Starting phenix.real_space_refine on Thu Jan 16 04:15:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uue_42580/01_2025/8uue_42580_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uue_42580/01_2025/8uue_42580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uue_42580/01_2025/8uue_42580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uue_42580/01_2025/8uue_42580.map" model { file = "/net/cci-nas-00/data/ceres_data/8uue_42580/01_2025/8uue_42580_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uue_42580/01_2025/8uue_42580_neut.cif" } resolution = 3.96 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= 0.039 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: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 5724 2.51 5 N 1517 2.21 5 O 1682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8984 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2239 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2255 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2268 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2222 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 16, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 6.49, per 1000 atoms: 0.72 Number of scatterers: 8984 At special positions: 0 Unit cell: (137.816, 128.4, 73.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 1682 8.00 N 1517 7.00 C 5724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 575 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 859 " - pdb=" SG CYS B 913 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.01 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 537 " - pdb=" SG CYS D 575 " distance=2.03 Simple disulfide: pdb=" SG CYS D 859 " - pdb=" SG CYS D 913 " distance=2.03 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: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 16 sheets defined 38.3% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 458 through 469 removed outlier: 3.539A pdb=" N THR A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 527 Processing helix chain 'A' and resid 669 through 674 removed outlier: 3.629A pdb=" N ARG A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 669 through 674' Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 699 through 708 removed outlier: 3.649A pdb=" N TYR A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 724 Processing helix chain 'A' and resid 732 through 742 Processing helix chain 'A' and resid 768 through 783 removed outlier: 3.583A pdb=" N VAL A 772 " --> pdb=" O TRP A 768 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 783 " --> pdb=" O SER A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'B' and resid 550 through 562 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 578 through 592 Processing helix chain 'B' and resid 614 through 622 Processing helix chain 'B' and resid 635 through 640 Processing helix chain 'B' and resid 782 through 786 Processing helix chain 'B' and resid 800 through 810 removed outlier: 3.587A pdb=" N TYR B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL B 806 " --> pdb=" O ALA B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 820 removed outlier: 3.876A pdb=" N MET B 817 " --> pdb=" O MET B 813 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR B 820 " --> pdb=" O TYR B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 833 Processing helix chain 'B' and resid 846 through 854 removed outlier: 3.710A pdb=" N SER B 854 " --> pdb=" O ASP B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 884 Processing helix chain 'B' and resid 885 through 897 removed outlier: 3.584A pdb=" N GLU B 889 " --> pdb=" O ALA B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 906 removed outlier: 3.840A pdb=" N MET B 902 " --> pdb=" O GLY B 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.542A pdb=" N GLY C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.659A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 707 removed outlier: 4.377A pdb=" N ARG C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.761A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 743 Processing helix chain 'C' and resid 769 through 781 removed outlier: 3.559A pdb=" N GLU C 781 " --> pdb=" O LEU C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'D' and resid 550 through 562 removed outlier: 3.775A pdb=" N LEU D 554 " --> pdb=" O ASP D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 573 Processing helix chain 'D' and resid 578 through 592 Processing helix chain 'D' and resid 614 through 622 Processing helix chain 'D' and resid 635 through 642 removed outlier: 4.066A pdb=" N VAL D 641 " --> pdb=" O ALA D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 787 removed outlier: 3.825A pdb=" N HIS D 787 " --> pdb=" O PRO D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 810 Processing helix chain 'D' and resid 810 through 821 removed outlier: 3.519A pdb=" N HIS D 814 " --> pdb=" O PHE D 810 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR D 820 " --> pdb=" O TYR D 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 826 No H-bonds generated for 'chain 'D' and resid 824 through 826' Processing helix chain 'D' and resid 827 through 833 removed outlier: 3.568A pdb=" N TYR D 831 " --> pdb=" O ASP D 827 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 856 Processing helix chain 'D' and resid 883 through 898 removed outlier: 3.601A pdb=" N ILE D 887 " --> pdb=" O LEU D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 898 through 908 Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 399 removed outlier: 7.255A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 409 through 412 Processing sheet with id=AA3, first strand: chain 'A' and resid 729 through 731 removed outlier: 3.723A pdb=" N PHE A 729 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 541 " --> pdb=" O PHE A 729 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 729 through 731 removed outlier: 3.723A pdb=" N PHE A 729 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 541 " --> pdb=" O PHE A 729 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 538 " --> pdb=" O PHE A 754 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N PHE A 754 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 573 through 576 removed outlier: 6.892A pdb=" N LEU B 542 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE B 599 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B 544 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET B 627 " --> pdb=" O ARG B 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 643 through 644 removed outlier: 3.503A pdb=" N ASP B 643 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 844 through 845 removed outlier: 3.650A pdb=" N ILE B 655 " --> pdb=" O VAL B 864 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 657 " --> pdb=" O LEU B 862 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 862 " --> pdb=" O VAL B 657 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 398 through 402 removed outlier: 6.999A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 434 through 436 Processing sheet with id=AB1, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AB2, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AB3, first strand: chain 'C' and resid 535 through 536 Processing sheet with id=AB4, first strand: chain 'C' and resid 710 through 711 removed outlier: 8.936A pdb=" N TYR C 711 " --> pdb=" O TYR C 681 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR C 683 " --> pdb=" O TYR C 711 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 542 " --> pdb=" O VAL C 747 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 747 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 543 through 544 removed outlier: 4.186A pdb=" N LEU D 515 " --> pdb=" O ASP D 594 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP D 596 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR D 598 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 643 through 644 removed outlier: 4.203A pdb=" N ASP D 643 " --> pdb=" O LEU D 877 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU D 877 " --> pdb=" O ASP D 643 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 844 through 845 removed outlier: 3.616A pdb=" N MET D 844 " --> pdb=" O GLY D 654 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU D 653 " --> pdb=" O ALA D 869 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA D 869 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N ILE D 655 " --> pdb=" O PRO D 867 " (cutoff:3.500A) removed outlier: 10.755A pdb=" N VAL D 657 " --> pdb=" O GLY D 865 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N GLY D 865 " --> pdb=" O VAL D 657 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 813 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: 2.38 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.03: 1 1.03 - 1.27: 1494 1.27 - 1.51: 4271 1.51 - 1.75: 3337 1.75 - 1.99: 95 Bond restraints: 9198 Sorted by residual: bond pdb=" CG PRO C 675 " pdb=" CD PRO C 675 " ideal model delta sigma weight residual 1.503 0.795 0.708 3.40e-02 8.65e+02 4.34e+02 bond pdb=" CA PRO C 675 " pdb=" CB PRO C 675 " ideal model delta sigma weight residual 1.531 1.323 0.208 1.67e-02 3.59e+03 1.55e+02 bond pdb=" N PRO C 675 " pdb=" CD PRO C 675 " ideal model delta sigma weight residual 1.473 1.646 -0.173 1.40e-02 5.10e+03 1.53e+02 bond pdb=" C ASN C 674 " pdb=" N PRO C 675 " ideal model delta sigma weight residual 1.326 1.474 -0.148 1.44e-02 4.82e+03 1.06e+02 bond pdb=" CB PRO C 675 " pdb=" CG PRO C 675 " ideal model delta sigma weight residual 1.492 1.992 -0.500 5.00e-02 4.00e+02 1.00e+02 ... (remaining 9193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 12458 21.21 - 42.42: 1 42.42 - 63.63: 1 63.63 - 84.84: 0 84.84 - 106.05: 1 Bond angle restraints: 12461 Sorted by residual: angle pdb=" CB PRO C 675 " pdb=" CG PRO C 675 " pdb=" CD PRO C 675 " ideal model delta sigma weight residual 106.10 0.05 106.05 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO C 675 " pdb=" N PRO C 675 " pdb=" CD PRO C 675 " ideal model delta sigma weight residual 112.00 76.53 35.47 1.40e+00 5.10e-01 6.42e+02 angle pdb=" CA ASN C 674 " pdb=" C ASN C 674 " pdb=" O ASN C 674 " ideal model delta sigma weight residual 120.08 106.91 13.17 1.14e+00 7.69e-01 1.33e+02 angle pdb=" C ASN C 674 " pdb=" N PRO C 675 " pdb=" CD PRO C 675 " ideal model delta sigma weight residual 125.00 170.58 -45.58 4.10e+00 5.95e-02 1.24e+02 angle pdb=" CA ASN C 674 " pdb=" C ASN C 674 " pdb=" N PRO C 675 " ideal model delta sigma weight residual 118.34 128.80 -10.46 1.03e+00 9.43e-01 1.03e+02 ... (remaining 12456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.52: 4844 23.52 - 47.05: 580 47.05 - 70.57: 62 70.57 - 94.09: 21 94.09 - 117.62: 1 Dihedral angle restraints: 5508 sinusoidal: 2171 harmonic: 3337 Sorted by residual: dihedral pdb=" CB CYS A 420 " pdb=" SG CYS A 420 " pdb=" SG CYS A 454 " pdb=" CB CYS A 454 " ideal model delta sinusoidal sigma weight residual 93.00 176.59 -83.59 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" SG CYS A 455 " pdb=" CB CYS A 455 " ideal model delta sinusoidal sigma weight residual 93.00 174.94 -81.94 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" N PRO C 675 " pdb=" CG PRO C 675 " pdb=" CD PRO C 675 " pdb=" CB PRO C 675 " ideal model delta sinusoidal sigma weight residual 30.00 147.62 -117.62 1 1.50e+01 4.44e-03 6.24e+01 ... (remaining 5505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1275 0.088 - 0.177: 86 0.177 - 0.265: 6 0.265 - 0.353: 3 0.353 - 0.441: 2 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CA GLU D 830 " pdb=" N GLU D 830 " pdb=" C GLU D 830 " pdb=" CB GLU D 830 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CA PRO C 675 " pdb=" N PRO C 675 " pdb=" C PRO C 675 " pdb=" CB PRO C 675 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CA MET B 902 " pdb=" N MET B 902 " pdb=" C MET B 902 " pdb=" CB MET B 902 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 1369 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 523 " -0.088 5.00e-02 4.00e+02 1.33e-01 2.84e+01 pdb=" N PRO D 524 " 0.231 5.00e-02 4.00e+02 pdb=" CA PRO D 524 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO D 524 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 908 " -0.024 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C TYR B 908 " 0.083 2.00e-02 2.50e+03 pdb=" O TYR B 908 " -0.032 2.00e-02 2.50e+03 pdb=" N ARG B 909 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 446 " -0.059 5.00e-02 4.00e+02 8.35e-02 1.11e+01 pdb=" N PRO A 447 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 447 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 447 " -0.047 5.00e-02 4.00e+02 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 299 2.68 - 3.24: 8874 3.24 - 3.79: 13271 3.79 - 4.35: 16274 4.35 - 4.90: 27326 Nonbonded interactions: 66044 Sorted by model distance: nonbonded pdb=" O ASP D 901 " pdb=" OD1 ASP D 905 " model vdw 2.131 3.040 nonbonded pdb=" O GLY B 618 " pdb=" NH1 ARG B 622 " model vdw 2.142 3.120 nonbonded pdb=" O LEU C 517 " pdb=" OG1 THR C 518 " model vdw 2.144 3.040 nonbonded pdb=" NE1 TRP C 498 " pdb=" OH TYR C 526 " model vdw 2.160 3.120 nonbonded pdb=" OG SER C 507 " pdb=" OE1 GLN C 509 " model vdw 2.180 3.040 ... (remaining 66039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 395 through 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or (resid 445 through 448 and (name N or name CA or \ name C or name O or name CB )) or resid 449 through 544 or resid 663 through 73 \ 1 or (resid 732 and (name N or name CA or name C or name O or name CB )) or resi \ d 733 through 745 or (resid 746 and (name N or name CA or name C or name O or na \ me CB )) or resid 747 through 798)) selection = (chain 'C' and (resid 395 through 397 or (resid 398 and (name N or name CA or na \ me C or name O or name CB )) or resid 399 through 431 or (resid 432 through 433 \ and (name N or name CA or name C or name O or name CB )) or resid 434 through 48 \ 7 or (resid 488 through 489 and (name N or name CA or name C or name O or name C \ B )) or resid 490 or (resid 491 through 496 and (name N or name CA or name C or \ name O or name CB )) or resid 497 through 510 or (resid 511 and (name N or name \ CA or name C or name O or name CB )) or resid 512 through 543 or (resid 544 and \ (name N or name CA or name C or name O or name CB )) or resid 663 through 693 or \ (resid 694 through 695 and (name N or name CA or name C or name O or name CB )) \ or resid 696 through 708 or (resid 709 and (name N or name CA or name C or name \ O or name CB )) or resid 710 through 787 or (resid 788 and (name N or name CA o \ r name C or name O or name CB )) or resid 789 through 798)) } ncs_group { reference = (chain 'B' and (resid 511 through 541 or (resid 542 and (name N or name CA or na \ me C or name O or name CB )) or resid 543 or (resid 544 through 545 and (name N \ or name CA or name C or name O or name CB )) or resid 546 through 596 or (resid \ 597 and (name N or name CA or name C or name O or name CB )) or resid 598 throug \ h 657 or (resid 658 through 777 and (name N or name CA or name C or name O or na \ me CB )) or resid 778 through 784 or (resid 785 and (name N or name CA or name C \ or name O or name CB )) or resid 786 through 855 or (resid 856 through 857 and \ (name N or name CA or name C or name O or name CB )) or resid 858 through 888 or \ (resid 889 and (name N or name CA or name C or name O or name CB )) or resid 89 \ 0 through 891 or (resid 892 through 894 and (name N or name CA or name C or name \ O or name CB )) or resid 895 through 901 or (resid 902 and (name N or name CA o \ r name C or name O or name CB )) or resid 903 through 913)) selection = (chain 'D' and (resid 511 through 565 or (resid 566 and (name N or name CA or na \ me C or name O or name CB )) or resid 567 through 642 or (resid 643 and (name N \ or name CA or name C or name O or name CB )) or resid 644 through 829 or (resid \ 830 and (name N or name CA or name C or name O or name CB )) or resid 831 throug \ h 844 or (resid 845 and (name N or name CA or name C or name O or name CB )) or \ resid 846 through 908 or (resid 909 and (name N or name CA or name C or name O o \ r name CB )) or resid 910 through 913)) } 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: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.350 Find NCS groups from input model: 0.390 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 0.708 9198 Z= 0.717 Angle : 1.339 106.049 12461 Z= 0.609 Chirality : 0.051 0.441 1372 Planarity : 0.006 0.133 1606 Dihedral : 18.947 117.617 3329 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.97 % Allowed : 10.76 % Favored : 88.27 % Rotamer: Outliers : 1.45 % Allowed : 39.26 % Favored : 59.30 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -2.50 (0.24), residues: 1134 helix: 0.07 (0.27), residues: 373 sheet: -1.13 (0.52), residues: 97 loop : -2.96 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 498 HIS 0.031 0.001 HIS D 626 PHE 0.020 0.001 PHE B 794 TYR 0.017 0.001 TYR C 703 ARG 0.004 0.000 ARG C 704 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 1.080 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 123 average time/residue: 0.2030 time to fit residues: 35.5099 Evaluate side-chains 125 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 586 LYS Chi-restraints excluded: chain B residue 622 ARG Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain D residue 586 LYS Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 622 ARG Chi-restraints excluded: chain D residue 626 HIS Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 844 MET Chi-restraints excluded: chain D residue 909 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0060 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 786 HIS C 440 ASN ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.133701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.110112 restraints weight = 19903.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.109987 restraints weight = 18648.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.110988 restraints weight = 16813.098| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 9198 Z= 0.246 Angle : 0.660 9.789 12461 Z= 0.348 Chirality : 0.044 0.239 1372 Planarity : 0.006 0.135 1606 Dihedral : 6.647 57.470 1267 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.97 % Allowed : 10.76 % Favored : 88.27 % Rotamer: Outliers : 6.30 % Allowed : 35.33 % Favored : 58.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -2.20 (0.25), residues: 1134 helix: 0.52 (0.27), residues: 379 sheet: -1.63 (0.44), residues: 139 loop : -2.86 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 498 HIS 0.003 0.001 HIS C 404 PHE 0.020 0.001 PHE B 794 TYR 0.018 0.001 TYR C 526 ARG 0.003 0.000 ARG C 704 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 126 time to evaluate : 0.989 Fit side-chains REVERT: A 475 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: A 536 GLN cc_start: 0.8335 (pp30) cc_final: 0.8083 (pp30) REVERT: B 622 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7735 (mpp80) REVERT: B 850 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7794 (t0) REVERT: C 440 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6892 (t0) REVERT: C 755 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8361 (mtt90) REVERT: D 636 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8204 (t) REVERT: D 640 GLN cc_start: 0.8374 (mm110) cc_final: 0.8140 (mm110) outliers start: 61 outliers final: 31 residues processed: 173 average time/residue: 0.1811 time to fit residues: 45.2700 Evaluate side-chains 150 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 622 ARG Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 866 LYS Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 484 PHE Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 755 ARG Chi-restraints excluded: chain D residue 514 HIS Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 657 VAL Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 861 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 0.0970 chunk 51 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 86 optimal weight: 0.0970 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 81 optimal weight: 0.0170 chunk 56 optimal weight: 0.6980 overall best weight: 0.2214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 786 HIS C 440 ASN C 686 GLN C 710 ASN ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.137914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.114533 restraints weight = 20302.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.115105 restraints weight = 17074.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.116395 restraints weight = 14865.765| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9198 Z= 0.169 Angle : 0.611 8.875 12461 Z= 0.320 Chirality : 0.042 0.242 1372 Planarity : 0.005 0.134 1606 Dihedral : 5.357 48.617 1238 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.64 % Favored : 90.56 % Rotamer: Outliers : 5.68 % Allowed : 35.64 % Favored : 58.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -1.95 (0.24), residues: 1134 helix: 0.77 (0.27), residues: 381 sheet: -0.87 (0.50), residues: 104 loop : -2.84 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 498 HIS 0.005 0.001 HIS C 404 PHE 0.022 0.001 PHE B 794 TYR 0.013 0.001 TYR C 526 ARG 0.003 0.000 ARG C 704 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 137 time to evaluate : 1.104 Fit side-chains REVERT: A 475 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7155 (tt0) REVERT: A 754 PHE cc_start: 0.7858 (t80) cc_final: 0.7577 (t80) REVERT: B 571 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8079 (mttm) REVERT: B 622 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7764 (mpp80) REVERT: C 399 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8234 (mtmt) REVERT: C 424 PHE cc_start: 0.6545 (OUTLIER) cc_final: 0.5789 (t80) outliers start: 55 outliers final: 24 residues processed: 176 average time/residue: 0.1901 time to fit residues: 48.3098 Evaluate side-chains 153 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 622 ARG Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 424 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain D residue 514 HIS Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 844 MET Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 890 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 40 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 440 ASN C 796 GLN ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.134868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.110140 restraints weight = 20078.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.110703 restraints weight = 16339.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.111548 restraints weight = 13760.138| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9198 Z= 0.201 Angle : 0.630 9.181 12461 Z= 0.330 Chirality : 0.043 0.236 1372 Planarity : 0.005 0.137 1606 Dihedral : 5.038 46.136 1235 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.70 % Favored : 89.51 % Rotamer: Outliers : 5.68 % Allowed : 35.64 % Favored : 58.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -1.84 (0.25), residues: 1134 helix: 0.85 (0.27), residues: 383 sheet: -1.09 (0.51), residues: 107 loop : -2.72 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 731 HIS 0.003 0.001 HIS C 404 PHE 0.022 0.001 PHE B 794 TYR 0.026 0.001 TYR C 692 ARG 0.002 0.000 ARG C 704 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 475 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: A 701 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.7076 (p) REVERT: A 754 PHE cc_start: 0.7930 (t80) cc_final: 0.7612 (t80) REVERT: B 850 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7948 (t0) REVERT: C 424 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6252 (t80) REVERT: D 541 GLN cc_start: 0.7768 (mp10) cc_final: 0.7549 (mp10) REVERT: D 595 PHE cc_start: 0.8360 (p90) cc_final: 0.7924 (p90) outliers start: 55 outliers final: 40 residues processed: 163 average time/residue: 0.1718 time to fit residues: 41.7619 Evaluate side-chains 164 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 120 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 622 ARG Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 866 LYS Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 484 PHE Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 514 HIS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 657 VAL Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 844 MET Chi-restraints excluded: chain D residue 854 SER Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 864 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 89 optimal weight: 0.0570 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 440 ASN C 686 GLN ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.129524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.103640 restraints weight = 19303.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.104883 restraints weight = 14006.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106327 restraints weight = 11350.356| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9198 Z= 0.180 Angle : 0.622 9.097 12461 Z= 0.324 Chirality : 0.043 0.235 1372 Planarity : 0.005 0.138 1606 Dihedral : 4.945 42.532 1235 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.82 % Favored : 90.39 % Rotamer: Outliers : 6.20 % Allowed : 35.12 % Favored : 58.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -1.77 (0.25), residues: 1134 helix: 0.91 (0.27), residues: 383 sheet: -1.08 (0.51), residues: 107 loop : -2.67 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 731 HIS 0.004 0.001 HIS C 404 PHE 0.022 0.001 PHE B 794 TYR 0.030 0.001 TYR C 692 ARG 0.002 0.000 ARG C 704 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 128 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 475 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: A 536 GLN cc_start: 0.8120 (pp30) cc_final: 0.7886 (pp30) REVERT: A 701 THR cc_start: 0.7385 (OUTLIER) cc_final: 0.7037 (p) REVERT: A 702 MET cc_start: 0.7466 (tpt) cc_final: 0.7087 (mtm) REVERT: A 754 PHE cc_start: 0.8072 (t80) cc_final: 0.7612 (t80) REVERT: B 571 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8350 (mttm) REVERT: B 622 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7273 (mpt-90) REVERT: B 850 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8175 (t0) REVERT: C 424 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.6490 (t80) REVERT: D 547 MET cc_start: 0.7176 (pmm) cc_final: 0.6692 (pmm) REVERT: D 595 PHE cc_start: 0.8387 (p90) cc_final: 0.7960 (p90) outliers start: 60 outliers final: 40 residues processed: 172 average time/residue: 0.1783 time to fit residues: 44.9521 Evaluate side-chains 166 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 120 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 622 ARG Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 514 HIS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 657 VAL Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 844 MET Chi-restraints excluded: chain D residue 854 SER Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 864 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 405 GLN C 440 ASN C 686 GLN ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.123808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100066 restraints weight = 19166.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.098895 restraints weight = 18771.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100069 restraints weight = 17976.839| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 9198 Z= 0.483 Angle : 0.822 10.845 12461 Z= 0.434 Chirality : 0.049 0.220 1372 Planarity : 0.006 0.146 1606 Dihedral : 5.995 47.394 1235 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.97 % Allowed : 11.90 % Favored : 87.13 % Rotamer: Outliers : 7.75 % Allowed : 34.81 % Favored : 57.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -2.32 (0.24), residues: 1134 helix: 0.40 (0.26), residues: 380 sheet: -1.70 (0.47), residues: 122 loop : -2.91 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 792 HIS 0.005 0.001 HIS C 477 PHE 0.027 0.003 PHE C 533 TYR 0.039 0.003 TYR B 579 ARG 0.004 0.001 ARG D 818 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 106 time to evaluate : 1.106 Fit side-chains REVERT: A 475 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7609 (pt0) REVERT: A 701 THR cc_start: 0.7358 (OUTLIER) cc_final: 0.7091 (p) REVERT: A 754 PHE cc_start: 0.8141 (t80) cc_final: 0.7832 (t80) REVERT: B 622 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7876 (mpp80) REVERT: B 850 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8119 (t0) REVERT: C 423 GLU cc_start: 0.7291 (tp30) cc_final: 0.7020 (tp30) REVERT: C 424 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6120 (t80) REVERT: C 692 TYR cc_start: 0.8250 (t80) cc_final: 0.7859 (t80) REVERT: D 595 PHE cc_start: 0.8356 (p90) cc_final: 0.8003 (p90) REVERT: D 636 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8454 (t) REVERT: D 781 HIS cc_start: 0.7758 (m-70) cc_final: 0.6704 (p90) REVERT: D 799 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8544 (pm20) REVERT: D 818 ARG cc_start: 0.7926 (ptt90) cc_final: 0.7705 (ptt90) outliers start: 75 outliers final: 47 residues processed: 169 average time/residue: 0.1651 time to fit residues: 42.1195 Evaluate side-chains 153 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 99 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 622 ARG Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 PHE Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 484 PHE Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 514 HIS Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 657 VAL Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 799 GLU Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 844 MET Chi-restraints excluded: chain D residue 854 SER Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 908 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN C 440 ASN C 453 GLN ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.132492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108572 restraints weight = 20238.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108694 restraints weight = 17752.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.109851 restraints weight = 16445.917| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9198 Z= 0.216 Angle : 0.685 9.767 12461 Z= 0.357 Chirality : 0.045 0.225 1372 Planarity : 0.006 0.145 1606 Dihedral : 5.445 42.460 1235 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.97 % Allowed : 9.52 % Favored : 89.51 % Rotamer: Outliers : 5.37 % Allowed : 38.53 % Favored : 56.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -2.02 (0.25), residues: 1134 helix: 0.63 (0.27), residues: 383 sheet: -1.42 (0.47), residues: 119 loop : -2.75 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 613 HIS 0.005 0.001 HIS C 404 PHE 0.022 0.001 PHE B 794 TYR 0.020 0.001 TYR B 579 ARG 0.002 0.000 ARG C 704 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 115 time to evaluate : 1.047 Fit side-chains REVERT: A 475 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: A 701 THR cc_start: 0.7282 (OUTLIER) cc_final: 0.7003 (p) REVERT: A 754 PHE cc_start: 0.8030 (t80) cc_final: 0.7750 (t80) REVERT: B 850 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7926 (t0) REVERT: C 424 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.5938 (t80) REVERT: C 692 TYR cc_start: 0.8038 (t80) cc_final: 0.7776 (t80) REVERT: D 547 MET cc_start: 0.6857 (pmm) cc_final: 0.6375 (pmm) REVERT: D 595 PHE cc_start: 0.8416 (p90) cc_final: 0.7915 (p90) REVERT: D 636 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8420 (t) REVERT: D 818 ARG cc_start: 0.7781 (ptt90) cc_final: 0.7352 (tmm160) REVERT: D 905 ASP cc_start: 0.7822 (t0) cc_final: 0.7515 (p0) outliers start: 52 outliers final: 39 residues processed: 152 average time/residue: 0.1627 time to fit residues: 37.4994 Evaluate side-chains 153 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 PHE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 514 HIS Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 657 VAL Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 884 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 15 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 626 HIS D 640 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.130695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.106966 restraints weight = 19242.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.107756 restraints weight = 15968.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.109141 restraints weight = 12922.326| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9198 Z= 0.189 Angle : 0.653 9.440 12461 Z= 0.339 Chirality : 0.043 0.229 1372 Planarity : 0.005 0.143 1606 Dihedral : 4.900 35.736 1231 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.79 % Allowed : 10.14 % Favored : 89.07 % Rotamer: Outliers : 5.06 % Allowed : 37.91 % Favored : 57.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -1.83 (0.25), residues: 1134 helix: 0.83 (0.27), residues: 383 sheet: -1.37 (0.46), residues: 119 loop : -2.65 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 768 HIS 0.005 0.001 HIS A 449 PHE 0.023 0.001 PHE B 794 TYR 0.013 0.001 TYR B 579 ARG 0.003 0.000 ARG C 704 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 120 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 701 THR cc_start: 0.7166 (OUTLIER) cc_final: 0.6904 (p) REVERT: A 754 PHE cc_start: 0.8096 (t80) cc_final: 0.7734 (t80) REVERT: C 424 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.6108 (t80) REVERT: C 692 TYR cc_start: 0.8163 (t80) cc_final: 0.7794 (t80) REVERT: D 595 PHE cc_start: 0.8404 (p90) cc_final: 0.7937 (p90) REVERT: D 640 GLN cc_start: 0.8536 (mm110) cc_final: 0.8331 (mm110) REVERT: D 818 ARG cc_start: 0.7599 (ptt90) cc_final: 0.7219 (tmm160) outliers start: 49 outliers final: 38 residues processed: 155 average time/residue: 0.1624 time to fit residues: 38.1561 Evaluate side-chains 152 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 PHE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 514 HIS Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 657 VAL Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 854 SER Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 884 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.129713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.104817 restraints weight = 19325.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.105069 restraints weight = 15465.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.105851 restraints weight = 12949.914| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9198 Z= 0.190 Angle : 0.656 8.920 12461 Z= 0.340 Chirality : 0.043 0.227 1372 Planarity : 0.005 0.142 1606 Dihedral : 4.788 35.869 1231 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.08 % Favored : 90.12 % Rotamer: Outliers : 5.06 % Allowed : 37.60 % Favored : 57.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -1.74 (0.25), residues: 1134 helix: 0.88 (0.27), residues: 383 sheet: -1.26 (0.46), residues: 119 loop : -2.60 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 498 HIS 0.022 0.001 HIS A 449 PHE 0.022 0.001 PHE B 794 TYR 0.014 0.001 TYR A 692 ARG 0.002 0.000 ARG C 704 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 120 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 399 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6783 (mtmt) REVERT: A 701 THR cc_start: 0.7283 (OUTLIER) cc_final: 0.6978 (p) REVERT: A 702 MET cc_start: 0.7908 (tpt) cc_final: 0.7627 (tpt) REVERT: A 754 PHE cc_start: 0.8211 (t80) cc_final: 0.7803 (t80) REVERT: B 622 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7416 (mpt-90) REVERT: C 399 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8335 (mtmt) REVERT: C 424 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6323 (t80) REVERT: C 692 TYR cc_start: 0.8168 (t80) cc_final: 0.7869 (t80) REVERT: D 547 MET cc_start: 0.7221 (pmm) cc_final: 0.6685 (pmm) REVERT: D 636 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8347 (t) REVERT: D 818 ARG cc_start: 0.7589 (ptt90) cc_final: 0.7279 (tmm160) outliers start: 49 outliers final: 36 residues processed: 158 average time/residue: 0.1757 time to fit residues: 41.0485 Evaluate side-chains 151 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 622 ARG Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 PHE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 514 HIS Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 657 VAL Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 854 SER Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 884 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 5 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 95 optimal weight: 0.0010 chunk 43 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.130019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.104644 restraints weight = 19282.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.106305 restraints weight = 14536.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.107660 restraints weight = 11781.094| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9198 Z= 0.193 Angle : 0.670 9.299 12461 Z= 0.346 Chirality : 0.043 0.225 1372 Planarity : 0.005 0.142 1606 Dihedral : 4.753 36.032 1231 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.61 % Favored : 89.59 % Rotamer: Outliers : 5.17 % Allowed : 37.71 % Favored : 57.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -1.73 (0.25), residues: 1134 helix: 0.87 (0.27), residues: 384 sheet: -1.16 (0.47), residues: 117 loop : -2.60 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 768 HIS 0.010 0.001 HIS A 449 PHE 0.022 0.001 PHE B 794 TYR 0.014 0.001 TYR B 579 ARG 0.002 0.000 ARG C 704 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 113 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 399 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6720 (mtmt) REVERT: A 701 THR cc_start: 0.7198 (OUTLIER) cc_final: 0.6900 (p) REVERT: A 754 PHE cc_start: 0.8145 (t80) cc_final: 0.7722 (t80) REVERT: B 622 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7425 (mpt-90) REVERT: C 399 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8279 (mtmt) REVERT: C 424 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6356 (t80) REVERT: D 547 MET cc_start: 0.7262 (pmm) cc_final: 0.6710 (pmm) REVERT: D 636 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8198 (t) REVERT: D 640 GLN cc_start: 0.8489 (mm110) cc_final: 0.8244 (mm110) outliers start: 50 outliers final: 41 residues processed: 152 average time/residue: 0.1866 time to fit residues: 42.0508 Evaluate side-chains 155 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 108 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 622 ARG Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 844 MET Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 PHE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 514 HIS Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 596 ASP Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 657 VAL Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 834 ASN Chi-restraints excluded: chain D residue 854 SER Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 864 VAL Chi-restraints excluded: chain D residue 884 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 78 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.127690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.103077 restraints weight = 19475.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.103951 restraints weight = 15360.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.104869 restraints weight = 14429.821| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9198 Z= 0.253 Angle : 0.696 9.242 12461 Z= 0.363 Chirality : 0.044 0.219 1372 Planarity : 0.006 0.144 1606 Dihedral : 4.967 36.546 1231 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.41 % Favored : 88.71 % Rotamer: Outliers : 5.27 % Allowed : 37.81 % Favored : 56.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -1.82 (0.25), residues: 1134 helix: 0.80 (0.27), residues: 384 sheet: -1.20 (0.47), residues: 119 loop : -2.66 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 731 HIS 0.003 0.001 HIS C 404 PHE 0.028 0.002 PHE C 754 TYR 0.027 0.002 TYR C 692 ARG 0.003 0.000 ARG D 818 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2515.01 seconds wall clock time: 46 minutes 21.71 seconds (2781.71 seconds total)