Starting phenix.real_space_refine on Fri Jul 3 10:27:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jao_61296/07_2026/9jao_61296.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jao_61296/07_2026/9jao_61296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jao_61296/07_2026/9jao_61296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jao_61296/07_2026/9jao_61296.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jao_61296/07_2026/9jao_61296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jao_61296/07_2026/9jao_61296.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12 atoms to isotropic. 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: 8 Type Number sf(0) Gaussians P 210 5.49 5 Mg 1 5.21 5 S 51 5.16 5 Be 1 3.05 5 C 8110 2.51 5 N 2549 2.21 5 O 2991 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13916 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 5030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5030 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 16, 'TRANS': 604} Chain breaks: 1 Chain: "D" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 750 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2123 Classifications: {'DNA': 104} Link IDs: {'rna3p': 103} Chain: "J" Number of atoms: 2141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2141 Classifications: {'DNA': 104} Link IDs: {'rna3p': 103} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 66 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.17, per 1000 atoms: 0.23 Number of scatterers: 13916 At special positions: 0 Unit cell: (120.157, 116.91, 149.385, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 51 16.00 P 210 15.00 Mg 1 11.99 F 3 9.00 O 2991 8.00 N 2549 7.00 C 8110 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 546.7 milliseconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2262 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 8 sheets defined 66.2% alpha, 4.8% beta 103 base pairs and 185 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'C' and resid 382 through 396 Processing helix chain 'C' and resid 397 through 403 Processing helix chain 'C' and resid 409 through 418 removed outlier: 3.577A pdb=" N ILE C 415 " --> pdb=" O LYS C 411 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 417 " --> pdb=" O GLN C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 439 through 476 removed outlier: 3.803A pdb=" N TRP C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP C 464 " --> pdb=" O ASN C 460 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR C 474 " --> pdb=" O THR C 470 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET C 475 " --> pdb=" O LYS C 471 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU C 476 " --> pdb=" O GLN C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 514 Processing helix chain 'C' and resid 527 through 542 Processing helix chain 'C' and resid 556 through 568 removed outlier: 3.894A pdb=" N ASN C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 592 Processing helix chain 'C' and resid 610 through 620 Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 638 through 646 removed outlier: 3.733A pdb=" N GLN C 642 " --> pdb=" O SER C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 675 removed outlier: 3.827A pdb=" N LEU C 667 " --> pdb=" O ASN C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 680 removed outlier: 3.703A pdb=" N PHE C 679 " --> pdb=" O MET C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 690 Processing helix chain 'C' and resid 701 through 716 Processing helix chain 'C' and resid 723 through 728 Processing helix chain 'C' and resid 744 through 761 removed outlier: 3.958A pdb=" N LYS C 760 " --> pdb=" O ASN C 756 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER C 761 " --> pdb=" O ARG C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 774 removed outlier: 4.042A pdb=" N VAL C 774 " --> pdb=" O MET C 771 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 771 through 774' Processing helix chain 'C' and resid 775 through 784 removed outlier: 4.171A pdb=" N MET C 781 " --> pdb=" O GLN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 788 removed outlier: 3.547A pdb=" N HIS C 788 " --> pdb=" O PRO C 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 785 through 788' Processing helix chain 'C' and resid 793 through 804 Processing helix chain 'C' and resid 805 through 811 Proline residue: C 808 - end of helix Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.722A pdb=" N GLU C 820 " --> pdb=" O ASP C 816 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL C 824 " --> pdb=" O GLU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 837 Processing helix chain 'C' and resid 840 through 844 removed outlier: 3.805A pdb=" N GLN C 844 " --> pdb=" O ASN C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 851 removed outlier: 3.547A pdb=" N ILE C 850 " --> pdb=" O ASP C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 869 removed outlier: 3.657A pdb=" N CYS C 861 " --> pdb=" O ARG C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 893 Processing helix chain 'C' and resid 905 through 907 No H-bonds generated for 'chain 'C' and resid 905 through 907' Processing helix chain 'C' and resid 908 through 919 Processing helix chain 'C' and resid 952 through 961 removed outlier: 4.191A pdb=" N ASP C 956 " --> pdb=" O ASN C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1002 removed outlier: 4.032A pdb=" N SER C 986 " --> pdb=" O THR C 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 57 Processing helix chain 'D' and resid 63 through 79 removed outlier: 3.616A pdb=" N PHE D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP D 77 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 114 removed outlier: 3.527A pdb=" N VAL D 89 " --> pdb=" O GLN D 85 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 114 " --> pdb=" O CYS D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.546A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.698A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.915A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.516A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.576A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.760A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.632A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.680A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'K' and resid 1019 through 1025 removed outlier: 3.822A pdb=" N MET K1024 " --> pdb=" O LEU K1020 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY K1025 " --> pdb=" O LYS K1021 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 573 through 575 removed outlier: 6.506A pdb=" N HIS C 548 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N THR C 602 " --> pdb=" O HIS C 548 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C 550 " --> pdb=" O THR C 602 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 626 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA C 625 " --> pdb=" O LEU C 653 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU C 655 " --> pdb=" O ALA C 625 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE C 627 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 519 " --> pdb=" O LEU C 720 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 737 through 741 removed outlier: 6.986A pdb=" N VAL C 873 " --> pdb=" O PHE C 925 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU C 927 " --> pdb=" O VAL C 873 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU C 875 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C 898 " --> pdb=" O LEU C 926 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N SER C 928 " --> pdb=" O LEU C 898 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU C 900 " --> pdb=" O SER C 928 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 83 through 84 removed outlier: 6.665A pdb=" N ARG D 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.865A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.219A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.991A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 541 hydrogen bonds defined for protein. 1599 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 268 hydrogen bonds 536 hydrogen bond angles 0 basepair planarities 103 basepair parallelities 185 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1806 1.30 - 1.43: 4750 1.43 - 1.56: 7514 1.56 - 1.69: 417 1.69 - 1.81: 90 Bond restraints: 14577 Sorted by residual: bond pdb=" F2 BEF C1102 " pdb="BE BEF C1102 " ideal model delta sigma weight residual 1.476 1.710 -0.234 2.00e-02 2.50e+03 1.36e+02 bond pdb=" F1 BEF C1102 " pdb="BE BEF C1102 " ideal model delta sigma weight residual 1.476 1.701 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" F3 BEF C1102 " pdb="BE BEF C1102 " ideal model delta sigma weight residual 1.476 1.690 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" CA HIS C 548 " pdb=" C HIS C 548 " ideal model delta sigma weight residual 1.521 1.467 0.054 1.19e-02 7.06e+03 2.09e+01 bond pdb=" C HIS C 548 " pdb=" O HIS C 548 " ideal model delta sigma weight residual 1.236 1.182 0.053 1.20e-02 6.94e+03 1.96e+01 ... (remaining 14572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.31: 20506 4.31 - 8.62: 41 8.62 - 12.93: 1 12.93 - 17.24: 1 17.24 - 21.55: 1 Bond angle restraints: 20550 Sorted by residual: angle pdb=" F1 BEF C1102 " pdb="BE BEF C1102 " pdb=" F3 BEF C1102 " ideal model delta sigma weight residual 120.12 98.57 21.55 3.00e+00 1.11e-01 5.16e+01 angle pdb=" N PHE C 421 " pdb=" CA PHE C 421 " pdb=" C PHE C 421 " ideal model delta sigma weight residual 112.24 105.63 6.61 1.28e+00 6.10e-01 2.66e+01 angle pdb=" N VAL G 27 " pdb=" CA VAL G 27 " pdb=" C VAL G 27 " ideal model delta sigma weight residual 112.96 108.08 4.88 1.00e+00 1.00e+00 2.38e+01 angle pdb=" F2 BEF C1102 " pdb="BE BEF C1102 " pdb=" F3 BEF C1102 " ideal model delta sigma weight residual 119.96 105.50 14.46 3.00e+00 1.11e-01 2.32e+01 angle pdb=" N3 DT J 105 " pdb=" C4 DT J 105 " pdb=" O4 DT J 105 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.09e+01 ... (remaining 20545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.59: 6671 25.59 - 51.19: 1280 51.19 - 76.78: 323 76.78 - 102.38: 11 102.38 - 127.97: 2 Dihedral angle restraints: 8287 sinusoidal: 4794 harmonic: 3493 Sorted by residual: dihedral pdb=" CA SER C 408 " pdb=" C SER C 408 " pdb=" N GLN C 409 " pdb=" CA GLN C 409 " ideal model delta harmonic sigma weight residual 180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 92.03 127.97 1 3.50e+01 8.16e-04 1.27e+01 dihedral pdb=" C4' DT J 89 " pdb=" C3' DT J 89 " pdb=" O3' DT J 89 " pdb=" P DA J 90 " ideal model delta sinusoidal sigma weight residual 220.00 96.30 123.70 1 3.50e+01 8.16e-04 1.22e+01 ... (remaining 8284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1930 0.057 - 0.114: 372 0.114 - 0.172: 31 0.172 - 0.229: 0 0.229 - 0.286: 2 Chirality restraints: 2335 Sorted by residual: chirality pdb=" CA ARG C 419 " pdb=" N ARG C 419 " pdb=" C ARG C 419 " pdb=" CB ARG C 419 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CG LEU C 549 " pdb=" CB LEU C 549 " pdb=" CD1 LEU C 549 " pdb=" CD2 LEU C 549 " both_signs ideal model delta sigma weight residual False -2.59 -2.85 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C3' DG I 34 " pdb=" C4' DG I 34 " pdb=" O3' DG I 34 " pdb=" C2' DG I 34 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 2332 not shown) Planarity restraints: 1878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 549 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C LEU C 549 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU C 549 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE C 550 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 417 " -0.014 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C GLU C 417 " 0.051 2.00e-02 2.50e+03 pdb=" O GLU C 417 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU C 418 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 80 " -0.011 2.00e-02 2.50e+03 1.49e-02 4.42e+00 pdb=" CG TYR H 80 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR H 80 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR H 80 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR H 80 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR H 80 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR H 80 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 80 " 0.002 2.00e-02 2.50e+03 ... (remaining 1875 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.79: 5 1.79 - 2.57: 96 2.57 - 3.34: 16451 3.34 - 4.12: 37984 4.12 - 4.90: 63286 Nonbonded interactions: 117822 Sorted by model distance: nonbonded pdb=" O3B ADP C1101 " pdb=" F1 BEF C1102 " model vdw 1.011 2.990 nonbonded pdb=" OE1 GLN C 394 " pdb=" CD2 PHE C 421 " model vdw 1.051 3.340 nonbonded pdb=" O3B ADP C1101 " pdb="BE BEF C1102 " model vdw 1.400 2.420 nonbonded pdb=" OD1 ASN C 422 " pdb=" CB ALA C 426 " model vdw 1.612 3.460 nonbonded pdb=" OE1 GLN C 394 " pdb=" CE2 PHE C 421 " model vdw 1.780 3.340 ... (remaining 117817 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 'B' selection = (chain 'F' and ((resid 20 and (name N or name CA or name C or name O or name CB \ )) or resid 21 through 101)) } ncs_group { reference = (chain 'D' and resid 40 through 134) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.010 Find NCS groups from input model: 0.110 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 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 : 0.007 0.374 14578 Z= 0.598 Angle : 0.798 21.549 20550 Z= 0.614 Chirality : 0.044 0.286 2335 Planarity : 0.004 0.044 1878 Dihedral : 24.272 127.973 6025 Min Nonbonded Distance : 1.011 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.79 % Favored : 97.12 % Rotamer: Outliers : 0.19 % Allowed : 0.29 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.24), residues: 1182 helix: 0.87 (0.19), residues: 753 sheet: -0.92 (0.68), residues: 62 loop : -0.98 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 92 TYR 0.036 0.002 TYR H 80 PHE 0.017 0.002 PHE C 535 TRP 0.007 0.001 TRP C 507 HIS 0.012 0.002 HIS C 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.51 (14577) covalent geometry : angle 0.79807 / 0.61 (20550) hydrogen bonds : bond 0.12911 / 8.26 ( 809) hydrogen bonds : angle 4.63459 / 3.33 ( 2135) Misc. bond : bond 0.37368 / 19.67 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 267 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 269 average time/residue: 0.1298 time to fit residues: 49.3693 Evaluate side-chains 207 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 545 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 GLN ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.094688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.070944 restraints weight = 43243.079| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.81 r_work: 0.3285 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14578 Z= 0.179 Angle : 0.692 9.606 20550 Z= 0.382 Chirality : 0.046 0.216 2335 Planarity : 0.005 0.091 1878 Dihedral : 28.250 132.872 3586 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.82 % Allowed : 8.60 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.25), residues: 1182 helix: 1.15 (0.19), residues: 764 sheet: -1.08 (0.63), residues: 60 loop : -0.93 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 872 TYR 0.015 0.002 TYR H 80 PHE 0.018 0.002 PHE C 421 TRP 0.021 0.002 TRP C 424 HIS 0.006 0.002 HIS C 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 (14577) covalent geometry : angle 0.69189 / 0.38 (20550) hydrogen bonds : bond 0.04958 / 3.32 ( 809) hydrogen bonds : angle 3.78938 / 2.71 ( 2135) Misc. bond : bond 0.00115 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 893 HIS cc_start: 0.8887 (OUTLIER) cc_final: 0.8563 (m-70) REVERT: D 59 GLU cc_start: 0.8252 (pm20) cc_final: 0.8035 (pm20) REVERT: B 64 ASN cc_start: 0.8981 (t0) cc_final: 0.8763 (t0) REVERT: H 65 ASP cc_start: 0.8533 (t70) cc_final: 0.8186 (t0) REVERT: H 87 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8049 (t) REVERT: H 90 GLU cc_start: 0.8297 (mp0) cc_final: 0.7762 (mp0) REVERT: H 102 GLU cc_start: 0.7485 (tp30) cc_final: 0.6955 (tp30) outliers start: 19 outliers final: 13 residues processed: 214 average time/residue: 0.1229 time to fit residues: 37.3642 Evaluate side-chains 212 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 893 HIS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 1022 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 46 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 81 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 128 optimal weight: 10.9990 chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 HIS ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN D 113 HIS D 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.095008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.071265 restraints weight = 42987.084| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.82 r_work: 0.3297 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14578 Z= 0.139 Angle : 0.613 6.586 20550 Z= 0.346 Chirality : 0.043 0.210 2335 Planarity : 0.004 0.072 1878 Dihedral : 28.265 134.989 3584 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.01 % Allowed : 10.80 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.25), residues: 1182 helix: 1.35 (0.19), residues: 765 sheet: -1.01 (0.62), residues: 60 loop : -0.87 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 96 TYR 0.032 0.002 TYR H 80 PHE 0.014 0.001 PHE C 679 TRP 0.007 0.001 TRP C 507 HIS 0.007 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (14577) covalent geometry : angle 0.61308 / 0.35 (20550) hydrogen bonds : bond 0.04270 / 2.86 ( 809) hydrogen bonds : angle 3.54566 / 2.55 ( 2135) Misc. bond : bond 0.00209 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 893 HIS cc_start: 0.8916 (OUTLIER) cc_final: 0.8586 (m-70) REVERT: D 86 SER cc_start: 0.8754 (p) cc_final: 0.8515 (t) REVERT: B 24 ASP cc_start: 0.6881 (t0) cc_final: 0.6566 (t0) REVERT: B 64 ASN cc_start: 0.9041 (t0) cc_final: 0.8672 (t0) REVERT: B 93 GLN cc_start: 0.8287 (tt0) cc_final: 0.7720 (tt0) REVERT: E 60 LEU cc_start: 0.8714 (mm) cc_final: 0.8339 (mm) REVERT: E 97 GLU cc_start: 0.8233 (mt-10) cc_final: 0.8007 (mt-10) REVERT: H 65 ASP cc_start: 0.8474 (t70) cc_final: 0.8139 (t0) REVERT: H 76 ARG cc_start: 0.8472 (mtm180) cc_final: 0.8100 (mtp-110) REVERT: H 102 GLU cc_start: 0.7776 (tp30) cc_final: 0.6740 (tp30) outliers start: 21 outliers final: 12 residues processed: 218 average time/residue: 0.1234 time to fit residues: 38.5302 Evaluate side-chains 210 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 893 HIS Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 1022 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 6 optimal weight: 30.0000 chunk 93 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 467 ASN ** C 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 773 ASN ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN B 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.094056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.070227 restraints weight = 43227.442| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.84 r_work: 0.3273 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14578 Z= 0.162 Angle : 0.623 9.343 20550 Z= 0.347 Chirality : 0.043 0.206 2335 Planarity : 0.004 0.063 1878 Dihedral : 28.301 135.154 3582 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.10 % Allowed : 12.14 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.25), residues: 1182 helix: 1.51 (0.19), residues: 765 sheet: -1.02 (0.61), residues: 60 loop : -0.82 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 99 TYR 0.026 0.002 TYR H 80 PHE 0.011 0.001 PHE E 67 TRP 0.008 0.001 TRP C 507 HIS 0.008 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (14577) covalent geometry : angle 0.62342 / 0.35 (20550) hydrogen bonds : bond 0.04442 / 3.00 ( 809) hydrogen bonds : angle 3.48641 / 2.51 ( 2135) Misc. bond : bond 0.00122 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 893 HIS cc_start: 0.8960 (OUTLIER) cc_final: 0.8652 (m-70) REVERT: D 59 GLU cc_start: 0.8191 (pm20) cc_final: 0.7640 (pm20) REVERT: D 86 SER cc_start: 0.8790 (p) cc_final: 0.8527 (t) REVERT: B 64 ASN cc_start: 0.9099 (t0) cc_final: 0.8685 (t0) REVERT: B 79 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8241 (mtmm) REVERT: B 93 GLN cc_start: 0.8457 (tt0) cc_final: 0.7811 (tt0) REVERT: F 88 TYR cc_start: 0.8650 (m-10) cc_final: 0.8317 (m-80) REVERT: F 91 LYS cc_start: 0.9160 (tttt) cc_final: 0.8907 (tttt) REVERT: G 91 GLU cc_start: 0.8158 (pm20) cc_final: 0.7430 (pm20) REVERT: G 92 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8020 (pm20) REVERT: H 65 ASP cc_start: 0.8633 (t70) cc_final: 0.8339 (t0) REVERT: H 76 ARG cc_start: 0.8414 (mtm180) cc_final: 0.8152 (mtp-110) REVERT: H 102 GLU cc_start: 0.7821 (tp30) cc_final: 0.7598 (tp30) REVERT: H 106 HIS cc_start: 0.7984 (m-70) cc_final: 0.7774 (m-70) outliers start: 22 outliers final: 16 residues processed: 214 average time/residue: 0.1290 time to fit residues: 39.2688 Evaluate side-chains 210 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 893 HIS Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 1022 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 103 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 56 optimal weight: 0.0770 chunk 84 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 126 optimal weight: 30.0000 chunk 25 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 128 optimal weight: 10.0000 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.094588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.070967 restraints weight = 43052.130| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.86 r_work: 0.3296 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14578 Z= 0.130 Angle : 0.599 7.019 20550 Z= 0.333 Chirality : 0.042 0.203 2335 Planarity : 0.004 0.054 1878 Dihedral : 28.261 136.142 3582 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.01 % Allowed : 12.81 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.25), residues: 1182 helix: 1.67 (0.19), residues: 765 sheet: -1.01 (0.62), residues: 60 loop : -0.76 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 99 TYR 0.014 0.001 TYR C 954 PHE 0.009 0.001 PHE E 67 TRP 0.007 0.001 TRP C 507 HIS 0.006 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 (14577) covalent geometry : angle 0.59862 / 0.33 (20550) hydrogen bonds : bond 0.03853 / 2.58 ( 809) hydrogen bonds : angle 3.37386 / 2.42 ( 2135) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 893 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.8710 (m-70) REVERT: D 57 SER cc_start: 0.7912 (OUTLIER) cc_final: 0.7226 (t) REVERT: D 59 GLU cc_start: 0.8335 (pm20) cc_final: 0.8036 (pm20) REVERT: D 85 GLN cc_start: 0.8154 (pt0) cc_final: 0.7937 (pt0) REVERT: D 86 SER cc_start: 0.8712 (p) cc_final: 0.8417 (t) REVERT: B 64 ASN cc_start: 0.9116 (t0) cc_final: 0.8792 (t0) REVERT: B 93 GLN cc_start: 0.8641 (tt0) cc_final: 0.8222 (tt0) REVERT: F 88 TYR cc_start: 0.8546 (m-10) cc_final: 0.8310 (m-80) REVERT: F 91 LYS cc_start: 0.9132 (tttt) cc_final: 0.8900 (tttt) REVERT: H 65 ASP cc_start: 0.8640 (t70) cc_final: 0.8428 (t70) REVERT: H 76 ARG cc_start: 0.8431 (mtm180) cc_final: 0.8176 (mtp-110) REVERT: H 90 GLU cc_start: 0.8404 (mp0) cc_final: 0.7958 (mp0) outliers start: 21 outliers final: 13 residues processed: 218 average time/residue: 0.1298 time to fit residues: 40.6106 Evaluate side-chains 211 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 893 HIS Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 1022 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 63 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 541 GLN ** C 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN F 75 HIS H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.093474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.069593 restraints weight = 42710.530| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.83 r_work: 0.3258 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14578 Z= 0.177 Angle : 0.649 14.891 20550 Z= 0.350 Chirality : 0.043 0.206 2335 Planarity : 0.004 0.051 1878 Dihedral : 28.274 135.311 3582 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.29 % Allowed : 14.05 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.25), residues: 1182 helix: 1.76 (0.19), residues: 765 sheet: -1.13 (0.61), residues: 60 loop : -0.82 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 99 TYR 0.021 0.001 TYR C 954 PHE 0.012 0.001 PHE D 67 TRP 0.008 0.001 TRP C 507 HIS 0.008 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.18 (14577) covalent geometry : angle 0.64947 / 0.35 (20550) hydrogen bonds : bond 0.04614 / 3.13 ( 809) hydrogen bonds : angle 3.40129 / 2.44 ( 2135) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 893 HIS cc_start: 0.9010 (OUTLIER) cc_final: 0.8751 (m-70) REVERT: D 59 GLU cc_start: 0.8382 (pm20) cc_final: 0.8178 (pm20) REVERT: D 85 GLN cc_start: 0.8329 (pt0) cc_final: 0.8116 (pt0) REVERT: D 86 SER cc_start: 0.8796 (p) cc_final: 0.8534 (t) REVERT: B 24 ASP cc_start: 0.7089 (t0) cc_final: 0.6863 (t0) REVERT: B 64 ASN cc_start: 0.9141 (t0) cc_final: 0.8938 (t0) REVERT: B 93 GLN cc_start: 0.8688 (tt0) cc_final: 0.8398 (tt0) REVERT: F 88 TYR cc_start: 0.8659 (m-10) cc_final: 0.8379 (m-80) REVERT: F 91 LYS cc_start: 0.9120 (tttt) cc_final: 0.8882 (tttt) REVERT: H 65 ASP cc_start: 0.8723 (t70) cc_final: 0.8436 (t0) REVERT: H 73 GLU cc_start: 0.8062 (tp30) cc_final: 0.7416 (tp30) REVERT: H 76 ARG cc_start: 0.8465 (mtm180) cc_final: 0.8224 (mtp-110) REVERT: H 90 GLU cc_start: 0.8455 (mp0) cc_final: 0.8058 (mp0) outliers start: 24 outliers final: 18 residues processed: 206 average time/residue: 0.1184 time to fit residues: 35.1046 Evaluate side-chains 200 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 893 HIS Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain K residue 1022 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 45 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** H 81 ASN ** 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 = 0.3978 r_free = 0.3978 target = 0.093274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.069454 restraints weight = 42729.925| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.82 r_work: 0.3257 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14578 Z= 0.173 Angle : 0.644 10.975 20550 Z= 0.349 Chirality : 0.043 0.207 2335 Planarity : 0.004 0.046 1878 Dihedral : 28.293 135.379 3582 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.01 % Allowed : 14.24 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.25), residues: 1182 helix: 1.83 (0.19), residues: 757 sheet: -1.16 (0.61), residues: 60 loop : -0.70 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 99 TYR 0.019 0.001 TYR C 954 PHE 0.009 0.001 PHE D 67 TRP 0.009 0.001 TRP C 507 HIS 0.007 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (14577) covalent geometry : angle 0.64427 / 0.35 (20550) hydrogen bonds : bond 0.04275 / 2.87 ( 809) hydrogen bonds : angle 3.40049 / 2.45 ( 2135) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 GLU cc_start: 0.8383 (pm20) cc_final: 0.8159 (pm20) REVERT: D 85 GLN cc_start: 0.8303 (pt0) cc_final: 0.8087 (pt0) REVERT: D 86 SER cc_start: 0.8795 (p) cc_final: 0.8536 (t) REVERT: B 24 ASP cc_start: 0.7113 (t0) cc_final: 0.6856 (t0) REVERT: B 64 ASN cc_start: 0.9164 (t0) cc_final: 0.8945 (t0) REVERT: B 93 GLN cc_start: 0.8722 (tt0) cc_final: 0.8491 (tt0) REVERT: F 88 TYR cc_start: 0.8656 (m-10) cc_final: 0.8170 (m-80) REVERT: G 92 GLU cc_start: 0.8438 (pm20) cc_final: 0.8229 (pm20) REVERT: H 65 ASP cc_start: 0.8742 (t70) cc_final: 0.8437 (t0) REVERT: H 73 GLU cc_start: 0.8081 (tp30) cc_final: 0.7423 (tp30) outliers start: 21 outliers final: 18 residues processed: 194 average time/residue: 0.1271 time to fit residues: 35.1968 Evaluate side-chains 198 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain K residue 1022 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 80 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 40.0000 chunk 130 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.093844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.070203 restraints weight = 42833.658| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.80 r_work: 0.3281 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14578 Z= 0.136 Angle : 0.625 10.124 20550 Z= 0.339 Chirality : 0.041 0.203 2335 Planarity : 0.003 0.047 1878 Dihedral : 28.239 136.129 3582 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.10 % Allowed : 14.44 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.25), residues: 1182 helix: 1.88 (0.19), residues: 757 sheet: -1.02 (0.63), residues: 60 loop : -0.66 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 99 TYR 0.019 0.001 TYR C 954 PHE 0.008 0.001 PHE F 61 TRP 0.007 0.001 TRP C 507 HIS 0.006 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (14577) covalent geometry : angle 0.62450 / 0.34 (20550) hydrogen bonds : bond 0.03800 / 2.53 ( 809) hydrogen bonds : angle 3.33004 / 2.39 ( 2135) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 SER cc_start: 0.8786 (p) cc_final: 0.8516 (t) REVERT: B 24 ASP cc_start: 0.7170 (t0) cc_final: 0.6896 (t0) REVERT: B 64 ASN cc_start: 0.9160 (t0) cc_final: 0.8907 (t0) REVERT: B 93 GLN cc_start: 0.8715 (tt0) cc_final: 0.8512 (tt0) REVERT: F 88 TYR cc_start: 0.8631 (m-10) cc_final: 0.8185 (m-80) REVERT: G 90 ASP cc_start: 0.7875 (t70) cc_final: 0.7591 (t70) REVERT: H 65 ASP cc_start: 0.8629 (t70) cc_final: 0.8369 (t0) REVERT: H 90 GLU cc_start: 0.8332 (mp0) cc_final: 0.7958 (mp0) outliers start: 22 outliers final: 19 residues processed: 202 average time/residue: 0.1269 time to fit residues: 36.8307 Evaluate side-chains 205 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 893 HIS Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain K residue 1022 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 0.0170 chunk 28 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 541 GLN ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.094096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.070417 restraints weight = 42996.100| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.81 r_work: 0.3288 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14578 Z= 0.133 Angle : 0.639 9.806 20550 Z= 0.347 Chirality : 0.042 0.214 2335 Planarity : 0.004 0.043 1878 Dihedral : 28.190 136.355 3582 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.91 % Allowed : 15.20 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.25), residues: 1182 helix: 1.91 (0.19), residues: 757 sheet: -0.89 (0.64), residues: 60 loop : -0.66 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 593 TYR 0.018 0.001 TYR C 954 PHE 0.017 0.001 PHE C 588 TRP 0.006 0.001 TRP C 507 HIS 0.006 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (14577) covalent geometry : angle 0.63913 / 0.35 (20550) hydrogen bonds : bond 0.03779 / 2.52 ( 809) hydrogen bonds : angle 3.30159 / 2.36 ( 2135) Misc. bond : bond 0.00060 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 SER cc_start: 0.8694 (p) cc_final: 0.8405 (t) REVERT: B 24 ASP cc_start: 0.7202 (t0) cc_final: 0.6945 (t0) REVERT: F 88 TYR cc_start: 0.8611 (m-10) cc_final: 0.8163 (m-80) REVERT: H 65 ASP cc_start: 0.8654 (t70) cc_final: 0.8405 (t0) REVERT: H 73 GLU cc_start: 0.8105 (tp30) cc_final: 0.7464 (tp30) REVERT: H 90 GLU cc_start: 0.8335 (mp0) cc_final: 0.7957 (mp0) outliers start: 20 outliers final: 17 residues processed: 200 average time/residue: 0.1166 time to fit residues: 33.5560 Evaluate side-chains 202 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 893 HIS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain K residue 1022 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 102 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.092614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.068792 restraints weight = 42744.187| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.79 r_work: 0.3241 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14578 Z= 0.212 Angle : 0.696 9.345 20550 Z= 0.372 Chirality : 0.044 0.213 2335 Planarity : 0.004 0.043 1878 Dihedral : 28.268 134.384 3582 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.82 % Allowed : 15.39 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.25), residues: 1182 helix: 1.85 (0.19), residues: 760 sheet: -1.08 (0.62), residues: 60 loop : -0.80 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 99 TYR 0.017 0.002 TYR C 954 PHE 0.017 0.002 PHE D 67 TRP 0.009 0.001 TRP C 507 HIS 0.007 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (14577) covalent geometry : angle 0.69601 / 0.37 (20550) hydrogen bonds : bond 0.04959 / 3.36 ( 809) hydrogen bonds : angle 3.45353 / 2.46 ( 2135) Misc. bond : bond 0.00067 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 SER cc_start: 0.8562 (p) cc_final: 0.8207 (t) REVERT: F 88 TYR cc_start: 0.8696 (m-10) cc_final: 0.8464 (m-10) REVERT: H 65 ASP cc_start: 0.8693 (t70) cc_final: 0.8424 (t0) REVERT: H 73 GLU cc_start: 0.8064 (tp30) cc_final: 0.7430 (tp30) REVERT: H 90 GLU cc_start: 0.8354 (mp0) cc_final: 0.8060 (mp0) outliers start: 19 outliers final: 18 residues processed: 189 average time/residue: 0.1187 time to fit residues: 32.2427 Evaluate side-chains 196 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 893 HIS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain K residue 1022 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 34 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.092588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.068756 restraints weight = 42833.588| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.80 r_work: 0.3241 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14578 Z= 0.194 Angle : 0.681 10.732 20550 Z= 0.364 Chirality : 0.043 0.209 2335 Planarity : 0.004 0.041 1878 Dihedral : 28.325 134.221 3582 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.91 % Allowed : 15.01 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.25), residues: 1182 helix: 1.85 (0.19), residues: 758 sheet: -1.09 (0.63), residues: 60 loop : -0.78 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 99 TYR 0.016 0.001 TYR C 954 PHE 0.014 0.001 PHE D 67 TRP 0.009 0.001 TRP C 507 HIS 0.008 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (14577) covalent geometry : angle 0.68121 / 0.36 (20550) hydrogen bonds : bond 0.04458 / 3.00 ( 809) hydrogen bonds : angle 3.42926 / 2.44 ( 2135) Misc. bond : bond 0.00043 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3621.53 seconds wall clock time: 62 minutes 41.52 seconds (3761.52 seconds total)