) hydrogen bonds : angle 3.81530 ( 820) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: A 156 MET cc_start: 0.7990 (tpp) cc_final: 0.7779 (tpt) REVERT: A 241 LYS cc_start: 0.8127 (tttp) cc_final: 0.7412 (tptp) REVERT: A 397 ASP cc_start: 0.7868 (t0) cc_final: 0.7316 (t70) REVERT: A 479 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8205 (tmmt) REVERT: A 538 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7758 (mm-30) REVERT: A 546 ASP cc_start: 0.8009 (t0) cc_final: 0.7743 (m-30) REVERT: A 682 GLU cc_start: 0.8569 (tp30) cc_final: 0.8357 (tp30) REVERT: A 832 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7213 (mt) REVERT: A 867 GLU cc_start: 0.7007 (mp0) cc_final: 0.6668 (mt-10) outliers start: 29 outliers final: 22 residues processed: 145 average time/residue: 0.0972 time to fit residues: 19.7422 Evaluate side-chains 139 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 911 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 90 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 77 optimal weight: 0.0470 chunk 53 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116629 restraints weight = 13303.149| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.79 r_work: 0.3241 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 9058 Z= 0.164 Angle : 0.595 8.599 12571 Z= 0.306 Chirality : 0.041 0.197 1459 Planarity : 0.004 0.049 1316 Dihedral : 17.157 92.427 2131 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.87 % Allowed : 20.36 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.28), residues: 852 helix: -0.88 (0.23), residues: 493 sheet: -3.30 (0.94), residues: 24 loop : -1.23 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 255 TYR 0.016 0.002 TYR A 416 PHE 0.018 0.002 PHE A 71 TRP 0.012 0.002 TRP A 297 HIS 0.005 0.001 HIS A 879 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9058) covalent geometry : angle 0.59460 (12571) hydrogen bonds : bond 0.03945 ( 306) hydrogen bonds : angle 3.82275 ( 820) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: A 397 ASP cc_start: 0.7884 (t0) cc_final: 0.7315 (t70) REVERT: A 479 LYS cc_start: 0.9032 (mtpp) cc_final: 0.8236 (tmmt) REVERT: A 487 ASP cc_start: 0.6843 (m-30) cc_final: 0.6572 (m-30) REVERT: A 491 LYS cc_start: 0.8448 (pttt) cc_final: 0.8217 (pttm) REVERT: A 538 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7794 (mm-30) REVERT: A 546 ASP cc_start: 0.8051 (t0) cc_final: 0.7699 (m-30) REVERT: A 832 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7261 (mt) REVERT: A 867 GLU cc_start: 0.6994 (mp0) cc_final: 0.6658 (mt-10) REVERT: A 897 ARG cc_start: 0.7719 (ttp80) cc_final: 0.7450 (ttp80) outliers start: 30 outliers final: 25 residues processed: 140 average time/residue: 0.0930 time to fit residues: 18.4175 Evaluate side-chains 139 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 920 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121037 restraints weight = 13146.839| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.76 r_work: 0.3299 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9058 Z= 0.117 Angle : 0.564 8.853 12571 Z= 0.287 Chirality : 0.038 0.159 1459 Planarity : 0.003 0.043 1316 Dihedral : 17.090 92.011 2131 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.74 % Allowed : 20.62 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.28), residues: 852 helix: -0.68 (0.24), residues: 500 sheet: -3.27 (0.93), residues: 24 loop : -1.15 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 255 TYR 0.015 0.001 TYR A 416 PHE 0.017 0.001 PHE A 848 TRP 0.009 0.001 TRP A 297 HIS 0.004 0.001 HIS A 879 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9058) covalent geometry : angle 0.56402 (12571) hydrogen bonds : bond 0.03601 ( 306) hydrogen bonds : angle 3.68168 ( 820) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 116 MET cc_start: 0.7764 (tpt) cc_final: 0.7382 (tpt) REVERT: A 127 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: A 397 ASP cc_start: 0.7901 (t0) cc_final: 0.7304 (t70) REVERT: A 479 LYS cc_start: 0.9006 (mtpp) cc_final: 0.8234 (tmmt) REVERT: A 487 ASP cc_start: 0.6796 (m-30) cc_final: 0.6539 (m-30) REVERT: A 491 LYS cc_start: 0.8394 (pttt) cc_final: 0.8178 (pttm) REVERT: A 538 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7734 (mm-30) REVERT: A 546 ASP cc_start: 0.7989 (t0) cc_final: 0.7747 (m-30) REVERT: A 553 TYR cc_start: 0.7861 (t80) cc_final: 0.7528 (t80) REVERT: A 682 GLU cc_start: 0.8315 (tp30) cc_final: 0.8066 (tp30) REVERT: A 832 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7194 (mt) REVERT: A 867 GLU cc_start: 0.6890 (mp0) cc_final: 0.6567 (mt-10) REVERT: A 897 ARG cc_start: 0.7710 (ttp80) cc_final: 0.7490 (ttp80) outliers start: 29 outliers final: 25 residues processed: 147 average time/residue: 0.0948 time to fit residues: 19.5183 Evaluate side-chains 147 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 920 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 88 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.134326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119123 restraints weight = 13263.160| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.74 r_work: 0.3271 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9058 Z= 0.142 Angle : 0.587 8.792 12571 Z= 0.298 Chirality : 0.040 0.154 1459 Planarity : 0.003 0.044 1316 Dihedral : 17.085 92.045 2131 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.48 % Allowed : 21.01 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.28), residues: 852 helix: -0.62 (0.24), residues: 501 sheet: -3.26 (0.93), residues: 24 loop : -1.14 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 255 TYR 0.016 0.002 TYR A 416 PHE 0.018 0.002 PHE A 71 TRP 0.011 0.002 TRP A 297 HIS 0.004 0.001 HIS A 879 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9058) covalent geometry : angle 0.58697 (12571) hydrogen bonds : bond 0.03719 ( 306) hydrogen bonds : angle 3.71348 ( 820) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: A 397 ASP cc_start: 0.7848 (t0) cc_final: 0.7301 (t70) REVERT: A 479 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8287 (tmmt) REVERT: A 538 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7829 (mm-30) REVERT: A 546 ASP cc_start: 0.8005 (t0) cc_final: 0.7789 (m-30) REVERT: A 682 GLU cc_start: 0.8333 (tp30) cc_final: 0.8009 (tp30) REVERT: A 832 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7306 (mt) REVERT: A 867 GLU cc_start: 0.6962 (mp0) cc_final: 0.6625 (mt-10) REVERT: A 897 ARG cc_start: 0.7740 (ttp80) cc_final: 0.7538 (ttp80) outliers start: 27 outliers final: 23 residues processed: 137 average time/residue: 0.0989 time to fit residues: 18.8210 Evaluate side-chains 146 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 920 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 0.0170 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 75 optimal weight: 0.0770 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.137600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121982 restraints weight = 13250.602| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.82 r_work: 0.3307 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9058 Z= 0.112 Angle : 0.562 8.906 12571 Z= 0.283 Chirality : 0.038 0.144 1459 Planarity : 0.003 0.043 1316 Dihedral : 17.037 91.661 2131 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.48 % Allowed : 21.01 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.29), residues: 852 helix: -0.48 (0.24), residues: 500 sheet: -2.94 (0.81), residues: 33 loop : -1.13 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 255 TYR 0.016 0.001 TYR A 416 PHE 0.016 0.001 PHE A 71 TRP 0.008 0.001 TRP A 297 HIS 0.004 0.001 HIS A 879 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9058) covalent geometry : angle 0.56206 (12571) hydrogen bonds : bond 0.03477 ( 306) hydrogen bonds : angle 3.60923 ( 820) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2028.29 seconds wall clock time: 35 minutes 48.43 seconds (2148.43 seconds total)