Starting phenix.real_space_refine on Sun Nov 17 09:12:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8x_34551/11_2024/8h8x_34551.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8x_34551/11_2024/8h8x_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8x_34551/11_2024/8h8x_34551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8x_34551/11_2024/8h8x_34551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8x_34551/11_2024/8h8x_34551.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8x_34551/11_2024/8h8x_34551.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 6.57, per 1000 atoms: 0.49 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: 3.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.07 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: 4.52 Time building geometry restraints manager: 4.10 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: 1.070 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: 0.180 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.680 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.470 ------------------------------------------------------------------------------- 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= 0.690 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 : 4.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (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 TRP 0.035 0.004 TRP A 796 HIS 0.014 0.003 HIS A 654 PHE 0.046 0.004 PHE A 459 TYR 0.028 0.003 TYR A 667 ARG 0.009 0.001 ARG A 66 *********************** 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 : 0.978 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: 0.5458 time to fit residues: 77.6913 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 : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.5980 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 257 GLN A 669 HIS A 697 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2843 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= 0.175 Angle : 0.621 5.982 9356 Z= 0.334 Chirality : 0.038 0.138 1044 Planarity : 0.005 0.052 1219 Dihedral : 6.070 27.517 917 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.53 % Allowed : 5.17 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.26), residues: 846 helix: -1.62 (0.20), residues: 437 sheet: -1.78 (1.04), residues: 19 loop : -1.66 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 600 HIS 0.005 0.001 HIS A 669 PHE 0.013 0.001 PHE A 327 TYR 0.017 0.001 TYR A 313 ARG 0.003 0.000 ARG A 107 *********************** 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 95 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8564 (t-100) cc_final: 0.7812 (t-100) REVERT: A 751 ARG cc_start: 0.7564 (tpt90) cc_final: 0.6857 (tpm170) outliers start: 4 outliers final: 3 residues processed: 93 average time/residue: 0.4569 time to fit residues: 56.0595 Evaluate side-chains 75 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 76 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 129 ASN A 536 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6899 Z= 0.217 Angle : 0.565 5.448 9356 Z= 0.304 Chirality : 0.037 0.136 1044 Planarity : 0.005 0.061 1219 Dihedral : 5.518 23.761 917 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.53 % Allowed : 7.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.27), residues: 846 helix: -0.90 (0.22), residues: 439 sheet: -1.19 (1.22), residues: 18 loop : -1.55 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 600 HIS 0.006 0.001 HIS A 558 PHE 0.013 0.001 PHE A 531 TYR 0.010 0.001 TYR A 313 ARG 0.005 0.000 ARG A 514 *********************** 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 85 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 1.091 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 146 LEU cc_start: 0.9126 (tt) cc_final: 0.8858 (tt) REVERT: A 742 GLN cc_start: 0.8848 (tp-100) cc_final: 0.8504 (tp-100) REVERT: A 751 ARG cc_start: 0.7541 (tpt90) cc_final: 0.6845 (tpm170) REVERT: A 879 MET cc_start: 0.8385 (ttt) cc_final: 0.8089 (tpp) REVERT: A 882 LEU cc_start: 0.8276 (mp) cc_final: 0.7592 (tp) outliers start: 4 outliers final: 3 residues processed: 83 average time/residue: 0.4910 time to fit residues: 53.7881 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 : 1.103 ------------------------------------------------------------------------------- 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 677 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6899 Z= 0.173 Angle : 0.532 5.937 9356 Z= 0.281 Chirality : 0.037 0.132 1044 Planarity : 0.004 0.049 1219 Dihedral : 5.190 24.479 917 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.66 % Allowed : 7.55 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.28), residues: 846 helix: -0.32 (0.23), residues: 441 sheet: -1.07 (0.97), residues: 29 loop : -1.49 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 796 HIS 0.004 0.001 HIS A 654 PHE 0.012 0.001 PHE A 531 TYR 0.018 0.001 TYR A 120 ARG 0.004 0.000 ARG A 514 *********************** 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 78 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 1.054 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: 0.8864 (tp-100) cc_final: 0.8518 (tp-100) REVERT: A 751 ARG cc_start: 0.7457 (tpt90) cc_final: 0.6779 (tpm170) REVERT: A 879 MET cc_start: 0.8400 (ttt) cc_final: 0.7962 (tpp) REVERT: A 882 LEU cc_start: 0.8192 (mp) cc_final: 0.7570 (tt) outliers start: 5 outliers final: 3 residues processed: 74 average time/residue: 0.4546 time to fit residues: 44.6020 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 : 1.044 ------------------------------------------------------------------------------- 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 677 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 0.0000 chunk 1 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 0.4980 chunk 73 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6899 Z= 0.141 Angle : 0.501 6.330 9356 Z= 0.262 Chirality : 0.036 0.130 1044 Planarity : 0.004 0.048 1219 Dihedral : 4.825 22.716 917 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.40 % Allowed : 7.68 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.29), residues: 846 helix: 0.23 (0.24), residues: 442 sheet: -0.85 (1.21), residues: 18 loop : -1.22 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 796 HIS 0.004 0.001 HIS A 517 PHE 0.009 0.001 PHE A 531 TYR 0.014 0.001 TYR A 120 ARG 0.001 0.000 ARG A 332 *********************** 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 70 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.951 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: 0.8864 (tp-100) cc_final: 0.8493 (tp-100) REVERT: A 751 ARG cc_start: 0.7392 (tpt90) cc_final: 0.6710 (tpm170) REVERT: A 879 MET cc_start: 0.8393 (ttt) cc_final: 0.7974 (tpp) outliers start: 3 outliers final: 1 residues processed: 67 average time/residue: 0.3895 time to fit residues: 37.1562 Evaluate side-chains 62 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 79 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4788 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= 0.251 Angle : 0.554 5.769 9356 Z= 0.296 Chirality : 0.038 0.132 1044 Planarity : 0.004 0.050 1219 Dihedral : 4.963 23.745 917 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.26 % Allowed : 8.61 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.29), residues: 846 helix: 0.17 (0.24), residues: 443 sheet: -0.91 (0.96), residues: 29 loop : -1.36 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 796 HIS 0.006 0.001 HIS A 654 PHE 0.017 0.002 PHE A 531 TYR 0.013 0.001 TYR A 120 ARG 0.002 0.000 ARG A 13 *********************** 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: 2 poor density : 67 time to evaluate : 1.036 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: A 742 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8485 (tp-100) REVERT: A 751 ARG cc_start: 0.7453 (tpt90) cc_final: 0.6770 (tpm170) REVERT: A 879 MET cc_start: 0.8346 (ttt) cc_final: 0.7994 (tpp) REVERT: A 882 LEU cc_start: 0.8331 (mp) cc_final: 0.7605 (tt) outliers start: 2 outliers final: 2 residues processed: 67 average time/residue: 0.4092 time to fit residues: 37.1400 Evaluate side-chains 64 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 693 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 51 optimal weight: 0.1980 chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6899 Z= 0.140 Angle : 0.498 5.926 9356 Z= 0.258 Chirality : 0.036 0.128 1044 Planarity : 0.004 0.048 1219 Dihedral : 4.691 23.279 917 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.53 % Allowed : 8.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.30), residues: 846 helix: 0.54 (0.24), residues: 451 sheet: -0.68 (0.97), residues: 29 loop : -1.25 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 817 HIS 0.004 0.001 HIS A 517 PHE 0.018 0.001 PHE A 331 TYR 0.011 0.001 TYR A 120 ARG 0.001 0.000 ARG A 107 *********************** 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 68 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 1.043 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: A 742 GLN cc_start: 0.8822 (tp-100) cc_final: 0.8494 (tp-100) REVERT: A 751 ARG cc_start: 0.7410 (tpt90) cc_final: 0.6694 (tpm170) REVERT: A 879 MET cc_start: 0.8369 (ttt) cc_final: 0.8052 (tpp) REVERT: A 882 LEU cc_start: 0.8363 (mp) cc_final: 0.7662 (tt) outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 0.4232 time to fit residues: 36.5465 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 : 1.101 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 74 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5147 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= 0.274 Angle : 0.560 5.414 9356 Z= 0.298 Chirality : 0.038 0.134 1044 Planarity : 0.004 0.050 1219 Dihedral : 4.897 23.771 917 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.93 % Allowed : 8.48 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.29), residues: 846 helix: 0.36 (0.24), residues: 445 sheet: -0.69 (0.99), residues: 29 loop : -1.33 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 796 HIS 0.006 0.001 HIS A 654 PHE 0.017 0.002 PHE A 531 TYR 0.012 0.002 TYR A 885 ARG 0.002 0.000 ARG A 13 *********************** 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 73 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 1.031 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: 0.8789 (tp-100) cc_final: 0.8459 (tp-100) REVERT: A 751 ARG cc_start: 0.7458 (tpt90) cc_final: 0.6733 (tpm170) REVERT: A 879 MET cc_start: 0.8401 (ttt) cc_final: 0.8029 (tpp) REVERT: A 882 LEU cc_start: 0.8340 (mp) cc_final: 0.7758 (tp) outliers start: 7 outliers final: 4 residues processed: 68 average time/residue: 0.4233 time to fit residues: 39.1862 Evaluate side-chains 70 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 0.0870 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 overall best weight: 1.1762 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6899 Z= 0.159 Angle : 0.500 5.474 9356 Z= 0.261 Chirality : 0.036 0.127 1044 Planarity : 0.004 0.049 1219 Dihedral : 4.704 23.918 917 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.53 % Allowed : 8.48 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.29), residues: 846 helix: 0.57 (0.24), residues: 456 sheet: -0.56 (0.98), residues: 29 loop : -1.29 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 796 HIS 0.003 0.001 HIS A 517 PHE 0.010 0.001 PHE A 531 TYR 0.011 0.001 TYR A 885 ARG 0.001 0.000 ARG A 107 *********************** 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 71 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 1.030 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: 0.8795 (tp-100) cc_final: 0.8471 (tp-100) REVERT: A 751 ARG cc_start: 0.7451 (tpt90) cc_final: 0.6704 (tpm170) REVERT: A 879 MET cc_start: 0.8364 (ttt) cc_final: 0.8001 (tpp) REVERT: A 882 LEU cc_start: 0.8346 (mp) cc_final: 0.7786 (tp) outliers start: 4 outliers final: 4 residues processed: 68 average time/residue: 0.4179 time to fit residues: 38.3887 Evaluate side-chains 68 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 67 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5462 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= 0.166 Angle : 0.507 7.540 9356 Z= 0.264 Chirality : 0.036 0.127 1044 Planarity : 0.004 0.049 1219 Dihedral : 4.624 23.575 917 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.53 % Allowed : 8.87 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.29), residues: 846 helix: 0.77 (0.25), residues: 451 sheet: -0.52 (0.99), residues: 29 loop : -1.31 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 137 HIS 0.004 0.001 HIS A 517 PHE 0.012 0.001 PHE A 531 TYR 0.011 0.001 TYR A 885 ARG 0.001 0.000 ARG A 107 ********************** 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 72 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.998 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: 0.7511 (tt0) cc_final: 0.7047 (pt0) REVERT: A 742 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8463 (tp-100) REVERT: A 751 ARG cc_start: 0.7412 (tpt90) cc_final: 0.6675 (tpm170) REVERT: A 879 MET cc_start: 0.8372 (ttt) cc_final: 0.8005 (tpp) REVERT: A 882 LEU cc_start: 0.8358 (mp) cc_final: 0.7805 (tp) outliers start: 4 outliers final: 4 residues processed: 69 average time/residue: 0.4435 time to fit residues: 41.1088 Evaluate side-chains 69 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 69 optimal weight: 0.0770 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 overall best weight: 1.5742 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.117021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.089026 restraints weight = 62001.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.091943 restraints weight = 30128.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.092668 restraints weight = 20784.077| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5581 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= 0.190 Angle : 0.514 6.540 9356 Z= 0.269 Chirality : 0.036 0.135 1044 Planarity : 0.004 0.048 1219 Dihedral : 4.624 23.166 917 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.53 % Allowed : 9.14 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.29), residues: 846 helix: 0.72 (0.25), residues: 449 sheet: -0.71 (1.00), residues: 30 loop : -1.24 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 796 HIS 0.004 0.001 HIS A 654 PHE 0.012 0.001 PHE A 531 TYR 0.015 0.001 TYR A 885 ARG 0.002 0.000 ARG A 840 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2995.33 seconds wall clock time: 54 minutes 36.07 seconds (3276.07 seconds total)