Starting phenix.real_space_refine on Thu May 15 22:11:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jao_61296/05_2025/9jao_61296.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jao_61296/05_2025/9jao_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jao_61296/05_2025/9jao_61296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jao_61296/05_2025/9jao_61296.map" model { file = "/net/cci-nas-00/data/ceres_data/9jao_61296/05_2025/9jao_61296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jao_61296/05_2025/9jao_61296.cif" } resolution = 3.1 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= 0.030 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.75, per 1000 atoms: 0.63 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: 3.40 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 6.77 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: 7.58 Time building geometry restraints manager: 4.01 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=" N LEU C 549 " pdb=" CA LEU C 549 " pdb=" C LEU C 549 " ideal model delta sigma weight residual 110.53 116.19 -5.66 1.29e+00 6.01e-01 1.93e+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: 2043 0.057 - 0.114: 273 0.114 - 0.172: 17 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=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 40.960 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 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 : 0.006 0.374 14578 Z= 0.418 Angle : 0.705 21.549 20550 Z= 0.408 Chirality : 0.039 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.24), 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 TRP 0.007 0.001 TRP C 507 HIS 0.012 0.002 HIS C 548 PHE 0.017 0.002 PHE C 535 TYR 0.036 0.002 TYR H 80 ARG 0.015 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.12911 ( 809) hydrogen bonds : angle 4.63459 ( 2135) covalent geometry : bond 0.00561 (14577) covalent geometry : angle 0.70510 (20550) Misc. bond : bond 0.37368 ( 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 : 1.259 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: 0.2988 time to fit residues: 111.3900 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 : 1.269 ------------------------------------------------------------------------------- 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 114 optimal weight: 0.0040 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 HIS ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.095500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.071955 restraints weight = 43140.619| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.80 r_work: 0.3316 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14578 Z= 0.152 Angle : 0.596 6.646 20550 Z= 0.336 Chirality : 0.037 0.137 2335 Planarity : 0.004 0.078 1878 Dihedral : 27.813 135.901 3586 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.28 % Favored : 97.63 % Rotamer: Outliers : 1.63 % Allowed : 8.99 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1182 helix: 1.37 (0.19), residues: 766 sheet: -0.95 (0.64), residues: 60 loop : -0.83 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 424 HIS 0.006 0.001 HIS C 895 PHE 0.013 0.001 PHE C 421 TYR 0.018 0.001 TYR F 88 ARG 0.006 0.001 ARG C 838 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 809) hydrogen bonds : angle 3.43467 ( 2135) covalent geometry : bond 0.00325 (14577) covalent geometry : angle 0.59594 (20550) Misc. bond : bond 0.00099 ( 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 230 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 840 ILE cc_start: 0.8567 (pt) cc_final: 0.8359 (pt) REVERT: C 893 HIS cc_start: 0.8882 (OUTLIER) cc_final: 0.8498 (m-70) REVERT: C 987 MET cc_start: 0.8397 (mtp) cc_final: 0.8107 (mtp) REVERT: D 59 GLU cc_start: 0.8295 (pm20) cc_final: 0.7676 (pm20) REVERT: D 86 SER cc_start: 0.8729 (p) cc_final: 0.8484 (t) REVERT: B 64 ASN cc_start: 0.9041 (t0) cc_final: 0.8832 (t0) REVERT: B 79 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8139 (mtpp) REVERT: B 93 GLN cc_start: 0.8411 (tt0) cc_final: 0.8114 (tt0) REVERT: B 98 TYR cc_start: 0.9029 (m-10) cc_final: 0.8723 (m-80) REVERT: F 20 LYS cc_start: 0.8418 (mmtp) cc_final: 0.8026 (mmtp) REVERT: G 75 LYS cc_start: 0.8319 (mmmt) cc_final: 0.8054 (mmmm) REVERT: H 65 ASP cc_start: 0.8495 (t70) cc_final: 0.8186 (t0) REVERT: H 102 GLU cc_start: 0.7668 (tp30) cc_final: 0.6106 (tp30) outliers start: 17 outliers final: 8 residues processed: 220 average time/residue: 0.2878 time to fit residues: 89.0468 Evaluate side-chains 206 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 197 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 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 G residue 114 VAL 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 20 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 111 optimal weight: 0.0270 chunk 8 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 chunk 87 optimal weight: 0.8980 overall best weight: 1.4040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 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 85 GLN D 113 HIS D 125 GLN E 93 GLN F 75 HIS H 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.093888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.070053 restraints weight = 42271.993| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.82 r_work: 0.3270 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14578 Z= 0.195 Angle : 0.587 9.249 20550 Z= 0.331 Chirality : 0.037 0.148 2335 Planarity : 0.004 0.056 1878 Dihedral : 27.807 134.666 3584 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.72 % Allowed : 11.19 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1182 helix: 1.56 (0.19), residues: 765 sheet: -1.00 (0.63), residues: 60 loop : -0.84 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 507 HIS 0.006 0.001 HIS F 18 PHE 0.011 0.001 PHE D 67 TYR 0.025 0.001 TYR F 88 ARG 0.005 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 809) hydrogen bonds : angle 3.38059 ( 2135) covalent geometry : bond 0.00430 (14577) covalent geometry : angle 0.58668 (20550) Misc. bond : bond 0.00073 ( 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 226 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 1.313 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: C 987 MET cc_start: 0.8424 (mtp) cc_final: 0.8112 (mtp) REVERT: D 59 GLU cc_start: 0.8352 (pm20) cc_final: 0.8104 (pm20) REVERT: D 86 SER cc_start: 0.8809 (p) cc_final: 0.8575 (t) REVERT: B 24 ASP cc_start: 0.6943 (t0) cc_final: 0.6685 (t0) REVERT: B 64 ASN cc_start: 0.9098 (t0) cc_final: 0.8806 (t0) REVERT: B 79 LYS cc_start: 0.8777 (mtpp) cc_final: 0.8256 (mtmm) REVERT: B 93 GLN cc_start: 0.8554 (tt0) cc_final: 0.8198 (tt0) REVERT: F 91 LYS cc_start: 0.9099 (tttt) cc_final: 0.8820 (tttt) REVERT: H 65 ASP cc_start: 0.8626 (t70) cc_final: 0.8322 (t0) REVERT: H 102 GLU cc_start: 0.7817 (tp30) cc_final: 0.6635 (tp30) REVERT: H 106 HIS cc_start: 0.7939 (m-70) cc_final: 0.7478 (m-70) outliers start: 18 outliers final: 12 residues processed: 215 average time/residue: 0.2935 time to fit residues: 89.0579 Evaluate side-chains 208 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 620 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 124 ILE 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 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 130 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 773 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 125 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.093761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.069871 restraints weight = 42686.756| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.85 r_work: 0.3266 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14578 Z= 0.187 Angle : 0.584 9.217 20550 Z= 0.328 Chirality : 0.037 0.167 2335 Planarity : 0.004 0.052 1878 Dihedral : 27.784 134.830 3584 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.10 % Allowed : 12.62 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1182 helix: 1.69 (0.19), residues: 765 sheet: -1.05 (0.61), residues: 60 loop : -0.77 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 507 HIS 0.006 0.001 HIS F 18 PHE 0.019 0.001 PHE C 679 TYR 0.032 0.002 TYR H 80 ARG 0.006 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 809) hydrogen bonds : angle 3.32297 ( 2135) covalent geometry : bond 0.00412 (14577) covalent geometry : angle 0.58435 (20550) Misc. bond : bond 0.00056 ( 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 221 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 875 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8778 (tt) REVERT: C 987 MET cc_start: 0.8447 (mtp) cc_final: 0.8121 (mtp) REVERT: D 86 SER cc_start: 0.8808 (p) cc_final: 0.8587 (t) REVERT: B 64 ASN cc_start: 0.9141 (t0) cc_final: 0.8901 (t0) REVERT: B 79 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8251 (mtmm) REVERT: B 93 GLN cc_start: 0.8671 (tt0) cc_final: 0.8447 (tt0) REVERT: F 91 LYS cc_start: 0.9030 (tttt) cc_final: 0.8800 (tttt) REVERT: H 65 ASP cc_start: 0.8692 (t70) cc_final: 0.8407 (t0) REVERT: H 73 GLU cc_start: 0.7974 (tp30) cc_final: 0.7387 (tp30) REVERT: H 90 GLU cc_start: 0.8279 (mp0) cc_final: 0.7916 (mp0) outliers start: 22 outliers final: 17 residues processed: 211 average time/residue: 0.2835 time to fit residues: 84.3790 Evaluate side-chains 203 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 667 LEU Chi-restraints excluded: chain C residue 875 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 E residue 124 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 73 THR 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 10 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 94 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.092909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.068977 restraints weight = 42808.040| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.80 r_work: 0.3247 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 14578 Z= 0.209 Angle : 0.591 7.745 20550 Z= 0.332 Chirality : 0.037 0.167 2335 Planarity : 0.004 0.043 1878 Dihedral : 27.796 133.765 3584 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.39 % Allowed : 13.29 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1182 helix: 1.82 (0.19), residues: 759 sheet: -1.15 (0.61), residues: 60 loop : -0.70 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 507 HIS 0.007 0.001 HIS F 18 PHE 0.013 0.001 PHE D 67 TYR 0.027 0.002 TYR H 80 ARG 0.005 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 809) hydrogen bonds : angle 3.30988 ( 2135) covalent geometry : bond 0.00461 (14577) covalent geometry : angle 0.59096 (20550) Misc. bond : bond 0.00058 ( 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 223 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 771 MET cc_start: 0.4748 (OUTLIER) cc_final: 0.4476 (tpt) REVERT: C 773 ASN cc_start: 0.6467 (m110) cc_final: 0.6065 (m-40) REVERT: C 840 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8298 (pt) REVERT: D 86 SER cc_start: 0.8848 (p) cc_final: 0.8647 (t) REVERT: F 10 LEU cc_start: 0.9106 (tp) cc_final: 0.8878 (tp) REVERT: H 65 ASP cc_start: 0.8687 (t70) cc_final: 0.8410 (t0) REVERT: H 73 GLU cc_start: 0.8037 (tp30) cc_final: 0.7474 (tp30) REVERT: H 90 GLU cc_start: 0.8266 (mp0) cc_final: 0.7875 (mp0) outliers start: 25 outliers final: 19 residues processed: 212 average time/residue: 0.2845 time to fit residues: 84.9927 Evaluate side-chains 205 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 667 LEU Chi-restraints excluded: chain C residue 771 MET Chi-restraints excluded: chain C residue 840 ILE Chi-restraints excluded: chain C residue 893 HIS Chi-restraints excluded: chain C residue 915 GLU 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 E residue 124 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 62 ILE 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 45 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 107 optimal weight: 0.0770 chunk 6 optimal weight: 7.9990 chunk 38 optimal weight: 0.2980 chunk 132 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 541 GLN ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.093698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.069854 restraints weight = 42975.969| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.87 r_work: 0.3276 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2967 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= 0.155 Angle : 0.578 9.470 20550 Z= 0.323 Chirality : 0.035 0.142 2335 Planarity : 0.004 0.042 1878 Dihedral : 27.751 134.811 3584 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.01 % Allowed : 14.91 % 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 (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: 1.50 (0.25), residues: 1182 helix: 1.92 (0.19), residues: 757 sheet: -0.99 (0.63), residues: 60 loop : -0.60 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 507 HIS 0.005 0.001 HIS F 18 PHE 0.010 0.001 PHE D 67 TYR 0.030 0.001 TYR F 88 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 809) hydrogen bonds : angle 3.23117 ( 2135) covalent geometry : bond 0.00341 (14577) covalent geometry : angle 0.57817 (20550) Misc. bond : bond 0.00044 ( 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 216 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 840 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8322 (pt) REVERT: D 86 SER cc_start: 0.8804 (p) cc_final: 0.8593 (t) REVERT: F 10 LEU cc_start: 0.8987 (tp) cc_final: 0.8760 (tp) REVERT: G 75 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8598 (mmmm) REVERT: G 91 GLU cc_start: 0.8379 (pm20) cc_final: 0.7707 (pm20) REVERT: G 92 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: H 65 ASP cc_start: 0.8656 (t70) cc_final: 0.8376 (t0) REVERT: H 73 GLU cc_start: 0.8024 (tp30) cc_final: 0.7499 (tp30) REVERT: H 90 GLU cc_start: 0.8237 (mp0) cc_final: 0.7814 (mp0) outliers start: 21 outliers final: 14 residues processed: 206 average time/residue: 0.2898 time to fit residues: 83.9574 Evaluate side-chains 200 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 840 ILE Chi-restraints excluded: chain C residue 893 HIS 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 E residue 124 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 103 LEU 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 87 optimal weight: 0.3980 chunk 113 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 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 = 0.3981 r_free = 0.3981 target = 0.093215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.069324 restraints weight = 43250.947| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.85 r_work: 0.3260 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3163 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= 0.182 Angle : 0.592 10.159 20550 Z= 0.329 Chirality : 0.036 0.140 2335 Planarity : 0.004 0.041 1878 Dihedral : 27.675 133.914 3584 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.20 % Allowed : 14.91 % 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 (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: 1.56 (0.25), residues: 1182 helix: 1.98 (0.19), residues: 758 sheet: -0.92 (0.64), residues: 60 loop : -0.61 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 507 HIS 0.005 0.001 HIS H 46 PHE 0.010 0.001 PHE D 67 TYR 0.022 0.001 TYR H 80 ARG 0.007 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 809) hydrogen bonds : angle 3.22197 ( 2135) covalent geometry : bond 0.00402 (14577) covalent geometry : angle 0.59203 (20550) Misc. bond : bond 0.00047 ( 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 215 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 840 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8356 (pt) REVERT: D 86 SER cc_start: 0.8857 (p) cc_final: 0.8652 (t) REVERT: G 75 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8644 (mmmm) REVERT: H 65 ASP cc_start: 0.8697 (t70) cc_final: 0.8408 (t0) REVERT: H 73 GLU cc_start: 0.8025 (tp30) cc_final: 0.7467 (tp30) REVERT: H 90 GLU cc_start: 0.8209 (mp0) cc_final: 0.7761 (mp0) outliers start: 23 outliers final: 18 residues processed: 203 average time/residue: 0.2852 time to fit residues: 81.5588 Evaluate side-chains 203 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 539 LEU Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 840 ILE Chi-restraints excluded: chain C residue 893 HIS Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain D residue 57 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 E residue 124 ILE 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 H residue 56 MET Chi-restraints excluded: chain H residue 103 LEU 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 18 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 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 541 GLN ** 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 ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.093741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.069981 restraints weight = 42784.441| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.80 r_work: 0.3278 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14578 Z= 0.152 Angle : 0.591 10.367 20550 Z= 0.329 Chirality : 0.035 0.153 2335 Planarity : 0.004 0.052 1878 Dihedral : 27.668 134.480 3584 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.20 % Allowed : 15.11 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.25), residues: 1182 helix: 1.98 (0.19), residues: 759 sheet: -0.86 (0.65), residues: 60 loop : -0.62 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 507 HIS 0.005 0.001 HIS F 18 PHE 0.010 0.001 PHE D 67 TYR 0.019 0.001 TYR F 88 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 809) hydrogen bonds : angle 3.17497 ( 2135) covalent geometry : bond 0.00332 (14577) covalent geometry : angle 0.59123 (20550) Misc. bond : bond 0.00036 ( 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 210 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 840 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8301 (pt) REVERT: D 86 SER cc_start: 0.8818 (p) cc_final: 0.8598 (t) REVERT: G 75 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8553 (mmmm) REVERT: G 91 GLU cc_start: 0.8444 (pm20) cc_final: 0.7654 (pm20) REVERT: G 92 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: H 65 ASP cc_start: 0.8700 (t70) cc_final: 0.8416 (t0) REVERT: H 73 GLU cc_start: 0.8021 (tp30) cc_final: 0.7543 (tp30) REVERT: H 90 GLU cc_start: 0.8180 (mp0) cc_final: 0.7628 (mp0) outliers start: 23 outliers final: 18 residues processed: 199 average time/residue: 0.2872 time to fit residues: 81.3773 Evaluate side-chains 200 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 539 LEU Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 840 ILE Chi-restraints excluded: chain C residue 893 HIS Chi-restraints excluded: chain D residue 57 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 91 LYS Chi-restraints excluded: chain E residue 124 ILE 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 H residue 56 MET Chi-restraints excluded: chain H residue 103 LEU 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 127 optimal weight: 3.9990 chunk 55 optimal weight: 0.1980 chunk 99 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 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 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 = 0.4003 r_free = 0.4003 target = 0.094383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.070691 restraints weight = 42727.702| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.83 r_work: 0.3297 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14578 Z= 0.148 Angle : 0.587 9.287 20550 Z= 0.324 Chirality : 0.035 0.166 2335 Planarity : 0.004 0.046 1878 Dihedral : 27.520 135.279 3584 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.82 % Allowed : 15.87 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.25), residues: 1182 helix: 2.08 (0.19), residues: 759 sheet: -0.75 (0.65), residues: 60 loop : -0.64 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 507 HIS 0.007 0.001 HIS H 106 PHE 0.012 0.001 PHE C 679 TYR 0.017 0.001 TYR F 88 ARG 0.006 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 809) hydrogen bonds : angle 3.12035 ( 2135) covalent geometry : bond 0.00321 (14577) covalent geometry : angle 0.58653 (20550) Misc. bond : bond 0.00031 ( 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 212 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 840 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8337 (pt) REVERT: D 86 SER cc_start: 0.8734 (p) cc_final: 0.8506 (t) REVERT: E 73 GLU cc_start: 0.8173 (tp30) cc_final: 0.7953 (tp30) REVERT: G 116 LEU cc_start: 0.9048 (mm) cc_final: 0.8833 (mt) REVERT: H 65 ASP cc_start: 0.8694 (t70) cc_final: 0.8421 (t0) REVERT: H 73 GLU cc_start: 0.8052 (tp30) cc_final: 0.7606 (tp30) REVERT: H 90 GLU cc_start: 0.8111 (mp0) cc_final: 0.7641 (mp0) outliers start: 19 outliers final: 17 residues processed: 202 average time/residue: 0.2788 time to fit residues: 80.0239 Evaluate side-chains 203 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 539 LEU Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 840 ILE Chi-restraints excluded: chain C residue 893 HIS Chi-restraints excluded: chain D residue 57 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 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 H residue 56 MET Chi-restraints excluded: chain H residue 103 LEU 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 6 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 35 optimal weight: 0.0870 chunk 109 optimal weight: 0.4980 chunk 133 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 F 93 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.094682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.071138 restraints weight = 42863.190| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.81 r_work: 0.3309 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14578 Z= 0.139 Angle : 0.606 10.845 20550 Z= 0.333 Chirality : 0.035 0.183 2335 Planarity : 0.004 0.050 1878 Dihedral : 27.506 135.590 3584 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.82 % Allowed : 17.02 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.25), residues: 1182 helix: 2.10 (0.19), residues: 759 sheet: -0.65 (0.65), residues: 60 loop : -0.61 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 507 HIS 0.005 0.001 HIS F 18 PHE 0.014 0.001 PHE C 679 TYR 0.015 0.001 TYR F 88 ARG 0.006 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 809) hydrogen bonds : angle 3.09877 ( 2135) covalent geometry : bond 0.00300 (14577) covalent geometry : angle 0.60553 (20550) Misc. bond : bond 0.00022 ( 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 211 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 840 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8320 (pt) REVERT: D 86 SER cc_start: 0.8688 (p) cc_final: 0.8463 (t) REVERT: B 25 ASN cc_start: 0.7307 (t0) cc_final: 0.7067 (t0) REVERT: E 73 GLU cc_start: 0.8215 (tp30) cc_final: 0.8003 (tp30) REVERT: G 75 LYS cc_start: 0.8732 (mmmm) cc_final: 0.8427 (mmmt) REVERT: G 116 LEU cc_start: 0.9038 (mm) cc_final: 0.8816 (mt) REVERT: H 65 ASP cc_start: 0.8698 (t70) cc_final: 0.8430 (t0) REVERT: H 73 GLU cc_start: 0.8044 (tp30) cc_final: 0.7644 (tp30) REVERT: H 90 GLU cc_start: 0.8072 (mp0) cc_final: 0.7576 (mp0) outliers start: 19 outliers final: 17 residues processed: 201 average time/residue: 0.2861 time to fit residues: 82.1377 Evaluate side-chains 208 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 539 LEU Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 840 ILE Chi-restraints excluded: chain C residue 893 HIS Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 103 LEU 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 52 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** F 93 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.094640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.071061 restraints weight = 43244.543| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.88 r_work: 0.3305 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 14578 Z= 0.199 Angle : 0.826 59.198 20550 Z= 0.490 Chirality : 0.036 0.256 2335 Planarity : 0.004 0.048 1878 Dihedral : 27.501 135.613 3584 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.63 % Allowed : 16.92 % Favored : 81.45 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.25), residues: 1182 helix: 2.08 (0.19), residues: 759 sheet: -0.63 (0.65), residues: 60 loop : -0.61 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 507 HIS 0.007 0.001 HIS H 106 PHE 0.011 0.001 PHE C 679 TYR 0.015 0.001 TYR F 88 ARG 0.005 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 809) hydrogen bonds : angle 3.10074 ( 2135) covalent geometry : bond 0.00412 (14577) covalent geometry : angle 0.82603 (20550) Misc. bond : bond 0.00039 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7814.69 seconds wall clock time: 135 minutes 31.22 seconds (8131.22 seconds total)