Starting phenix.real_space_refine on Sat Aug 23 16:39:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8x_34551/08_2025/8h8x_34551.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8x_34551/08_2025/8h8x_34551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h8x_34551/08_2025/8h8x_34551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8x_34551/08_2025/8h8x_34551.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h8x_34551/08_2025/8h8x_34551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8x_34551/08_2025/8h8x_34551.map" } resolution = 3.92 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= 1.000 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: 5 Type Number sf(0) Gaussians S 49 5.16 5 C 4274 2.51 5 N 1166 2.21 5 O 1262 1.98 5 H 6667 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 13418 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 13418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 13418 Classifications: {'peptide': 850} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 39, 'TRANS': 810} Chain breaks: 1 Time building chain proxies: 2.64, per 1000 atoms: 0.20 Number of scatterers: 13418 At special positions: 0 Unit cell: (75.5392, 100.433, 156.229, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 O 1262 8.00 N 1166 7.00 C 4274 6.00 H 6667 1.00 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: 1.23 Conformation dependent library (CDL) restraints added in 416.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 4 sheets defined 63.9% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 3 through 17 removed outlier: 4.401A pdb=" N LEU A 11 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER A 14 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 40 removed outlier: 4.182A pdb=" N TYR A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Proline residue: A 36 - end of helix Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 67 through 76 removed outlier: 3.546A pdb=" N ILE A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.934A pdb=" N LEU A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 109 removed outlier: 3.986A pdb=" N LEU A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.529A pdb=" N LEU A 117 " --> pdb=" O CYS A 113 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 118 " --> pdb=" O MET A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 144 through 152 removed outlier: 3.523A pdb=" N GLN A 152 " --> pdb=" O HIS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 199 through 208 removed outlier: 3.556A pdb=" N PHE A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 232 through 240 removed outlier: 3.612A pdb=" N CYS A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 252 removed outlier: 3.888A pdb=" N CYS A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.888A pdb=" N THR A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 284 removed outlier: 3.538A pdb=" N LEU A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLN A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 308 removed outlier: 4.133A pdb=" N LYS A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 334 removed outlier: 3.898A pdb=" N GLN A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 321 " --> pdb=" O MET A 317 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N MET A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 360 through 382 removed outlier: 3.666A pdb=" N TRP A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 369 " --> pdb=" O HIS A 365 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TRP A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 464 removed outlier: 3.738A pdb=" N ALA A 449 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 454 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 455 " --> pdb=" O ARG A 451 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS A 463 " --> pdb=" O PHE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 483 removed outlier: 3.560A pdb=" N ILE A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 479 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS A 483 " --> pdb=" O PHE A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.562A pdb=" N LYS A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N CYS A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 508 through 515 Processing helix chain 'A' and resid 515 through 520 removed outlier: 4.058A pdb=" N ILE A 519 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 520 " --> pdb=" O MET A 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 515 through 520' Processing helix chain 'A' and resid 524 through 530 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 561 through 573 removed outlier: 3.894A pdb=" N GLU A 568 " --> pdb=" O ARG A 564 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 571 " --> pdb=" O CYS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 596 through 608 removed outlier: 3.750A pdb=" N TRP A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 629 through 634 removed outlier: 4.152A pdb=" N TYR A 632 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 633 " --> pdb=" O ASN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 654 removed outlier: 3.639A pdb=" N PHE A 643 " --> pdb=" O ASN A 639 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 644 " --> pdb=" O TYR A 640 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 645 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 646 " --> pdb=" O ARG A 642 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 649 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 650 " --> pdb=" O GLN A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 671 removed outlier: 3.778A pdb=" N TYR A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 668 " --> pdb=" O ARG A 664 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 683 removed outlier: 3.774A pdb=" N SER A 682 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 697 removed outlier: 3.837A pdb=" N ALA A 688 " --> pdb=" O ASP A 684 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 694 " --> pdb=" O ASN A 690 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 702 removed outlier: 3.566A pdb=" N ASP A 701 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 765 removed outlier: 3.519A pdb=" N THR A 745 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET A 749 " --> pdb=" O THR A 745 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A 752 " --> pdb=" O ARG A 748 " (cutoff:3.500A) Proline residue: A 755 - end of helix removed outlier: 3.611A pdb=" N ASN A 758 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA A 759 " --> pdb=" O PRO A 755 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 774 removed outlier: 4.052A pdb=" N ILE A 773 " --> pdb=" O PRO A 769 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN A 774 " --> pdb=" O PRO A 770 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 769 through 774' Processing helix chain 'A' and resid 780 through 787 removed outlier: 4.047A pdb=" N LEU A 784 " --> pdb=" O GLU A 780 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 785 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 799 removed outlier: 3.512A pdb=" N ASN A 799 " --> pdb=" O ASP A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 821 removed outlier: 3.604A pdb=" N TRP A 817 " --> pdb=" O ILE A 813 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 818 " --> pdb=" O GLN A 814 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 819 " --> pdb=" O TRP A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 837 removed outlier: 3.728A pdb=" N ARG A 828 " --> pdb=" O THR A 824 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU A 830 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 849 removed outlier: 3.916A pdb=" N ALA A 847 " --> pdb=" O GLY A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 904 removed outlier: 4.772A pdb=" N LEU A 896 " --> pdb=" O LYS A 892 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N HIS A 900 " --> pdb=" O LEU A 896 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 555 through 557 Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 618 Processing sheet with id=AA3, first strand: chain 'A' and resid 709 through 713 removed outlier: 3.587A pdb=" N VAL A 721 " --> pdb=" O VAL A 710 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 801 through 802 removed outlier: 6.684A pdb=" N GLU A 801 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N ALA A 862 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR A 859 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LEU A 882 " --> pdb=" O THR A 859 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA A 861 " --> pdb=" O LEU A 882 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 6645 1.03 - 1.22: 23 1.22 - 1.42: 2892 1.42 - 1.61: 3930 1.61 - 1.81: 76 Bond restraints: 13566 Sorted by residual: bond pdb=" CB VAL A 324 " pdb=" CG1 VAL A 324 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.40e+00 bond pdb=" CA ASP A 621 " pdb=" C ASP A 621 " ideal model delta sigma weight residual 1.523 1.487 0.036 1.41e-02 5.03e+03 6.55e+00 bond pdb=" CG LEU A 320 " pdb=" CD1 LEU A 320 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.35e+00 bond pdb=" CG LEU A 321 " pdb=" CD2 LEU A 321 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.80e+00 bond pdb=" CA PHE A 524 " pdb=" CB PHE A 524 " ideal model delta sigma weight residual 1.534 1.500 0.034 1.45e-02 4.76e+03 5.35e+00 ... (remaining 13561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 23093 1.66 - 3.32: 1278 3.32 - 4.98: 107 4.98 - 6.64: 16 6.64 - 8.30: 3 Bond angle restraints: 24497 Sorted by residual: angle pdb=" N LEU A 535 " pdb=" CA LEU A 535 " pdb=" C LEU A 535 " ideal model delta sigma weight residual 113.18 107.77 5.41 1.33e+00 5.65e-01 1.65e+01 angle pdb=" N LYS A 350 " pdb=" CA LYS A 350 " pdb=" CB LYS A 350 " ideal model delta sigma weight residual 114.17 109.88 4.29 1.14e+00 7.69e-01 1.41e+01 angle pdb=" N THR A 623 " pdb=" CA THR A 623 " pdb=" C THR A 623 " ideal model delta sigma weight residual 113.55 109.34 4.21 1.26e+00 6.30e-01 1.11e+01 angle pdb=" N ASP A 541 " pdb=" CA ASP A 541 " pdb=" C ASP A 541 " ideal model delta sigma weight residual 111.55 107.72 3.83 1.37e+00 5.33e-01 7.82e+00 angle pdb=" N ILE A 498 " pdb=" CA ILE A 498 " pdb=" CB ILE A 498 " ideal model delta sigma weight residual 111.23 106.85 4.38 1.65e+00 3.67e-01 7.06e+00 ... (remaining 24492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.63: 5719 14.63 - 29.27: 489 29.27 - 43.90: 139 43.90 - 58.53: 57 58.53 - 73.16: 5 Dihedral angle restraints: 6409 sinusoidal: 3493 harmonic: 2916 Sorted by residual: dihedral pdb=" CA HIS A 534 " pdb=" C HIS A 534 " pdb=" N LEU A 535 " pdb=" CA LEU A 535 " ideal model delta harmonic sigma weight residual 180.00 144.57 35.43 0 5.00e+00 4.00e-02 5.02e+01 dihedral pdb=" CA LEU A 706 " pdb=" C LEU A 706 " pdb=" N THR A 707 " pdb=" CA THR A 707 " ideal model delta harmonic sigma weight residual -180.00 -148.92 -31.08 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA PRO A 540 " pdb=" C PRO A 540 " pdb=" N ASP A 541 " pdb=" CA ASP A 541 " ideal model delta harmonic sigma weight residual 180.00 151.38 28.62 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 6406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 603 0.036 - 0.071: 295 0.071 - 0.107: 100 0.107 - 0.143: 40 0.143 - 0.179: 6 Chirality restraints: 1044 Sorted by residual: chirality pdb=" CB VAL A 455 " pdb=" CA VAL A 455 " pdb=" CG1 VAL A 455 " pdb=" CG2 VAL A 455 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CG LEU A 321 " pdb=" CB LEU A 321 " pdb=" CD1 LEU A 321 " pdb=" CD2 LEU A 321 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA PRO A 540 " pdb=" N PRO A 540 " pdb=" C PRO A 540 " pdb=" CB PRO A 540 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 1041 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 459 " -0.022 2.00e-02 2.50e+03 1.57e-02 7.37e+00 pdb=" CG PHE A 459 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 459 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 459 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 459 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 459 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 459 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 459 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE A 459 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 459 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 459 " -0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 459 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 534 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C HIS A 534 " -0.045 2.00e-02 2.50e+03 pdb=" O HIS A 534 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU A 535 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 547 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 548 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 548 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 548 " -0.031 5.00e-02 4.00e+02 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1587 2.25 - 2.84: 30500 2.84 - 3.43: 32464 3.43 - 4.01: 42752 4.01 - 4.60: 67443 Nonbonded interactions: 174746 Sorted by model distance: nonbonded pdb=" O PRO A 335 " pdb=" H ASP A 343 " model vdw 1.663 2.450 nonbonded pdb=" O ILE A 753 " pdb=" H GLN A 756 " model vdw 1.668 2.450 nonbonded pdb=" O PHE A 708 " pdb=" H LEU A 723 " model vdw 1.688 2.450 nonbonded pdb=" O HIS A 534 " pdb="HE21 GLN A 539 " model vdw 1.690 2.450 nonbonded pdb=" HG SER A 619 " pdb=" OG1 THR A 624 " model vdw 1.691 2.450 ... (remaining 174741 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.080 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 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 0.090 6899 Z= 0.446 Angle : 0.894 8.290 9356 Z= 0.508 Chirality : 0.050 0.179 1044 Planarity : 0.006 0.056 1219 Dihedral : 9.886 73.163 2558 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.57 (0.25), residues: 846 helix: -3.12 (0.18), residues: 378 sheet: -2.02 (1.01), residues: 19 loop : -1.61 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 66 TYR 0.028 0.003 TYR A 667 PHE 0.046 0.004 PHE A 459 TRP 0.035 0.004 TRP A 796 HIS 0.014 0.003 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.01074 ( 6899) covalent geometry : angle 0.89390 ( 9356) hydrogen bonds : bond 0.32507 ( 259) hydrogen bonds : angle 10.80296 ( 720) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8846 (mtp) cc_final: 0.8589 (mmm) REVERT: A 524 PHE cc_start: 0.7147 (m-80) cc_final: 0.6905 (m-10) REVERT: A 751 ARG cc_start: 0.7671 (tpt90) cc_final: 0.7033 (tpm170) REVERT: A 822 ASP cc_start: 0.7983 (m-30) cc_final: 0.7780 (t0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2627 time to fit residues: 37.2916 Evaluate side-chains 74 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 257 GLN A 536 HIS A 697 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.119926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.093190 restraints weight = 65527.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.096748 restraints weight = 33621.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.098943 restraints weight = 21945.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.100340 restraints weight = 16820.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.101066 restraints weight = 14271.775| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6899 Z= 0.159 Angle : 0.639 5.881 9356 Z= 0.346 Chirality : 0.038 0.137 1044 Planarity : 0.005 0.054 1219 Dihedral : 6.181 28.157 917 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.53 % Allowed : 5.56 % Favored : 93.91 % 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 aren not related in a simple way. whole: -2.69 (0.25), residues: 846 helix: -1.71 (0.20), residues: 436 sheet: -1.87 (1.02), residues: 19 loop : -1.74 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 107 TYR 0.017 0.001 TYR A 313 PHE 0.015 0.001 PHE A 531 TRP 0.011 0.002 TRP A 600 HIS 0.005 0.001 HIS A 669 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 6899) covalent geometry : angle 0.63866 ( 9356) hydrogen bonds : bond 0.05742 ( 259) hydrogen bonds : angle 6.44911 ( 720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 TRP cc_start: 0.8574 (t-100) cc_final: 0.7942 (t-100) REVERT: A 741 VAL cc_start: 0.7252 (t) cc_final: 0.7001 (p) REVERT: A 751 ARG cc_start: 0.7587 (tpt90) cc_final: 0.6925 (tpm170) REVERT: A 818 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7827 (mt-10) outliers start: 4 outliers final: 3 residues processed: 90 average time/residue: 0.2173 time to fit residues: 25.5817 Evaluate side-chains 69 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 677 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.120431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.092866 restraints weight = 65303.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.096522 restraints weight = 32847.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.098739 restraints weight = 21366.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.100151 restraints weight = 16417.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.100836 restraints weight = 13966.842| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6899 Z= 0.123 Angle : 0.548 5.185 9356 Z= 0.293 Chirality : 0.037 0.138 1044 Planarity : 0.005 0.074 1219 Dihedral : 5.498 24.462 917 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.66 % Allowed : 7.15 % Favored : 92.19 % 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: -1.79 (0.27), residues: 846 helix: -0.83 (0.22), residues: 439 sheet: -0.97 (1.28), residues: 18 loop : -1.53 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.010 0.001 TYR A 313 PHE 0.018 0.001 PHE A 816 TRP 0.008 0.001 TRP A 600 HIS 0.005 0.001 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6899) covalent geometry : angle 0.54753 ( 9356) hydrogen bonds : bond 0.04503 ( 259) hydrogen bonds : angle 5.57788 ( 720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 GLN cc_start: 0.8807 (tp-100) cc_final: 0.8494 (tp-100) REVERT: A 751 ARG cc_start: 0.7516 (tpt90) cc_final: 0.6852 (tpm170) REVERT: A 827 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6798 (mt-10) REVERT: A 879 MET cc_start: 0.8387 (ttt) cc_final: 0.8144 (tpp) outliers start: 5 outliers final: 4 residues processed: 80 average time/residue: 0.1972 time to fit residues: 21.3793 Evaluate side-chains 67 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 677 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 129 ASN A 252 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.117530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.089760 restraints weight = 64943.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.093248 restraints weight = 33036.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.095455 restraints weight = 21761.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.096607 restraints weight = 16784.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.097515 restraints weight = 14511.606| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6899 Z= 0.198 Angle : 0.587 6.073 9356 Z= 0.318 Chirality : 0.038 0.134 1044 Planarity : 0.004 0.053 1219 Dihedral : 5.427 26.176 917 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.66 % Allowed : 7.95 % Favored : 91.39 % 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: -1.66 (0.28), residues: 846 helix: -0.62 (0.23), residues: 441 sheet: -1.24 (0.98), residues: 29 loop : -1.60 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 514 TYR 0.012 0.002 TYR A 202 PHE 0.018 0.002 PHE A 531 TRP 0.009 0.001 TRP A 796 HIS 0.007 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 6899) covalent geometry : angle 0.58719 ( 9356) hydrogen bonds : bond 0.04434 ( 259) hydrogen bonds : angle 5.71070 ( 720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8529 (tp-100) REVERT: A 751 ARG cc_start: 0.7478 (tpt90) cc_final: 0.6834 (tpm170) REVERT: A 879 MET cc_start: 0.8384 (ttt) cc_final: 0.7803 (tpp) REVERT: A 882 LEU cc_start: 0.8252 (mp) cc_final: 0.7454 (tt) outliers start: 5 outliers final: 3 residues processed: 68 average time/residue: 0.2029 time to fit residues: 18.6136 Evaluate side-chains 66 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 525 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 63 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.118401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.090860 restraints weight = 64939.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.094388 restraints weight = 32362.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.096634 restraints weight = 21135.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.097953 restraints weight = 16176.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.098688 restraints weight = 13813.868| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6899 Z= 0.129 Angle : 0.522 5.387 9356 Z= 0.276 Chirality : 0.037 0.134 1044 Planarity : 0.004 0.051 1219 Dihedral : 5.082 25.249 917 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.66 % Allowed : 7.81 % Favored : 91.52 % 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: -1.17 (0.29), residues: 846 helix: -0.12 (0.24), residues: 443 sheet: -0.96 (0.97), residues: 29 loop : -1.51 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 514 TYR 0.008 0.001 TYR A 802 PHE 0.013 0.001 PHE A 816 TRP 0.008 0.001 TRP A 817 HIS 0.005 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6899) covalent geometry : angle 0.52194 ( 9356) hydrogen bonds : bond 0.03768 ( 259) hydrogen bonds : angle 5.22803 ( 720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 GLN cc_start: 0.8880 (tp-100) cc_final: 0.8539 (tp-100) REVERT: A 751 ARG cc_start: 0.7427 (tpt90) cc_final: 0.6773 (tpm170) REVERT: A 879 MET cc_start: 0.8402 (ttt) cc_final: 0.7991 (tpp) REVERT: A 882 LEU cc_start: 0.8234 (mp) cc_final: 0.7424 (tt) outliers start: 5 outliers final: 3 residues processed: 72 average time/residue: 0.1848 time to fit residues: 18.4582 Evaluate side-chains 68 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 592 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 GLN A 758 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.116210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.091242 restraints weight = 64567.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.091699 restraints weight = 31390.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.093669 restraints weight = 24600.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.093702 restraints weight = 20717.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.093742 restraints weight = 19312.085| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6899 Z= 0.197 Angle : 0.575 4.857 9356 Z= 0.309 Chirality : 0.038 0.135 1044 Planarity : 0.004 0.053 1219 Dihedral : 5.196 26.229 917 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.93 % Allowed : 8.34 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.29), residues: 846 helix: -0.20 (0.24), residues: 443 sheet: -1.01 (0.98), residues: 29 loop : -1.53 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 514 TYR 0.011 0.001 TYR A 202 PHE 0.017 0.002 PHE A 531 TRP 0.010 0.001 TRP A 796 HIS 0.006 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 6899) covalent geometry : angle 0.57499 ( 9356) hydrogen bonds : bond 0.04192 ( 259) hydrogen bonds : angle 5.45312 ( 720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 GLN cc_start: 0.8946 (tp-100) cc_final: 0.8622 (tp-100) REVERT: A 751 ARG cc_start: 0.7603 (tpt90) cc_final: 0.6914 (tpm170) REVERT: A 879 MET cc_start: 0.8585 (ttt) cc_final: 0.8062 (tpp) REVERT: A 882 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7454 (tt) outliers start: 7 outliers final: 4 residues processed: 64 average time/residue: 0.1962 time to fit residues: 17.2441 Evaluate side-chains 66 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 693 TRP Chi-restraints excluded: chain A residue 882 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 66 optimal weight: 0.0470 chunk 52 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 48 optimal weight: 0.1980 chunk 33 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.119180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.091657 restraints weight = 65091.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.095296 restraints weight = 32142.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.097478 restraints weight = 20828.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.098773 restraints weight = 16048.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.099592 restraints weight = 13719.895| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6899 Z= 0.091 Angle : 0.497 5.464 9356 Z= 0.258 Chirality : 0.036 0.129 1044 Planarity : 0.004 0.050 1219 Dihedral : 4.818 25.290 917 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.66 % Allowed : 8.61 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.29), residues: 846 helix: 0.27 (0.24), residues: 455 sheet: -0.61 (1.00), residues: 29 loop : -1.38 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.008 0.001 TYR A 532 PHE 0.011 0.001 PHE A 816 TRP 0.012 0.001 TRP A 817 HIS 0.003 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 6899) covalent geometry : angle 0.49697 ( 9356) hydrogen bonds : bond 0.03294 ( 259) hydrogen bonds : angle 4.85732 ( 720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 GLN cc_start: 0.8881 (tp-100) cc_final: 0.8520 (tp-100) REVERT: A 751 ARG cc_start: 0.7443 (tpt90) cc_final: 0.6757 (tpm170) REVERT: A 827 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7194 (mt-10) REVERT: A 879 MET cc_start: 0.8378 (ttt) cc_final: 0.8057 (tpp) REVERT: A 882 LEU cc_start: 0.8314 (mp) cc_final: 0.7550 (tt) outliers start: 5 outliers final: 5 residues processed: 68 average time/residue: 0.1923 time to fit residues: 18.1478 Evaluate side-chains 69 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 677 TYR Chi-restraints excluded: chain A residue 693 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 54 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 59 optimal weight: 0.4980 chunk 52 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.117140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.089578 restraints weight = 63952.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.092944 restraints weight = 32228.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.095042 restraints weight = 21288.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.096334 restraints weight = 16536.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.097058 restraints weight = 14171.034| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6899 Z= 0.144 Angle : 0.523 4.708 9356 Z= 0.276 Chirality : 0.037 0.130 1044 Planarity : 0.004 0.050 1219 Dihedral : 4.864 24.614 917 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.79 % Allowed : 9.01 % Favored : 90.20 % 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 aren not related in a simple way. whole: -0.73 (0.29), residues: 846 helix: 0.24 (0.24), residues: 450 sheet: -0.75 (0.98), residues: 29 loop : -1.33 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.008 0.001 TYR A 202 PHE 0.013 0.001 PHE A 531 TRP 0.008 0.001 TRP A 796 HIS 0.004 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6899) covalent geometry : angle 0.52295 ( 9356) hydrogen bonds : bond 0.03603 ( 259) hydrogen bonds : angle 5.00233 ( 720) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8496 (tp-100) REVERT: A 751 ARG cc_start: 0.7417 (tpt90) cc_final: 0.6712 (tpm170) REVERT: A 879 MET cc_start: 0.8402 (ttt) cc_final: 0.8064 (tpp) REVERT: A 882 LEU cc_start: 0.8340 (mp) cc_final: 0.7581 (tt) outliers start: 6 outliers final: 5 residues processed: 66 average time/residue: 0.1961 time to fit residues: 17.6433 Evaluate side-chains 69 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 693 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 68 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 27 optimal weight: 0.0980 chunk 58 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.117657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.090086 restraints weight = 64403.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.093586 restraints weight = 31944.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.095750 restraints weight = 20866.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.097046 restraints weight = 16027.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.097691 restraints weight = 13702.261| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6899 Z= 0.107 Angle : 0.502 4.902 9356 Z= 0.261 Chirality : 0.036 0.127 1044 Planarity : 0.004 0.049 1219 Dihedral : 4.750 25.003 917 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.66 % Allowed : 8.87 % Favored : 90.46 % 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: -0.65 (0.29), residues: 846 helix: 0.30 (0.24), residues: 455 sheet: -0.70 (0.98), residues: 29 loop : -1.31 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 840 TYR 0.008 0.001 TYR A 532 PHE 0.011 0.001 PHE A 531 TRP 0.010 0.001 TRP A 817 HIS 0.003 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 6899) covalent geometry : angle 0.50218 ( 9356) hydrogen bonds : bond 0.03370 ( 259) hydrogen bonds : angle 4.82527 ( 720) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 GLN cc_start: 0.7485 (tt0) cc_final: 0.7021 (pt0) REVERT: A 742 GLN cc_start: 0.8842 (tp-100) cc_final: 0.8514 (tp-100) REVERT: A 751 ARG cc_start: 0.7404 (tpt90) cc_final: 0.6699 (tpm170) REVERT: A 827 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7134 (mt-10) REVERT: A 879 MET cc_start: 0.8436 (ttt) cc_final: 0.8073 (tpp) REVERT: A 882 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7614 (tt) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 0.1914 time to fit residues: 18.1811 Evaluate side-chains 72 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 693 TRP Chi-restraints excluded: chain A residue 882 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 54 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 60 optimal weight: 0.3980 chunk 76 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.119156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.091423 restraints weight = 64003.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.095067 restraints weight = 31594.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.097301 restraints weight = 20469.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.098606 restraints weight = 15771.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.099327 restraints weight = 13490.579| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6899 Z= 0.091 Angle : 0.498 7.408 9356 Z= 0.255 Chirality : 0.036 0.132 1044 Planarity : 0.004 0.049 1219 Dihedral : 4.542 23.871 917 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.53 % Allowed : 9.67 % Favored : 89.80 % 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: -0.30 (0.29), residues: 846 helix: 0.62 (0.24), residues: 457 sheet: -0.72 (0.99), residues: 30 loop : -1.19 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.011 0.001 TYR A 661 PHE 0.012 0.001 PHE A 816 TRP 0.011 0.001 TRP A 817 HIS 0.003 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 6899) covalent geometry : angle 0.49765 ( 9356) hydrogen bonds : bond 0.03076 ( 259) hydrogen bonds : angle 4.60733 ( 720) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 GLN cc_start: 0.7493 (tt0) cc_final: 0.7038 (pt0) REVERT: A 742 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8464 (tp-100) REVERT: A 751 ARG cc_start: 0.7402 (tpt90) cc_final: 0.6683 (tpm170) REVERT: A 827 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 879 MET cc_start: 0.8449 (ttt) cc_final: 0.8017 (tpp) REVERT: A 882 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7695 (tp) outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 0.2068 time to fit residues: 19.8996 Evaluate side-chains 73 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 693 TRP Chi-restraints excluded: chain A residue 882 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 0.0020 chunk 43 optimal weight: 0.0970 chunk 46 optimal weight: 0.0870 chunk 11 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.119966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.092657 restraints weight = 64678.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.096266 restraints weight = 32078.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.098440 restraints weight = 20874.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.099726 restraints weight = 16091.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.100567 restraints weight = 13744.103| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6899 Z= 0.086 Angle : 0.487 6.089 9356 Z= 0.250 Chirality : 0.035 0.125 1044 Planarity : 0.004 0.048 1219 Dihedral : 4.373 22.964 917 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.79 % Allowed : 9.27 % Favored : 89.93 % 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: -0.03 (0.30), residues: 846 helix: 0.89 (0.25), residues: 456 sheet: -0.78 (0.96), residues: 30 loop : -1.10 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 332 TYR 0.011 0.001 TYR A 885 PHE 0.012 0.001 PHE A 816 TRP 0.011 0.001 TRP A 817 HIS 0.005 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 6899) covalent geometry : angle 0.48745 ( 9356) hydrogen bonds : bond 0.02938 ( 259) hydrogen bonds : angle 4.46703 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2608.90 seconds wall clock time: 45 minutes 17.81 seconds (2717.81 seconds total)