Starting phenix.real_space_refine on Thu Jun 12 07:12:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jao_61296/06_2025/9jao_61296.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jao_61296/06_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_61296/06_2025/9jao_61296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jao_61296/06_2025/9jao_61296.map" model { file = "/net/cci-nas-00/data/ceres_data/9jao_61296/06_2025/9jao_61296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jao_61296/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.22, per 1000 atoms: 0.59 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: 3.41 Conformation dependent library (CDL) restraints added in 1.2 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: 5.52 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: 7.98 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 39.030 Find NCS groups from input model: 0.260 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.440 ------------------------------------------------------------------------------- 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 : 1.287 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: 0.2941 time to fit residues: 109.7489 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 : 1.249 ------------------------------------------------------------------------------- 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 = 0.095499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.071958 restraints weight = 43141.327| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.80 r_work: 0.3316 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1794 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 6.659 20550 Z= 0.336 Chirality : 0.037 0.137 2335 Planarity : 0.004 0.078 1878 Dihedral : 27.813 135.896 3586 Min Nonbonded Distance : 1.900 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 3.43486 ( 2135) covalent geometry : bond 0.00325 (14577) covalent geometry : angle 0.59590 (20550) Misc. bond : bond 0.00098 ( 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 : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 893 HIS cc_start: 0.8882 (OUTLIER) cc_final: 0.8499 (m-70) REVERT: C 987 MET cc_start: 0.8382 (mtp) cc_final: 0.8104 (mtp) REVERT: D 59 GLU cc_start: 0.8300 (pm20) cc_final: 0.7678 (pm20) REVERT: D 86 SER cc_start: 0.8727 (p) cc_final: 0.8483 (t) REVERT: B 64 ASN cc_start: 0.9042 (t0) cc_final: 0.8833 (t0) REVERT: B 79 LYS cc_start: 0.8740 (mtpp) cc_final: 0.8119 (mtpp) REVERT: B 93 GLN cc_start: 0.8415 (tt0) cc_final: 0.8116 (tt0) REVERT: B 98 TYR cc_start: 0.9029 (m-10) cc_final: 0.8723 (m-80) REVERT: F 20 LYS cc_start: 0.8415 (mmtp) cc_final: 0.8025 (mmtp) REVERT: G 75 LYS cc_start: 0.8317 (mmmt) cc_final: 0.8053 (mmmm) REVERT: H 65 ASP cc_start: 0.8497 (t70) cc_final: 0.8186 (t0) REVERT: H 102 GLU cc_start: 0.7673 (tp30) cc_final: 0.6114 (tp30) outliers start: 17 outliers final: 8 residues processed: 220 average time/residue: 0.2961 time to fit residues: 92.1146 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 : 1.255 ------------------------------------------------------------------------------- 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: 0.6980 chunk 8 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS D 125 GLN E 93 GLN F 75 HIS H 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.092474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.068578 restraints weight = 42235.616| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.80 r_work: 0.3236 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 14578 Z= 0.250 Angle : 0.624 9.073 20550 Z= 0.349 Chirality : 0.039 0.160 2335 Planarity : 0.004 0.053 1878 Dihedral : 27.954 133.044 3584 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.91 % Allowed : 11.66 % Favored : 86.42 % 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: 0.94 (0.25), residues: 1182 helix: 1.50 (0.19), residues: 767 sheet: -1.13 (0.61), residues: 60 loop : -0.95 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 507 HIS 0.007 0.001 HIS F 18 PHE 0.013 0.002 PHE D 67 TYR 0.030 0.002 TYR H 80 ARG 0.006 0.001 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04977 ( 809) hydrogen bonds : angle 3.46609 ( 2135) covalent geometry : bond 0.00556 (14577) covalent geometry : angle 0.62370 (20550) Misc. bond : bond 0.00094 ( 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 220 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 1.286 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: 0.8938 (OUTLIER) cc_final: 0.8640 (m-70) REVERT: D 59 GLU cc_start: 0.8398 (pm20) cc_final: 0.8180 (pm20) REVERT: B 79 LYS cc_start: 0.8809 (mtpp) cc_final: 0.8286 (mtmm) REVERT: F 91 LYS cc_start: 0.9141 (tttt) cc_final: 0.8914 (tttt) REVERT: H 65 ASP cc_start: 0.8730 (t70) cc_final: 0.8401 (t0) REVERT: H 102 GLU cc_start: 0.7735 (tp30) cc_final: 0.6684 (tp30) outliers start: 20 outliers final: 12 residues processed: 210 average time/residue: 0.3168 time to fit residues: 93.5247 Evaluate side-chains 192 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 667 LEU Chi-restraints excluded: chain C residue 678 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 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: 1.9990 chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** C 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN E 68 GLN H 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.094187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.070473 restraints weight = 42720.427| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.84 r_work: 0.3288 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14578 Z= 0.149 Angle : 0.563 7.348 20550 Z= 0.317 Chirality : 0.036 0.134 2335 Planarity : 0.004 0.051 1878 Dihedral : 27.780 135.918 3584 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.72 % Allowed : 13.58 % Favored : 84.70 % 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: 1.36 (0.25), residues: 1182 helix: 1.82 (0.19), residues: 757 sheet: -1.07 (0.61), residues: 60 loop : -0.67 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 507 HIS 0.006 0.001 HIS F 18 PHE 0.012 0.001 PHE D 67 TYR 0.026 0.001 TYR F 88 ARG 0.006 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 809) hydrogen bonds : angle 3.23482 ( 2135) covalent geometry : bond 0.00322 (14577) covalent geometry : angle 0.56342 (20550) Misc. bond : bond 0.00035 ( 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 214 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 675 MET cc_start: 0.7996 (mmm) cc_final: 0.7723 (mmt) REVERT: C 840 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8289 (pt) REVERT: C 875 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8770 (tt) REVERT: E 62 ILE cc_start: 0.8970 (mp) cc_final: 0.7923 (mp) REVERT: E 133 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6825 (mt-10) REVERT: F 91 LYS cc_start: 0.9026 (tttt) cc_final: 0.8807 (tttt) REVERT: G 90 ASP cc_start: 0.7783 (t70) cc_final: 0.7520 (t70) REVERT: H 65 ASP cc_start: 0.8629 (t70) cc_final: 0.8381 (t0) REVERT: H 73 GLU cc_start: 0.8019 (tp30) cc_final: 0.7464 (tp30) outliers start: 18 outliers final: 12 residues processed: 207 average time/residue: 0.3104 time to fit residues: 93.4321 Evaluate side-chains 200 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 875 LEU 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 F residue 44 LYS Chi-restraints excluded: chain F residue 60 VAL 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: 5.9990 chunk 130 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 94 optimal weight: 0.9990 chunk 51 optimal weight: 0.0570 chunk 50 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- 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** ** 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 = 0.3988 r_free = 0.3988 target = 0.093596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.069749 restraints weight = 42805.520| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.87 r_work: 0.3267 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14578 Z= 0.176 Angle : 0.579 8.591 20550 Z= 0.325 Chirality : 0.036 0.144 2335 Planarity : 0.004 0.040 1878 Dihedral : 27.703 134.716 3584 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.91 % Allowed : 14.15 % Favored : 83.94 % 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: 1.49 (0.25), residues: 1182 helix: 1.95 (0.19), residues: 756 sheet: -1.03 (0.61), residues: 60 loop : -0.66 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 507 HIS 0.006 0.001 HIS F 18 PHE 0.011 0.001 PHE D 67 TYR 0.024 0.002 TYR C 594 ARG 0.006 0.000 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 809) hydrogen bonds : angle 3.23984 ( 2135) covalent geometry : bond 0.00389 (14577) covalent geometry : angle 0.57880 (20550) Misc. bond : bond 0.00053 ( 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 214 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 840 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8316 (pt) REVERT: C 875 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8776 (tt) REVERT: D 94 GLU cc_start: 0.7933 (tp30) cc_final: 0.7733 (tt0) REVERT: B 25 ASN cc_start: 0.7483 (m-40) cc_final: 0.7057 (m-40) REVERT: E 133 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6865 (mt-10) REVERT: F 12 LYS cc_start: 0.6268 (tttt) cc_final: 0.6044 (tttm) REVERT: F 91 LYS cc_start: 0.9049 (tttt) cc_final: 0.8823 (tttt) REVERT: G 75 LYS cc_start: 0.8852 (mmmm) cc_final: 0.8565 (mmmm) REVERT: H 65 ASP cc_start: 0.8689 (t70) cc_final: 0.8406 (t0) REVERT: H 73 GLU cc_start: 0.8046 (tp30) cc_final: 0.7517 (tp30) REVERT: H 90 GLU cc_start: 0.8237 (mp0) cc_final: 0.7909 (mp0) outliers start: 20 outliers final: 13 residues processed: 206 average time/residue: 0.2865 time to fit residues: 83.4973 Evaluate side-chains 200 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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 875 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 F residue 44 LYS 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: 1.9990 chunk 14 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.091253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.066992 restraints weight = 43078.542| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.88 r_work: 0.3194 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 14578 Z= 0.326 Angle : 0.661 8.766 20550 Z= 0.366 Chirality : 0.041 0.140 2335 Planarity : 0.004 0.039 1878 Dihedral : 27.932 129.689 3584 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.49 % Allowed : 14.53 % Favored : 82.98 % 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: 1.10 (0.25), residues: 1182 helix: 1.67 (0.19), residues: 765 sheet: -1.29 (0.61), residues: 60 loop : -0.94 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 507 HIS 0.012 0.002 HIS H 46 PHE 0.013 0.002 PHE D 67 TYR 0.027 0.002 TYR H 80 ARG 0.006 0.001 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.05503 ( 809) hydrogen bonds : angle 3.51979 ( 2135) covalent geometry : bond 0.00724 (14577) covalent geometry : angle 0.66094 (20550) Misc. bond : bond 0.00074 ( 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 209 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 678 MET cc_start: 0.8245 (tmm) cc_final: 0.7984 (tmm) REVERT: B 25 ASN cc_start: 0.7573 (m-40) cc_final: 0.7128 (m-40) REVERT: B 93 GLN cc_start: 0.8615 (tt0) cc_final: 0.8397 (tt0) REVERT: E 133 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7015 (mt-10) REVERT: G 75 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8635 (mmmt) REVERT: G 92 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8054 (pm20) REVERT: H 65 ASP cc_start: 0.8770 (t70) cc_final: 0.8463 (t0) REVERT: H 73 GLU cc_start: 0.7976 (tp30) cc_final: 0.7397 (tp30) REVERT: H 90 GLU cc_start: 0.8302 (mp0) cc_final: 0.7937 (mp0) outliers start: 26 outliers final: 17 residues processed: 198 average time/residue: 0.2916 time to fit residues: 81.8112 Evaluate side-chains 199 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 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 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 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: 0.7980 chunk 113 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.092819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.068679 restraints weight = 43211.950| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.88 r_work: 0.3235 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14578 Z= 0.186 Angle : 0.607 10.221 20550 Z= 0.335 Chirality : 0.036 0.142 2335 Planarity : 0.004 0.035 1878 Dihedral : 27.839 132.680 3584 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.10 % Allowed : 15.97 % Favored : 81.93 % 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: 1.40 (0.25), residues: 1182 helix: 1.90 (0.19), residues: 759 sheet: -1.15 (0.63), residues: 60 loop : -0.79 (0.34), residues: 363 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 0.012 0.001 PHE D 67 TYR 0.025 0.001 TYR H 80 ARG 0.006 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 809) hydrogen bonds : angle 3.27636 ( 2135) covalent geometry : bond 0.00410 (14577) covalent geometry : angle 0.60711 (20550) Misc. bond : bond 0.00042 ( 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 210 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 678 MET cc_start: 0.8291 (tmm) cc_final: 0.8043 (tmm) REVERT: B 25 ASN cc_start: 0.7492 (m-40) cc_final: 0.7024 (m-40) REVERT: E 133 GLU cc_start: 0.7253 (mt-10) cc_final: 0.7003 (mt-10) REVERT: G 75 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8596 (mmmt) REVERT: G 92 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8106 (pm20) REVERT: G 116 LEU cc_start: 0.9155 (mm) cc_final: 0.8927 (mt) REVERT: H 65 ASP cc_start: 0.8716 (t70) cc_final: 0.8420 (t0) REVERT: H 73 GLU cc_start: 0.7979 (tp30) cc_final: 0.7426 (tp30) REVERT: H 90 GLU cc_start: 0.8269 (mp0) cc_final: 0.7870 (mp0) outliers start: 22 outliers final: 20 residues processed: 198 average time/residue: 0.2962 time to fit residues: 83.2378 Evaluate side-chains 206 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 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 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 E residue 126 LEU 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 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: 0.6980 chunk 22 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.093271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.069340 restraints weight = 42817.130| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.86 r_work: 0.3253 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14578 Z= 0.166 Angle : 0.596 10.502 20550 Z= 0.329 Chirality : 0.036 0.151 2335 Planarity : 0.003 0.035 1878 Dihedral : 27.733 133.850 3584 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.10 % Allowed : 16.83 % Favored : 81.07 % 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: 2.01 (0.19), residues: 758 sheet: -0.97 (0.64), residues: 60 loop : -0.68 (0.34), residues: 364 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 0.014 0.001 TYR C 594 ARG 0.006 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 809) hydrogen bonds : angle 3.20791 ( 2135) covalent geometry : bond 0.00364 (14577) covalent geometry : angle 0.59645 (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 213 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 678 MET cc_start: 0.8317 (tmm) cc_final: 0.8042 (tmm) REVERT: C 776 MET cc_start: 0.7756 (mmm) cc_final: 0.7518 (tpp) REVERT: C 840 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8397 (pt) REVERT: B 25 ASN cc_start: 0.7396 (m-40) cc_final: 0.6886 (m-40) REVERT: E 133 GLU cc_start: 0.7250 (mt-10) cc_final: 0.7008 (mt-10) REVERT: F 91 LYS cc_start: 0.9004 (tttt) cc_final: 0.8765 (tttt) REVERT: G 75 LYS cc_start: 0.8982 (mmmm) cc_final: 0.8769 (mmmm) REVERT: G 91 GLU cc_start: 0.8435 (pm20) cc_final: 0.7819 (pm20) REVERT: G 116 LEU cc_start: 0.9139 (mm) cc_final: 0.8912 (mt) REVERT: H 65 ASP cc_start: 0.8715 (t70) cc_final: 0.8425 (t0) REVERT: H 73 GLU cc_start: 0.7983 (tp30) cc_final: 0.7512 (tp30) REVERT: H 90 GLU cc_start: 0.8211 (mp0) cc_final: 0.7802 (mp0) outliers start: 22 outliers final: 17 residues processed: 201 average time/residue: 0.2968 time to fit residues: 85.1986 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 : 1.443 ------------------------------------------------------------------------------- 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 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 E residue 126 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 62 ILE 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: 7.9990 chunk 99 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** 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 = 0.3976 r_free = 0.3976 target = 0.092945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.069099 restraints weight = 42485.450| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.85 r_work: 0.3251 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3497 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= 0.186 Angle : 0.615 11.705 20550 Z= 0.338 Chirality : 0.036 0.175 2335 Planarity : 0.004 0.033 1878 Dihedral : 27.696 133.017 3584 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.91 % Allowed : 17.30 % Favored : 80.78 % 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: 1.58 (0.25), residues: 1182 helix: 2.03 (0.19), residues: 758 sheet: -0.99 (0.64), residues: 60 loop : -0.69 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 507 HIS 0.006 0.001 HIS H 106 PHE 0.008 0.001 PHE F 61 TYR 0.013 0.001 TYR C 594 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 809) hydrogen bonds : angle 3.21305 ( 2135) covalent geometry : bond 0.00410 (14577) covalent geometry : angle 0.61503 (20550) Misc. bond : bond 0.00027 ( 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 207 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 459 MET cc_start: 0.6761 (mmm) cc_final: 0.6536 (mtt) REVERT: C 678 MET cc_start: 0.8253 (tmm) cc_final: 0.7969 (tmm) REVERT: C 893 HIS cc_start: 0.8905 (OUTLIER) cc_final: 0.8645 (t-90) REVERT: E 73 GLU cc_start: 0.8214 (tp30) cc_final: 0.7993 (tp30) REVERT: E 133 GLU cc_start: 0.7252 (mt-10) cc_final: 0.7004 (mt-10) REVERT: G 75 LYS cc_start: 0.8971 (mmmm) cc_final: 0.8764 (mmmm) REVERT: G 116 LEU cc_start: 0.9184 (mm) cc_final: 0.8952 (mt) REVERT: H 65 ASP cc_start: 0.8713 (t70) cc_final: 0.8428 (t0) REVERT: H 73 GLU cc_start: 0.8063 (tp30) cc_final: 0.7598 (tp30) REVERT: H 90 GLU cc_start: 0.8188 (mp0) cc_final: 0.7778 (mp0) outliers start: 20 outliers final: 15 residues processed: 195 average time/residue: 0.2862 time to fit residues: 78.8863 Evaluate side-chains 201 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 62 ILE 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: 0.5980 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 35 optimal weight: 0.0010 chunk 109 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 overall best weight: 1.1190 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.093126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.069386 restraints weight = 42763.399| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.85 r_work: 0.3263 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14578 Z= 0.172 Angle : 0.609 14.868 20550 Z= 0.333 Chirality : 0.036 0.170 2335 Planarity : 0.003 0.032 1878 Dihedral : 27.644 133.281 3582 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.53 % Allowed : 17.40 % Favored : 81.07 % 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: 1.60 (0.25), residues: 1182 helix: 2.04 (0.19), residues: 759 sheet: -0.93 (0.65), residues: 60 loop : -0.69 (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 H 106 PHE 0.010 0.001 PHE D 67 TYR 0.013 0.001 TYR H 80 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 809) hydrogen bonds : angle 3.17991 ( 2135) covalent geometry : bond 0.00381 (14577) covalent geometry : angle 0.60939 (20550) Misc. bond : bond 0.00016 ( 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 208 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 459 MET cc_start: 0.6920 (mmm) cc_final: 0.6718 (mtt) REVERT: C 678 MET cc_start: 0.8275 (tmm) cc_final: 0.7974 (tmm) REVERT: C 804 MET cc_start: 0.8620 (ptm) cc_final: 0.8242 (tmm) REVERT: C 893 HIS cc_start: 0.8898 (OUTLIER) cc_final: 0.8650 (t-90) REVERT: E 73 GLU cc_start: 0.8247 (tp30) cc_final: 0.8036 (tp30) REVERT: E 133 GLU cc_start: 0.7245 (mt-10) cc_final: 0.7008 (mt-10) REVERT: G 75 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8763 (mmmm) REVERT: G 116 LEU cc_start: 0.9204 (mm) cc_final: 0.8975 (mt) REVERT: H 65 ASP cc_start: 0.8713 (t70) cc_final: 0.8433 (t0) REVERT: H 73 GLU cc_start: 0.8007 (tp30) cc_final: 0.7616 (tp30) REVERT: H 90 GLU cc_start: 0.8160 (mp0) cc_final: 0.7648 (mp0) outliers start: 16 outliers final: 14 residues processed: 198 average time/residue: 0.2837 time to fit residues: 79.7490 Evaluate side-chains 204 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 56 MET 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: 2.9990 chunk 80 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.3980 chunk 122 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 E 68 GLN H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.093100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.069251 restraints weight = 43114.374| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.91 r_work: 0.3257 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14578 Z= 0.181 Angle : 0.619 12.100 20550 Z= 0.339 Chirality : 0.036 0.197 2335 Planarity : 0.003 0.031 1878 Dihedral : 27.624 132.866 3582 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.63 % Allowed : 17.59 % Favored : 80.78 % 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: 1.60 (0.25), residues: 1182 helix: 2.05 (0.19), residues: 759 sheet: -0.89 (0.65), residues: 60 loop : -0.72 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 507 HIS 0.017 0.001 HIS H 106 PHE 0.013 0.001 PHE D 67 TYR 0.015 0.001 TYR F 88 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 809) hydrogen bonds : angle 3.20696 ( 2135) covalent geometry : bond 0.00400 (14577) covalent geometry : angle 0.61863 (20550) Misc. bond : bond 0.00020 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8318.76 seconds wall clock time: 142 minutes 34.88 seconds (8554.88 seconds total)