Starting phenix.real_space_refine on Wed Apr 30 01:04:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uue_42580/04_2025/8uue_42580_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uue_42580/04_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_42580/04_2025/8uue_42580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uue_42580/04_2025/8uue_42580.map" model { file = "/net/cci-nas-00/data/ceres_data/8uue_42580/04_2025/8uue_42580_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uue_42580/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 6.66, per 1000 atoms: 0.74 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: 2.15 Conformation dependent library (CDL) restraints added in 1.0 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: 0.94 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: 2.18 Time building geometry restraints manager: 2.58 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: 4.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.550 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.370 ------------------------------------------------------------------------------- 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 9207 Z= 0.411 Angle : 1.338 106.049 12479 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 Details of bonding type rmsd hydrogen bonds : bond 0.18507 ( 284) hydrogen bonds : angle 7.82023 ( 813) SS BOND : bond 0.00847 ( 9) SS BOND : angle 0.68896 ( 18) covalent geometry : bond 0.01096 ( 9198) covalent geometry : angle 1.33889 (12461) *********************** 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 : 1.418 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 123 average time/residue: 0.2110 time to fit residues: 36.7896 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 : 0.970 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.133685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.110070 restraints weight = 19896.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.109952 restraints weight = 18568.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.110948 restraints weight = 16748.483| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 9207 Z= 0.152 Angle : 0.659 9.789 12479 Z= 0.347 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 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 284) hydrogen bonds : angle 5.75460 ( 813) SS BOND : bond 0.00158 ( 9) SS BOND : angle 0.50143 ( 18) covalent geometry : bond 0.00366 ( 9198) covalent geometry : angle 0.65962 (12461) *********************** 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 : 1.720 Fit side-chains REVERT: A 475 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: A 536 GLN cc_start: 0.8332 (pp30) cc_final: 0.8081 (pp30) REVERT: B 622 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7737 (mpp80) REVERT: B 850 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7799 (t0) REVERT: C 440 ASN cc_start: 0.7197 (OUTLIER) cc_final: 0.6891 (t0) REVERT: C 755 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8362 (mtt90) REVERT: D 636 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8204 (t) REVERT: D 640 GLN cc_start: 0.8376 (mm110) cc_final: 0.8141 (mm110) outliers start: 61 outliers final: 31 residues processed: 173 average time/residue: 0.1956 time to fit residues: 49.3345 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 : 0.957 ------------------------------------------------------------------------------- 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: 0.2980 chunk 51 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 86 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 43 optimal weight: 0.1980 chunk 81 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 626 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.136798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.112979 restraints weight = 20320.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.113431 restraints weight = 17377.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.114966 restraints weight = 14959.697| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9207 Z= 0.113 Angle : 0.615 8.978 12479 Z= 0.322 Chirality : 0.043 0.241 1372 Planarity : 0.005 0.135 1606 Dihedral : 5.424 49.288 1238 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.99 % Favored : 90.21 % Rotamer: Outliers : 5.89 % Allowed : 35.64 % Favored : 58.47 % 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 (0.25), residues: 1134 helix: 0.75 (0.27), residues: 382 sheet: -1.14 (0.50), residues: 107 loop : -2.78 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 498 HIS 0.004 0.001 HIS C 404 PHE 0.021 0.001 PHE B 794 TYR 0.014 0.001 TYR C 692 ARG 0.002 0.000 ARG C 704 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 284) hydrogen bonds : angle 5.41310 ( 813) SS BOND : bond 0.00155 ( 9) SS BOND : angle 0.34774 ( 18) covalent geometry : bond 0.00261 ( 9198) covalent geometry : angle 0.61573 (12461) *********************** 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 188 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 131 time to evaluate : 0.971 Fit side-chains REVERT: A 475 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7228 (tt0) REVERT: A 794 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6865 (pmt-80) REVERT: B 622 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7812 (mpp80) REVERT: C 424 PHE cc_start: 0.6687 (OUTLIER) cc_final: 0.5942 (t80) REVERT: C 502 MET cc_start: 0.8212 (mmt) cc_final: 0.7884 (mmt) REVERT: D 598 TYR cc_start: 0.8081 (p90) cc_final: 0.7849 (p90) REVERT: D 830 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7997 (pp20) outliers start: 57 outliers final: 26 residues processed: 173 average time/residue: 0.1820 time to fit residues: 45.8641 Evaluate side-chains 149 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 A residue 794 ARG 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 844 MET 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 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 810 PHE Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 844 MET Chi-restraints excluded: chain D residue 864 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 C 796 GLN ** D 612 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 = 0.3784 r_free = 0.3784 target = 0.130816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.105656 restraints weight = 18837.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.107258 restraints weight = 15752.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108294 restraints weight = 12616.456| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9207 Z= 0.125 Angle : 0.625 9.312 12479 Z= 0.327 Chirality : 0.043 0.235 1372 Planarity : 0.005 0.137 1606 Dihedral : 5.304 46.189 1238 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.70 % Favored : 89.51 % Rotamer: Outliers : 6.20 % Allowed : 35.23 % Favored : 58.57 % 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: 0.88 (0.27), residues: 382 sheet: -1.08 (0.51), residues: 107 loop : -2.73 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 768 HIS 0.003 0.001 HIS C 404 PHE 0.022 0.001 PHE B 794 TYR 0.027 0.001 TYR C 692 ARG 0.002 0.000 ARG C 704 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 284) hydrogen bonds : angle 5.29955 ( 813) SS BOND : bond 0.00123 ( 9) SS BOND : angle 0.37383 ( 18) covalent geometry : bond 0.00296 ( 9198) covalent geometry : angle 0.62554 (12461) *********************** 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 182 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 122 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 475 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: A 701 THR cc_start: 0.7336 (OUTLIER) cc_final: 0.7067 (p) REVERT: A 754 PHE cc_start: 0.8000 (t80) cc_final: 0.7650 (t80) REVERT: A 794 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6781 (pmt-80) REVERT: B 571 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8293 (mttm) REVERT: B 850 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8059 (t0) REVERT: C 399 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8268 (mtmt) REVERT: C 424 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.6298 (t80) outliers start: 60 outliers final: 38 residues processed: 168 average time/residue: 0.1700 time to fit residues: 41.9397 Evaluate side-chains 161 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 A residue 794 ARG 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 796 THR 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 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 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: 3.9990 chunk 62 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 89 optimal weight: 0.0970 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3785 r_free = 0.3785 target = 0.130921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.107536 restraints weight = 18932.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.107579 restraints weight = 16685.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108485 restraints weight = 14726.242| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9207 Z= 0.126 Angle : 0.631 9.403 12479 Z= 0.329 Chirality : 0.043 0.234 1372 Planarity : 0.005 0.139 1606 Dihedral : 5.000 42.900 1235 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.35 % Favored : 89.86 % Rotamer: Outliers : 6.30 % Allowed : 35.23 % Favored : 58.47 % 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: -1.79 (0.25), residues: 1134 helix: 0.90 (0.27), residues: 383 sheet: -1.12 (0.50), residues: 107 loop : -2.68 (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 0.025 0.001 TYR C 692 ARG 0.002 0.000 ARG C 704 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 284) hydrogen bonds : angle 5.20064 ( 813) SS BOND : bond 0.00108 ( 9) SS BOND : angle 0.36729 ( 18) covalent geometry : bond 0.00300 ( 9198) covalent geometry : angle 0.63101 (12461) *********************** 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 182 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 121 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 475 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: A 701 THR cc_start: 0.7362 (OUTLIER) cc_final: 0.7076 (p) REVERT: A 754 PHE cc_start: 0.8004 (t80) cc_final: 0.7623 (t80) REVERT: A 794 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6716 (pmt-80) REVERT: B 571 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8215 (mttm) REVERT: B 622 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7397 (mpt-90) REVERT: B 850 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.8022 (t0) REVERT: C 399 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8238 (mtmt) REVERT: C 424 PHE cc_start: 0.6851 (OUTLIER) cc_final: 0.6413 (t80) outliers start: 61 outliers final: 40 residues processed: 167 average time/residue: 0.1830 time to fit residues: 44.0434 Evaluate side-chains 160 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 112 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 777 LEU Chi-restraints excluded: chain A residue 794 ARG 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 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 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: 4.9990 chunk 72 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.127957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.103913 restraints weight = 18713.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.104122 restraints weight = 16575.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.105005 restraints weight = 15313.584| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9207 Z= 0.184 Angle : 0.695 10.023 12479 Z= 0.364 Chirality : 0.045 0.226 1372 Planarity : 0.006 0.142 1606 Dihedral : 5.347 42.707 1235 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.93 % Favored : 88.18 % Rotamer: Outliers : 7.23 % Allowed : 34.81 % Favored : 57.95 % 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: -1.96 (0.25), residues: 1134 helix: 0.75 (0.27), residues: 382 sheet: -1.42 (0.45), residues: 133 loop : -2.76 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 792 HIS 0.003 0.001 HIS C 477 PHE 0.021 0.002 PHE B 794 TYR 0.026 0.002 TYR B 579 ARG 0.003 0.000 ARG D 818 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 284) hydrogen bonds : angle 5.27430 ( 813) SS BOND : bond 0.00245 ( 9) SS BOND : angle 0.70019 ( 18) covalent geometry : bond 0.00438 ( 9198) covalent geometry : angle 0.69528 (12461) *********************** 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 183 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 113 time to evaluate : 0.992 Fit side-chains REVERT: A 475 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: A 701 THR cc_start: 0.7330 (OUTLIER) cc_final: 0.7067 (p) REVERT: A 710 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7763 (m-40) REVERT: A 754 PHE cc_start: 0.8087 (t80) cc_final: 0.7706 (t80) REVERT: A 762 MET cc_start: 0.8038 (pmm) cc_final: 0.7790 (pmm) REVERT: A 794 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6282 (ptt-90) REVERT: B 850 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8076 (t0) REVERT: C 424 PHE cc_start: 0.7074 (OUTLIER) cc_final: 0.6269 (t80) REVERT: D 547 MET cc_start: 0.6965 (pmm) cc_final: 0.6427 (pmm) outliers start: 70 outliers final: 48 residues processed: 170 average time/residue: 0.1687 time to fit residues: 42.9011 Evaluate side-chains 162 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 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 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 701 THR Chi-restraints excluded: chain A residue 710 ASN 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 A residue 749 THR Chi-restraints excluded: chain A residue 794 ARG 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 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 484 PHE 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 748 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 596 ASP Chi-restraints excluded: chain D residue 631 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.128853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.105066 restraints weight = 19033.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105427 restraints weight = 16545.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.106414 restraints weight = 13933.143| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9207 Z= 0.157 Angle : 0.679 9.649 12479 Z= 0.354 Chirality : 0.044 0.229 1372 Planarity : 0.005 0.143 1606 Dihedral : 5.102 35.155 1231 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.70 % Favored : 89.42 % Rotamer: Outliers : 6.92 % Allowed : 35.74 % 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: -1.89 (0.25), residues: 1134 helix: 0.80 (0.27), residues: 382 sheet: -1.38 (0.47), residues: 119 loop : -2.70 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 792 HIS 0.003 0.001 HIS C 404 PHE 0.022 0.002 PHE B 794 TYR 0.021 0.002 TYR B 579 ARG 0.002 0.000 ARG D 818 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 284) hydrogen bonds : angle 5.22127 ( 813) SS BOND : bond 0.00192 ( 9) SS BOND : angle 0.76981 ( 18) covalent geometry : bond 0.00373 ( 9198) covalent geometry : angle 0.67880 (12461) *********************** 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 177 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 110 time to evaluate : 1.051 Fit side-chains REVERT: A 475 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: A 701 THR cc_start: 0.7300 (OUTLIER) cc_final: 0.7019 (p) REVERT: A 710 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7734 (m-40) REVERT: A 754 PHE cc_start: 0.8141 (t80) cc_final: 0.7800 (t80) REVERT: A 794 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6328 (ptt-90) REVERT: B 622 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7484 (mpt-90) REVERT: B 850 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8044 (t0) REVERT: C 424 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6047 (t80) REVERT: D 818 ARG cc_start: 0.7673 (ptt90) cc_final: 0.7430 (tmm160) outliers start: 67 outliers final: 49 residues processed: 162 average time/residue: 0.1758 time to fit residues: 41.8618 Evaluate side-chains 166 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 110 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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 710 ASN 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 794 ARG 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 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 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 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 486 THR 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 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 568 VAL Chi-restraints excluded: chain D residue 631 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.129232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.105561 restraints weight = 19050.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.105793 restraints weight = 16552.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.106598 restraints weight = 15310.978| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9207 Z= 0.153 Angle : 0.678 9.653 12479 Z= 0.352 Chirality : 0.044 0.229 1372 Planarity : 0.005 0.143 1606 Dihedral : 5.051 35.355 1231 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.97 % Allowed : 10.14 % Favored : 88.89 % Rotamer: Outliers : 7.13 % Allowed : 35.64 % Favored : 57.23 % 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: -1.88 (0.25), residues: 1134 helix: 0.77 (0.27), residues: 384 sheet: -1.39 (0.47), residues: 119 loop : -2.68 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 792 HIS 0.003 0.001 HIS C 404 PHE 0.022 0.002 PHE B 794 TYR 0.020 0.002 TYR B 579 ARG 0.002 0.000 ARG D 818 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 284) hydrogen bonds : angle 5.19847 ( 813) SS BOND : bond 0.00171 ( 9) SS BOND : angle 0.60949 ( 18) covalent geometry : bond 0.00364 ( 9198) covalent geometry : angle 0.67771 (12461) *********************** 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 182 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 113 time to evaluate : 0.957 Fit side-chains REVERT: A 475 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: A 701 THR cc_start: 0.7299 (OUTLIER) cc_final: 0.7027 (p) REVERT: A 710 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7783 (m-40) REVERT: A 754 PHE cc_start: 0.8147 (t80) cc_final: 0.7844 (t80) REVERT: A 794 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6328 (ptt-90) REVERT: B 580 CYS cc_start: 0.8078 (t) cc_final: 0.7865 (t) REVERT: B 622 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7527 (mpt-90) REVERT: B 850 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8127 (t0) REVERT: C 424 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.6212 (t80) REVERT: C 692 TYR cc_start: 0.8087 (t80) cc_final: 0.7763 (t80) REVERT: D 636 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8265 (t) REVERT: D 640 GLN cc_start: 0.8521 (mm110) cc_final: 0.8272 (mm110) REVERT: D 818 ARG cc_start: 0.7736 (ptt90) cc_final: 0.7451 (tmm160) REVERT: D 905 ASP cc_start: 0.7896 (t0) cc_final: 0.7580 (p0) outliers start: 69 outliers final: 55 residues processed: 168 average time/residue: 0.1623 time to fit residues: 40.4007 Evaluate side-chains 171 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 108 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 426 VAL Chi-restraints excluded: chain A residue 436 CYS 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 710 ASN 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 794 ARG 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 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 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 486 THR 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 748 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 596 ASP Chi-restraints excluded: chain D residue 629 VAL 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 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 884 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 44 optimal weight: 0.3980 chunk 9 optimal weight: 0.0040 chunk 24 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** 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 = 0.3767 r_free = 0.3767 target = 0.129899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105623 restraints weight = 19200.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.106319 restraints weight = 15565.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.107414 restraints weight = 13458.954| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9207 Z= 0.122 Angle : 0.657 9.695 12479 Z= 0.340 Chirality : 0.043 0.232 1372 Planarity : 0.005 0.142 1606 Dihedral : 4.855 34.714 1231 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.82 % Favored : 90.39 % Rotamer: Outliers : 6.71 % Allowed : 36.05 % Favored : 57.23 % 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: -1.76 (0.25), residues: 1134 helix: 0.86 (0.27), residues: 385 sheet: -1.33 (0.48), residues: 113 loop : -2.59 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 498 HIS 0.004 0.001 HIS C 404 PHE 0.022 0.001 PHE B 794 TYR 0.015 0.001 TYR B 579 ARG 0.002 0.000 ARG C 704 Details of bonding type rmsd hydrogen bonds : bond 0.02962 ( 284) hydrogen bonds : angle 5.04006 ( 813) SS BOND : bond 0.00128 ( 9) SS BOND : angle 0.52998 ( 18) covalent geometry : bond 0.00290 ( 9198) covalent geometry : angle 0.65698 (12461) *********************** 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 185 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 120 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 536 GLN cc_start: 0.8098 (pp30) cc_final: 0.7810 (pp30) REVERT: A 701 THR cc_start: 0.7327 (OUTLIER) cc_final: 0.7058 (p) REVERT: A 754 PHE cc_start: 0.8163 (t80) cc_final: 0.7788 (t80) REVERT: A 794 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6087 (ptt-90) REVERT: B 622 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7440 (mpt-90) REVERT: B 850 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8115 (t0) REVERT: C 399 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8277 (mtmt) REVERT: C 424 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.6300 (t80) REVERT: C 692 TYR cc_start: 0.7993 (t80) cc_final: 0.7698 (t80) REVERT: D 547 MET cc_start: 0.6946 (pmm) cc_final: 0.6334 (pmm) outliers start: 65 outliers final: 48 residues processed: 171 average time/residue: 0.1734 time to fit residues: 43.4773 Evaluate side-chains 161 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 107 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 426 VAL Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 680 ILE 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 A residue 794 ARG 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 850 ASP 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 486 THR 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 748 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 561 LEU Chi-restraints excluded: chain D residue 596 ASP 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 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: 3.9990 chunk 89 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 95 optimal weight: 0.0980 chunk 43 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.129864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.104620 restraints weight = 19308.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.105044 restraints weight = 16104.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106219 restraints weight = 13244.891| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9207 Z= 0.128 Angle : 0.674 8.923 12479 Z= 0.348 Chirality : 0.044 0.231 1372 Planarity : 0.005 0.142 1606 Dihedral : 4.785 34.970 1231 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.61 % Favored : 89.59 % Rotamer: Outliers : 5.79 % Allowed : 35.95 % Favored : 58.26 % 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: -1.75 (0.25), residues: 1134 helix: 0.84 (0.27), residues: 385 sheet: -1.20 (0.47), residues: 117 loop : -2.60 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 731 HIS 0.004 0.001 HIS C 404 PHE 0.022 0.001 PHE B 794 TYR 0.016 0.001 TYR A 692 ARG 0.002 0.000 ARG D 818 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 284) hydrogen bonds : angle 5.10448 ( 813) SS BOND : bond 0.00134 ( 9) SS BOND : angle 0.52495 ( 18) covalent geometry : bond 0.00306 ( 9198) covalent geometry : angle 0.67417 (12461) ********************** 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 173 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 117 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 536 GLN cc_start: 0.8051 (pp30) cc_final: 0.7794 (pp30) REVERT: A 701 THR cc_start: 0.7381 (OUTLIER) cc_final: 0.7082 (p) REVERT: A 754 PHE cc_start: 0.8205 (t80) cc_final: 0.7789 (t80) REVERT: A 794 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6144 (ptt-90) REVERT: B 622 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7502 (mpt-90) REVERT: B 850 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8141 (t0) REVERT: C 399 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8302 (mtmt) REVERT: C 424 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6423 (t80) REVERT: C 692 TYR cc_start: 0.8096 (t80) cc_final: 0.7787 (t80) REVERT: D 547 MET cc_start: 0.7047 (pmm) cc_final: 0.6479 (pmm) REVERT: D 636 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8233 (t) REVERT: D 640 GLN cc_start: 0.8469 (mm110) cc_final: 0.8219 (mm110) outliers start: 56 outliers final: 47 residues processed: 162 average time/residue: 0.1739 time to fit residues: 41.4034 Evaluate side-chains 166 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 112 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 426 VAL Chi-restraints excluded: chain A residue 436 CYS 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 A residue 794 ARG 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 850 ASP 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 486 THR 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 748 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 561 LEU Chi-restraints excluded: chain D residue 596 ASP 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 834 ASN 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 884 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0470 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3751 r_free = 0.3751 target = 0.128709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.104708 restraints weight = 19473.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.105245 restraints weight = 15060.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106271 restraints weight = 14600.247| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9207 Z= 0.142 Angle : 0.683 9.188 12479 Z= 0.354 Chirality : 0.044 0.229 1372 Planarity : 0.005 0.143 1606 Dihedral : 4.871 35.251 1231 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.96 % Favored : 89.24 % Rotamer: Outliers : 5.99 % Allowed : 36.16 % Favored : 57.85 % 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: -1.80 (0.25), residues: 1134 helix: 0.80 (0.27), residues: 384 sheet: -1.29 (0.46), residues: 119 loop : -2.60 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 792 HIS 0.004 0.001 HIS C 404 PHE 0.022 0.001 PHE B 794 TYR 0.018 0.001 TYR B 579 ARG 0.002 0.000 ARG D 818 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 284) hydrogen bonds : angle 5.10384 ( 813) SS BOND : bond 0.00155 ( 9) SS BOND : angle 0.54350 ( 18) covalent geometry : bond 0.00342 ( 9198) covalent geometry : angle 0.68301 (12461) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2743.69 seconds wall clock time: 48 minutes 46.85 seconds (2926.85 seconds total)