Starting phenix.real_space_refine on Thu Aug 6 04:20:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rzc_54399/08_2026/9rzc_54399.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rzc_54399/08_2026/9rzc_54399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rzc_54399/08_2026/9rzc_54399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rzc_54399/08_2026/9rzc_54399.map" model { file = "/net/cci-nas-00/data/ceres_data/9rzc_54399/08_2026/9rzc_54399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rzc_54399/08_2026/9rzc_54399.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 256 5.49 5 S 32 5.16 5 C 7495 2.51 5 N 2462 2.21 5 O 2990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13235 Number of models: 1 Model: "" Number of chains: 12 Chain: "N" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 2662 Classifications: {'DNA': 129} Link IDs: {'rna3p': 128} Chain: "O" Number of atoms: 1993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1993 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 7, 'TRANS': 237} Chain: "T" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2586 Classifications: {'DNA': 127} Link IDs: {'rna3p': 126} Chain: "a" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 821 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "b" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "c" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 801 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "d" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "f" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "h" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "k" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Chain: "e" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 782 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Time building chain proxies: 2.45, per 1000 atoms: 0.19 Number of scatterers: 13235 At special positions: 0 Unit cell: (89.25, 127.05, 131.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 256 15.00 O 2990 8.00 N 2462 7.00 C 7495 6.00 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=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 287.2 milliseconds 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 13 sheets defined 59.7% alpha, 6.2% beta 126 base pairs and 220 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'O' and resid 1630 through 1634 removed outlier: 4.332A pdb=" N ARG O1633 " --> pdb=" O ASP O1630 " (cutoff:3.500A) Processing helix chain 'O' and resid 1657 through 1662 Processing helix chain 'O' and resid 1672 through 1676 removed outlier: 4.013A pdb=" N CYS O1676 " --> pdb=" O GLY O1673 " (cutoff:3.500A) Processing helix chain 'O' and resid 1722 through 1734 removed outlier: 4.159A pdb=" N LYS O1727 " --> pdb=" O HIS O1723 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA O1728 " --> pdb=" O LYS O1724 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS O1731 " --> pdb=" O LYS O1727 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA O1734 " --> pdb=" O VAL O1730 " (cutoff:3.500A) Processing helix chain 'O' and resid 1735 through 1737 No H-bonds generated for 'chain 'O' and resid 1735 through 1737' Processing helix chain 'O' and resid 1759 through 1764 removed outlier: 3.859A pdb=" N PHE O1763 " --> pdb=" O CYS O1760 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 77 removed outlier: 3.975A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 113 Processing helix chain 'a' and resid 114 through 116 No H-bonds generated for 'chain 'a' and resid 114 through 116' Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 24 through 29 removed outlier: 4.050A pdb=" N GLN b 27 " --> pdb=" O ASP b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.565A 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 'c' and resid 16 through 22 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.152A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.554A pdb=" N ASN c 89 " --> pdb=" O LEU c 85 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 85 Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 103 through 123 removed outlier: 4.034A pdb=" N LYS d 108 " --> pdb=" O GLY d 104 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.555A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.275A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 removed outlier: 3.533A pdb=" N LEU g 83 " --> pdb=" O ILE g 79 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP g 90 " --> pdb=" O ALA g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'g' and resid 112 through 116 Processing helix chain 'h' and resid 37 through 49 removed outlier: 3.903A pdb=" N GLN h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL h 48 " --> pdb=" O VAL h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 55 through 84 Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 103 through 122 Processing helix chain 'k' and resid 939 through 944 Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 76 Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 Processing sheet with id=AA1, first strand: chain 'O' and resid 1617 through 1618 removed outlier: 7.522A pdb=" N VAL O1617 " --> pdb=" O VAL O1720 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'O' and resid 1664 through 1665 removed outlier: 7.206A pdb=" N VAL O1785 " --> pdb=" O GLU O1715 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU O1715 " --> pdb=" O VAL O1785 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE O1787 " --> pdb=" O VAL O1713 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 1689 through 1695 removed outlier: 4.259A pdb=" N THR O1694 " --> pdb=" O GLY O1698 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLY O1698 " --> pdb=" O THR O1694 " (cutoff:3.500A) removed outlier: 13.439A pdb=" N TRP O1699 " --> pdb=" O PHE O1801 " (cutoff:3.500A) removed outlier: 10.494A pdb=" N PHE O1801 " --> pdb=" O TRP O1699 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU O1701 " --> pdb=" O LEU O1799 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASN O1765 " --> pdb=" O PHE O1801 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 83 through 84 removed outlier: 7.391A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'b' and resid 96 through 98 removed outlier: 6.540A pdb=" N THR b 96 " --> pdb=" O THR g 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.127A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'c' and resid 101 through 102 removed outlier: 6.553A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'f' and resid 45 through 46 removed outlier: 7.199A pdb=" N ARG f 45 " --> pdb=" O ILE e 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'f' and resid 80 through 81 Processing sheet with id=AB3, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.753A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'g' and resid 77 through 78 440 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 326 hydrogen bonds 652 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 220 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2803 1.33 - 1.45: 4098 1.45 - 1.57: 6532 1.57 - 1.69: 511 1.69 - 1.82: 48 Bond restraints: 13992 Sorted by residual: bond pdb=" C3' DA T 71 " pdb=" C2' DA T 71 " ideal model delta sigma weight residual 1.516 1.559 -0.043 8.00e-03 1.56e+04 2.91e+01 bond pdb=" C3' DC N 74 " pdb=" C2' DC N 74 " ideal model delta sigma weight residual 1.516 1.557 -0.041 8.00e-03 1.56e+04 2.69e+01 bond pdb=" C3' DT N 27 " pdb=" C2' DT N 27 " ideal model delta sigma weight residual 1.516 1.557 -0.041 8.00e-03 1.56e+04 2.58e+01 bond pdb=" C1' DT N 41 " pdb=" N1 DT N 41 " ideal model delta sigma weight residual 1.468 1.534 -0.066 1.40e-02 5.10e+03 2.20e+01 bond pdb=" C1' DT T 109 " pdb=" N1 DT T 109 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.17e+01 ... (remaining 13987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 17764 2.01 - 4.01: 1825 4.01 - 6.02: 323 6.02 - 8.03: 53 8.03 - 10.03: 7 Bond angle restraints: 19972 Sorted by residual: angle pdb=" O4' DC N 103 " pdb=" C1' DC N 103 " pdb=" N1 DC N 103 " ideal model delta sigma weight residual 108.00 115.46 -7.46 7.00e-01 2.04e+00 1.13e+02 angle pdb=" O5' DT N 104 " pdb=" C5' DT N 104 " pdb=" C4' DT N 104 " ideal model delta sigma weight residual 109.40 117.66 -8.26 8.00e-01 1.56e+00 1.07e+02 angle pdb=" O4' DA N 90 " pdb=" C1' DA N 90 " pdb=" N9 DA N 90 " ideal model delta sigma weight residual 108.00 101.52 6.48 7.00e-01 2.04e+00 8.57e+01 angle pdb=" O4' DG T 150 " pdb=" C1' DG T 150 " pdb=" N9 DG T 150 " ideal model delta sigma weight residual 108.00 113.91 -5.91 7.00e-01 2.04e+00 7.12e+01 angle pdb=" O4' DA N 120 " pdb=" C1' DA N 120 " pdb=" N9 DA N 120 " ideal model delta sigma weight residual 108.00 102.38 5.62 7.00e-01 2.04e+00 6.45e+01 ... (remaining 19967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.18: 6639 34.18 - 68.36: 1099 68.36 - 102.54: 27 102.54 - 136.72: 0 136.72 - 170.89: 2 Dihedral angle restraints: 7767 sinusoidal: 4866 harmonic: 2901 Sorted by residual: dihedral pdb=" C4' DG N 93 " pdb=" C3' DG N 93 " pdb=" O3' DG N 93 " pdb=" P DG N 94 " ideal model delta sinusoidal sigma weight residual 220.00 49.11 170.89 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG N 81 " pdb=" C3' DG N 81 " pdb=" O3' DG N 81 " pdb=" P DT N 82 " ideal model delta sinusoidal sigma weight residual 220.00 56.61 163.39 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" CG ARG O1784 " pdb=" CD ARG O1784 " pdb=" NE ARG O1784 " pdb=" CZ ARG O1784 " ideal model delta sinusoidal sigma weight residual -180.00 -135.03 -44.97 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 7764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1493 0.067 - 0.134: 549 0.134 - 0.200: 168 0.200 - 0.267: 25 0.267 - 0.334: 2 Chirality restraints: 2237 Sorted by residual: chirality pdb=" C3' DG N 81 " pdb=" C4' DG N 81 " pdb=" O3' DG N 81 " pdb=" C2' DG N 81 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" C3' DG N 93 " pdb=" C4' DG N 93 " pdb=" O3' DG N 93 " pdb=" C2' DG N 93 " both_signs ideal model delta sigma weight residual False -2.73 -2.42 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA ILE e 74 " pdb=" N ILE e 74 " pdb=" C ILE e 74 " pdb=" CB ILE e 74 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2234 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC N 47 " 0.063 2.00e-02 2.50e+03 4.43e-02 4.41e+01 pdb=" N1 DC N 47 " -0.107 2.00e-02 2.50e+03 pdb=" C2 DC N 47 " 0.041 2.00e-02 2.50e+03 pdb=" O2 DC N 47 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DC N 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC N 47 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC N 47 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DC N 47 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DC N 47 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC N 92 " -0.047 2.00e-02 2.50e+03 3.73e-02 3.13e+01 pdb=" N1 DC N 92 " 0.092 2.00e-02 2.50e+03 pdb=" C2 DC N 92 " -0.039 2.00e-02 2.50e+03 pdb=" O2 DC N 92 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DC N 92 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC N 92 " -0.006 2.00e-02 2.50e+03 pdb=" N4 DC N 92 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DC N 92 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DC N 92 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT N 27 " -0.058 2.00e-02 2.50e+03 3.49e-02 3.04e+01 pdb=" N1 DT N 27 " 0.088 2.00e-02 2.50e+03 pdb=" C2 DT N 27 " -0.025 2.00e-02 2.50e+03 pdb=" O2 DT N 27 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DT N 27 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT N 27 " -0.008 2.00e-02 2.50e+03 pdb=" O4 DT N 27 " -0.012 2.00e-02 2.50e+03 pdb=" C5 DT N 27 " 0.006 2.00e-02 2.50e+03 pdb=" C7 DT N 27 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DT N 27 " 0.004 2.00e-02 2.50e+03 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4366 2.90 - 3.40: 12556 3.40 - 3.90: 25366 3.90 - 4.40: 29405 4.40 - 4.90: 40975 Nonbonded interactions: 112668 Sorted by model distance: nonbonded pdb=" NH1 ARG a 116 " pdb=" O THR a 118 " model vdw 2.396 3.120 nonbonded pdb=" CZ ARG f 92 " pdb=" OE1 GLU h 76 " model vdw 2.526 3.270 nonbonded pdb=" NH1 ARG f 92 " pdb=" OE1 GLU h 76 " model vdw 2.532 3.120 nonbonded pdb=" N ASP e 77 " pdb=" OD1 ASP e 77 " model vdw 2.555 3.120 nonbonded pdb=" O ARG e 72 " pdb=" CG GLN e 76 " model vdw 2.565 3.440 ... (remaining 112663 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and resid 39 through 133) selection = chain 'e' } ncs_group { reference = chain 'b' selection = chain 'f' } ncs_group { reference = (chain 'c' and resid 15 through 117) selection = chain 'g' } ncs_group { reference = (chain 'd' and resid 35 through 123) selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.900 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.008 0.098 13992 Z= 0.674 Angle : 1.303 10.034 19972 Z= 0.966 Chirality : 0.075 0.334 2237 Planarity : 0.015 0.132 1664 Dihedral : 24.859 170.895 5899 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.12 % Allowed : 0.24 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.23), residues: 983 helix: -0.52 (0.19), residues: 562 sheet: -1.21 (0.66), residues: 43 loop : -1.52 (0.26), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.053 0.004 ARG f 92 TYR 0.027 0.007 TYR a 41 PHE 0.054 0.004 PHE c 25 TRP 0.019 0.005 TRP O1597 HIS 0.029 0.004 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00825 / 0.67 (13992) covalent geometry : angle 1.30346 / 0.97 (19972) hydrogen bonds : bond 0.11601 / 13.47 ( 766) hydrogen bonds : angle 4.65857 / 6.31 ( 1933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 350 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1623 LYS cc_start: 0.5221 (pttm) cc_final: 0.4759 (tptm) REVERT: O 1634 MET cc_start: 0.6304 (ptm) cc_final: 0.5906 (ptp) REVERT: O 1742 TYR cc_start: 0.4780 (m-80) cc_final: 0.4467 (m-10) REVERT: b 53 GLU cc_start: 0.7442 (tp30) cc_final: 0.6949 (tp30) REVERT: b 59 LYS cc_start: 0.8436 (ttpp) cc_final: 0.7646 (tttp) REVERT: b 64 ASN cc_start: 0.8074 (m-40) cc_final: 0.7728 (m110) REVERT: b 68 ASP cc_start: 0.7957 (m-30) cc_final: 0.7738 (m-30) REVERT: b 85 ASP cc_start: 0.8128 (m-30) cc_final: 0.7926 (m-30) REVERT: c 56 GLU cc_start: 0.8302 (tt0) cc_final: 0.8020 (tt0) REVERT: c 95 LYS cc_start: 0.8647 (tttt) cc_final: 0.8303 (tptp) REVERT: c 104 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7377 (mm-40) REVERT: d 79 ARG cc_start: 0.8186 (ttm110) cc_final: 0.7940 (mtm180) REVERT: d 100 LEU cc_start: 0.9147 (mt) cc_final: 0.8743 (mt) REVERT: f 96 THR cc_start: 0.8933 (m) cc_final: 0.8591 (t) REVERT: g 39 TYR cc_start: 0.8434 (m-80) cc_final: 0.7812 (m-80) REVERT: g 64 GLU cc_start: 0.8082 (tp30) cc_final: 0.7862 (tm-30) REVERT: g 73 ASN cc_start: 0.8404 (m-40) cc_final: 0.8115 (m110) REVERT: g 76 THR cc_start: 0.8434 (p) cc_final: 0.8135 (t) REVERT: g 101 THR cc_start: 0.9064 (m) cc_final: 0.8572 (p) REVERT: g 111 ILE cc_start: 0.8183 (mt) cc_final: 0.7777 (tt) REVERT: g 114 VAL cc_start: 0.9122 (m) cc_final: 0.8847 (p) REVERT: h 59 MET cc_start: 0.8452 (tpp) cc_final: 0.8214 (tpp) REVERT: e 56 LYS cc_start: 0.8442 (ttpp) cc_final: 0.8044 (tttp) outliers start: 1 outliers final: 0 residues processed: 351 average time/residue: 0.1307 time to fit residues: 61.3016 Evaluate side-chains 194 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.0170 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1740 HIS ** O1780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 113 HIS ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 47 GLN ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 HIS e 68 GLN e 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.075400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.054099 restraints weight = 49204.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.055524 restraints weight = 24092.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.056396 restraints weight = 15992.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.056867 restraints weight = 12908.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.057031 restraints weight = 11620.324| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13992 Z= 0.184 Angle : 0.846 9.510 19972 Z= 0.473 Chirality : 0.056 0.257 2237 Planarity : 0.006 0.053 1664 Dihedral : 29.568 172.687 3901 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.36 % Allowed : 10.26 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 983 helix: 1.27 (0.21), residues: 569 sheet: -0.15 (0.79), residues: 28 loop : -1.35 (0.27), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG g 35 TYR 0.029 0.003 TYR O1716 PHE 0.029 0.003 PHE c 25 TRP 0.033 0.006 TRP O1699 HIS 0.011 0.002 HIS a 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.18 (13992) covalent geometry : angle 0.84569 / 0.47 (19972) hydrogen bonds : bond 0.05504 / 6.26 ( 766) hydrogen bonds : angle 3.71336 / 5.00 ( 1933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1623 LYS cc_start: 0.5097 (pttm) cc_final: 0.4668 (tptm) REVERT: O 1691 VAL cc_start: 0.7702 (p) cc_final: 0.7464 (t) REVERT: O 1739 ILE cc_start: 0.5536 (pt) cc_final: 0.4748 (mt) REVERT: O 1764 MET cc_start: 0.7411 (tpp) cc_final: 0.7188 (tpp) REVERT: a 123 ASP cc_start: 0.8738 (m-30) cc_final: 0.8172 (m-30) REVERT: b 53 GLU cc_start: 0.7954 (tp30) cc_final: 0.7733 (tp30) REVERT: b 59 LYS cc_start: 0.8369 (ttpp) cc_final: 0.8158 (tttp) REVERT: b 63 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7484 (mt-10) REVERT: b 77 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8654 (mmtp) REVERT: c 41 GLU cc_start: 0.7649 (tp30) cc_final: 0.7420 (tp30) REVERT: d 113 GLU cc_start: 0.7937 (tp30) cc_final: 0.7730 (tp30) REVERT: d 116 LYS cc_start: 0.8955 (ttpt) cc_final: 0.8722 (ptpt) REVERT: f 96 THR cc_start: 0.8875 (m) cc_final: 0.8583 (t) REVERT: g 73 ASN cc_start: 0.8731 (m-40) cc_final: 0.8330 (m110) REVERT: g 76 THR cc_start: 0.8552 (p) cc_final: 0.8278 (t) REVERT: g 101 THR cc_start: 0.8987 (m) cc_final: 0.8454 (p) REVERT: g 111 ILE cc_start: 0.8105 (mt) cc_final: 0.7786 (tt) REVERT: g 114 VAL cc_start: 0.9131 (m) cc_final: 0.8871 (p) REVERT: h 71 GLU cc_start: 0.8107 (tp30) cc_final: 0.7564 (tp30) REVERT: e 56 LYS cc_start: 0.8504 (ttpp) cc_final: 0.8154 (tttm) outliers start: 20 outliers final: 11 residues processed: 224 average time/residue: 0.1029 time to fit residues: 33.3344 Evaluate side-chains 194 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1702 ARG Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain f residue 45 ARG Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain h residue 68 ASP Chi-restraints excluded: chain k residue 936 GLU Chi-restraints excluded: chain e residue 124 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 71 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1682 GLN O1780 ASN O1782 GLN ** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 GLN d 84 ASN e 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.074462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.052985 restraints weight = 49289.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.054388 restraints weight = 24438.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.055255 restraints weight = 16284.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.055729 restraints weight = 13130.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055947 restraints weight = 11798.816| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13992 Z= 0.174 Angle : 0.734 8.340 19972 Z= 0.417 Chirality : 0.048 0.296 2237 Planarity : 0.005 0.045 1664 Dihedral : 29.885 169.259 3901 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.59 % Allowed : 10.85 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 983 helix: 1.69 (0.21), residues: 568 sheet: -1.66 (0.66), residues: 43 loop : -1.14 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O1683 TYR 0.020 0.002 TYR g 39 PHE 0.013 0.002 PHE c 25 TRP 0.050 0.005 TRP O1699 HIS 0.006 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (13992) covalent geometry : angle 0.73362 / 0.42 (19972) hydrogen bonds : bond 0.04841 / 5.50 ( 766) hydrogen bonds : angle 3.50674 / 4.75 ( 1933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 1623 LYS cc_start: 0.5208 (pttm) cc_final: 0.4825 (tptm) REVERT: b 59 LYS cc_start: 0.8323 (ttpp) cc_final: 0.7891 (tttm) REVERT: b 63 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7586 (mt-10) REVERT: b 68 ASP cc_start: 0.8176 (m-30) cc_final: 0.7914 (m-30) REVERT: b 84 MET cc_start: 0.7938 (mmm) cc_final: 0.7567 (tpp) REVERT: b 88 TYR cc_start: 0.8135 (m-10) cc_final: 0.7282 (m-10) REVERT: c 41 GLU cc_start: 0.7705 (tp30) cc_final: 0.7440 (tp30) REVERT: d 100 LEU cc_start: 0.9261 (mt) cc_final: 0.8955 (mt) REVERT: d 101 LEU cc_start: 0.9000 (tp) cc_final: 0.8563 (tt) REVERT: d 116 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8658 (ptpt) REVERT: f 96 THR cc_start: 0.8908 (m) cc_final: 0.8600 (t) REVERT: g 73 ASN cc_start: 0.8746 (m-40) cc_final: 0.8308 (m110) REVERT: g 76 THR cc_start: 0.8559 (p) cc_final: 0.8260 (t) REVERT: g 101 THR cc_start: 0.9009 (m) cc_final: 0.8490 (p) REVERT: g 111 ILE cc_start: 0.8293 (mt) cc_final: 0.8005 (tt) REVERT: g 114 VAL cc_start: 0.9122 (m) cc_final: 0.8851 (p) REVERT: h 46 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8352 (mmmt) REVERT: h 71 GLU cc_start: 0.8263 (tp30) cc_final: 0.7687 (tp30) REVERT: h 93 GLU cc_start: 0.8230 (mm-30) cc_final: 0.8001 (mm-30) REVERT: e 56 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8149 (tttm) REVERT: e 120 MET cc_start: 0.8313 (mtm) cc_final: 0.7950 (mtm) outliers start: 22 outliers final: 16 residues processed: 208 average time/residue: 0.1017 time to fit residues: 31.1145 Evaluate side-chains 192 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1740 HIS Chi-restraints excluded: chain O residue 1774 THR Chi-restraints excluded: chain O residue 1789 THR Chi-restraints excluded: chain O residue 1825 TYR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain f residue 45 ARG Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 64 SER Chi-restraints excluded: chain k residue 936 GLU Chi-restraints excluded: chain e residue 124 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 36 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1686 HIS ** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 93 GLN h 63 ASN k 949 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.074618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.053251 restraints weight = 49133.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.054664 restraints weight = 24150.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055522 restraints weight = 16072.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.055993 restraints weight = 12964.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.056180 restraints weight = 11665.337| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13992 Z= 0.156 Angle : 0.687 10.326 19972 Z= 0.393 Chirality : 0.047 0.284 2237 Planarity : 0.004 0.045 1664 Dihedral : 29.921 168.953 3901 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.30 % Allowed : 12.74 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.26), residues: 983 helix: 1.88 (0.21), residues: 571 sheet: -1.42 (0.70), residues: 43 loop : -1.08 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O1702 TYR 0.033 0.002 TYR d 83 PHE 0.011 0.001 PHE k 948 TRP 0.049 0.004 TRP O1699 HIS 0.005 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.16 (13992) covalent geometry : angle 0.68703 / 0.39 (19972) hydrogen bonds : bond 0.04359 / 4.98 ( 766) hydrogen bonds : angle 3.33686 / 4.50 ( 1933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 1623 LYS cc_start: 0.5026 (pttm) cc_final: 0.4682 (tptm) REVERT: O 1764 MET cc_start: 0.7019 (tpp) cc_final: 0.6634 (tpp) REVERT: O 1775 GLN cc_start: 0.7775 (mt0) cc_final: 0.7329 (mt0) REVERT: O 1808 TYR cc_start: 0.6448 (t80) cc_final: 0.6130 (t80) REVERT: b 59 LYS cc_start: 0.8326 (ttpp) cc_final: 0.7848 (tttp) REVERT: b 68 ASP cc_start: 0.8112 (m-30) cc_final: 0.7879 (m-30) REVERT: c 41 GLU cc_start: 0.7723 (tp30) cc_final: 0.7436 (tp30) REVERT: d 83 TYR cc_start: 0.7709 (m-10) cc_final: 0.7412 (m-80) REVERT: d 100 LEU cc_start: 0.9365 (mt) cc_final: 0.9007 (mt) REVERT: d 101 LEU cc_start: 0.8964 (tp) cc_final: 0.8572 (tt) REVERT: d 113 GLU cc_start: 0.8055 (tp30) cc_final: 0.7766 (tp30) REVERT: g 73 ASN cc_start: 0.8765 (m-40) cc_final: 0.8322 (m110) REVERT: g 76 THR cc_start: 0.8560 (p) cc_final: 0.8276 (t) REVERT: g 101 THR cc_start: 0.8971 (m) cc_final: 0.8447 (p) REVERT: g 111 ILE cc_start: 0.8334 (mt) cc_final: 0.8050 (tt) REVERT: g 114 VAL cc_start: 0.9119 (m) cc_final: 0.8848 (p) REVERT: h 46 LYS cc_start: 0.8781 (mmmt) cc_final: 0.8559 (mmmt) REVERT: h 71 GLU cc_start: 0.8323 (tp30) cc_final: 0.7729 (tp30) REVERT: e 56 LYS cc_start: 0.8513 (ttpp) cc_final: 0.8199 (tttm) REVERT: e 73 GLU cc_start: 0.8007 (pt0) cc_final: 0.7707 (pt0) REVERT: e 120 MET cc_start: 0.8265 (mtm) cc_final: 0.8010 (mtm) outliers start: 28 outliers final: 18 residues processed: 205 average time/residue: 0.0977 time to fit residues: 29.2387 Evaluate side-chains 195 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1740 HIS Chi-restraints excluded: chain O residue 1772 CYS Chi-restraints excluded: chain O residue 1774 THR Chi-restraints excluded: chain O residue 1825 TYR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain c residue 104 GLN Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain f residue 45 ARG Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain h residue 64 SER Chi-restraints excluded: chain k residue 936 GLU Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain e residue 124 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 HIS a 76 GLN b 64 ASN d 82 HIS h 47 GLN h 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.074300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.052858 restraints weight = 49339.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.054249 restraints weight = 24441.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.055107 restraints weight = 16343.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.055560 restraints weight = 13211.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.055726 restraints weight = 11920.692| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13992 Z= 0.166 Angle : 0.681 8.334 19972 Z= 0.388 Chirality : 0.046 0.288 2237 Planarity : 0.005 0.057 1664 Dihedral : 29.937 168.134 3901 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.83 % Allowed : 13.92 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.27), residues: 983 helix: 2.04 (0.21), residues: 571 sheet: -1.37 (0.71), residues: 43 loop : -1.05 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG g 29 TYR 0.040 0.002 TYR d 83 PHE 0.012 0.002 PHE c 25 TRP 0.037 0.004 TRP O1699 HIS 0.005 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.17 (13992) covalent geometry : angle 0.68124 / 0.39 (19972) hydrogen bonds : bond 0.04278 / 4.90 ( 766) hydrogen bonds : angle 3.36064 / 4.59 ( 1933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 1623 LYS cc_start: 0.5096 (pttm) cc_final: 0.4808 (tptm) REVERT: O 1702 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7225 (ttm-80) REVERT: O 1764 MET cc_start: 0.6945 (tpp) cc_final: 0.6571 (tpp) REVERT: O 1808 TYR cc_start: 0.6480 (t80) cc_final: 0.6184 (t80) REVERT: a 82 LEU cc_start: 0.8598 (tp) cc_final: 0.8393 (tp) REVERT: b 68 ASP cc_start: 0.8180 (m-30) cc_final: 0.7970 (m-30) REVERT: c 41 GLU cc_start: 0.7752 (tp30) cc_final: 0.7446 (tp30) REVERT: d 83 TYR cc_start: 0.7850 (m-10) cc_final: 0.7349 (m-80) REVERT: d 100 LEU cc_start: 0.9375 (mt) cc_final: 0.9013 (mt) REVERT: d 101 LEU cc_start: 0.8963 (tp) cc_final: 0.8590 (tt) REVERT: d 116 LYS cc_start: 0.8982 (ptpt) cc_final: 0.8728 (ptpt) REVERT: g 73 ASN cc_start: 0.8784 (m-40) cc_final: 0.8320 (m110) REVERT: g 76 THR cc_start: 0.8584 (p) cc_final: 0.8275 (t) REVERT: g 101 THR cc_start: 0.8965 (m) cc_final: 0.8454 (p) REVERT: g 111 ILE cc_start: 0.8444 (mt) cc_final: 0.8110 (tt) REVERT: g 114 VAL cc_start: 0.9121 (m) cc_final: 0.8827 (p) REVERT: h 71 GLU cc_start: 0.8334 (tp30) cc_final: 0.7696 (tp30) REVERT: e 56 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8205 (tttm) outliers start: 24 outliers final: 19 residues processed: 194 average time/residue: 0.0942 time to fit residues: 27.1441 Evaluate side-chains 191 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1702 ARG Chi-restraints excluded: chain O residue 1740 HIS Chi-restraints excluded: chain O residue 1774 THR Chi-restraints excluded: chain O residue 1789 THR Chi-restraints excluded: chain O residue 1825 TYR Chi-restraints excluded: chain a residue 39 HIS Chi-restraints excluded: chain a residue 41 TYR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain c residue 104 GLN Chi-restraints excluded: chain d residue 90 THR Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain f residue 45 ARG Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain h residue 64 SER Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain k residue 936 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 33 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 37 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O1813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 HIS d 82 HIS g 31 HIS ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.073996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.052836 restraints weight = 49240.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.054186 restraints weight = 24729.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.055000 restraints weight = 16706.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055441 restraints weight = 13600.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.055630 restraints weight = 12299.819| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13992 Z= 0.167 Angle : 0.676 9.523 19972 Z= 0.383 Chirality : 0.045 0.287 2237 Planarity : 0.005 0.047 1664 Dihedral : 29.927 167.885 3901 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.07 % Allowed : 14.86 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.27), residues: 983 helix: 2.12 (0.22), residues: 571 sheet: -1.02 (0.72), residues: 38 loop : -1.08 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O1702 TYR 0.031 0.002 TYR d 83 PHE 0.012 0.001 PHE e 67 TRP 0.038 0.004 TRP O1699 HIS 0.018 0.002 HIS a 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (13992) covalent geometry : angle 0.67608 / 0.38 (19972) hydrogen bonds : bond 0.04195 / 4.81 ( 766) hydrogen bonds : angle 3.37330 / 4.65 ( 1933) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 1623 LYS cc_start: 0.5110 (pttm) cc_final: 0.4853 (tptm) REVERT: O 1764 MET cc_start: 0.6995 (tpp) cc_final: 0.6654 (tpp) REVERT: O 1808 TYR cc_start: 0.6502 (t80) cc_final: 0.6208 (t80) REVERT: b 68 ASP cc_start: 0.8176 (m-30) cc_final: 0.7947 (m-30) REVERT: b 84 MET cc_start: 0.7843 (tpp) cc_final: 0.7484 (tpp) REVERT: c 41 GLU cc_start: 0.7676 (tp30) cc_final: 0.7358 (tp30) REVERT: d 83 TYR cc_start: 0.7837 (m-10) cc_final: 0.7459 (m-80) REVERT: d 100 LEU cc_start: 0.9393 (mt) cc_final: 0.9067 (mt) REVERT: d 101 LEU cc_start: 0.8956 (tp) cc_final: 0.8594 (tt) REVERT: g 73 ASN cc_start: 0.8737 (m-40) cc_final: 0.8284 (m110) REVERT: g 76 THR cc_start: 0.8536 (p) cc_final: 0.8235 (t) REVERT: g 101 THR cc_start: 0.8969 (m) cc_final: 0.8456 (p) REVERT: g 111 ILE cc_start: 0.8456 (mt) cc_final: 0.8150 (tt) REVERT: g 114 VAL cc_start: 0.9115 (m) cc_final: 0.8808 (p) REVERT: h 71 GLU cc_start: 0.8265 (tp30) cc_final: 0.7681 (tp30) REVERT: e 56 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8212 (tttm) outliers start: 26 outliers final: 24 residues processed: 195 average time/residue: 0.0937 time to fit residues: 27.3261 Evaluate side-chains 193 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1740 HIS Chi-restraints excluded: chain O residue 1772 CYS Chi-restraints excluded: chain O residue 1774 THR Chi-restraints excluded: chain O residue 1789 THR Chi-restraints excluded: chain O residue 1825 TYR Chi-restraints excluded: chain a residue 41 TYR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain d residue 90 THR Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain f residue 45 ARG Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 64 SER Chi-restraints excluded: chain h residue 68 ASP Chi-restraints excluded: chain h residue 113 GLU Chi-restraints excluded: chain k residue 936 GLU Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 112 ILE Chi-restraints excluded: chain e residue 124 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 32 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 0.0000 chunk 62 optimal weight: 0.7980 chunk 117 optimal weight: 0.0670 chunk 78 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.5726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1686 HIS O1813 GLN d 82 HIS h 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.074823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.053663 restraints weight = 49112.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.055079 restraints weight = 23969.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055910 restraints weight = 15952.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.056326 restraints weight = 12896.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.056604 restraints weight = 11679.410| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13992 Z= 0.137 Angle : 0.647 8.036 19972 Z= 0.373 Chirality : 0.044 0.284 2237 Planarity : 0.004 0.049 1664 Dihedral : 29.765 167.600 3901 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.36 % Allowed : 16.27 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.27), residues: 983 helix: 2.23 (0.22), residues: 573 sheet: -0.96 (0.70), residues: 38 loop : -0.97 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O1702 TYR 0.026 0.002 TYR d 83 PHE 0.011 0.001 PHE e 67 TRP 0.042 0.003 TRP O1699 HIS 0.006 0.001 HIS a 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (13992) covalent geometry : angle 0.64711 / 0.37 (19972) hydrogen bonds : bond 0.03869 / 4.44 ( 766) hydrogen bonds : angle 3.23763 / 4.44 ( 1933) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: O 1623 LYS cc_start: 0.5356 (pttm) cc_final: 0.5058 (tptm) REVERT: O 1764 MET cc_start: 0.7007 (tpp) cc_final: 0.6657 (tpp) REVERT: O 1775 GLN cc_start: 0.7866 (mt0) cc_final: 0.7445 (mt0) REVERT: O 1808 TYR cc_start: 0.6470 (t80) cc_final: 0.6179 (t80) REVERT: b 68 ASP cc_start: 0.8249 (m-30) cc_final: 0.8004 (m-30) REVERT: b 84 MET cc_start: 0.7936 (tpp) cc_final: 0.7630 (tpp) REVERT: c 41 GLU cc_start: 0.7714 (tp30) cc_final: 0.7383 (tp30) REVERT: d 83 TYR cc_start: 0.7837 (m-10) cc_final: 0.7382 (m-80) REVERT: d 86 ARG cc_start: 0.7374 (mmp80) cc_final: 0.6850 (mmp80) REVERT: d 100 LEU cc_start: 0.9408 (mt) cc_final: 0.9151 (mt) REVERT: d 101 LEU cc_start: 0.8941 (tp) cc_final: 0.8577 (tt) REVERT: d 105 GLU cc_start: 0.6474 (tp30) cc_final: 0.6222 (tp30) REVERT: d 108 LYS cc_start: 0.8415 (tmtt) cc_final: 0.8065 (ttpp) REVERT: g 73 ASN cc_start: 0.8778 (m-40) cc_final: 0.8306 (m110) REVERT: g 76 THR cc_start: 0.8522 (p) cc_final: 0.8226 (t) REVERT: g 101 THR cc_start: 0.8946 (m) cc_final: 0.8430 (p) REVERT: g 111 ILE cc_start: 0.8402 (mt) cc_final: 0.8105 (tt) REVERT: g 114 VAL cc_start: 0.9105 (m) cc_final: 0.8803 (p) REVERT: e 56 LYS cc_start: 0.8526 (ttpp) cc_final: 0.8155 (tttm) REVERT: e 73 GLU cc_start: 0.7737 (pt0) cc_final: 0.7362 (pt0) outliers start: 20 outliers final: 18 residues processed: 193 average time/residue: 0.0859 time to fit residues: 24.6944 Evaluate side-chains 189 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1711 THR Chi-restraints excluded: chain O residue 1740 HIS Chi-restraints excluded: chain O residue 1774 THR Chi-restraints excluded: chain O residue 1825 TYR Chi-restraints excluded: chain a residue 39 HIS Chi-restraints excluded: chain a residue 41 TYR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain a residue 133 GLU Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain f residue 45 ARG Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 113 GLU Chi-restraints excluded: chain k residue 936 GLU Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 124 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 25 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 0.0570 chunk 10 optimal weight: 9.9990 overall best weight: 1.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1686 HIS f 25 ASN h 47 GLN ** h 63 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 = 0.3499 r_free = 0.3499 target = 0.073448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.052225 restraints weight = 49197.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.053544 restraints weight = 25073.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054321 restraints weight = 17135.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.054775 restraints weight = 14064.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.054969 restraints weight = 12699.225| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13992 Z= 0.207 Angle : 0.719 11.132 19972 Z= 0.397 Chirality : 0.046 0.295 2237 Planarity : 0.005 0.049 1664 Dihedral : 29.982 166.626 3901 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.66 % Allowed : 15.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.27), residues: 983 helix: 2.01 (0.21), residues: 573 sheet: -1.18 (0.68), residues: 39 loop : -1.15 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG f 95 TYR 0.023 0.002 TYR d 83 PHE 0.017 0.002 PHE c 25 TRP 0.040 0.004 TRP O1699 HIS 0.007 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.21 (13992) covalent geometry : angle 0.71941 / 0.40 (19972) hydrogen bonds : bond 0.04717 / 5.34 ( 766) hydrogen bonds : angle 3.40205 / 4.71 ( 1933) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: O 1775 GLN cc_start: 0.7896 (mt0) cc_final: 0.7481 (mt0) REVERT: O 1808 TYR cc_start: 0.6485 (t80) cc_final: 0.6202 (t80) REVERT: b 84 MET cc_start: 0.7984 (tpp) cc_final: 0.7143 (tpp) REVERT: c 41 GLU cc_start: 0.7644 (tp30) cc_final: 0.7311 (tp30) REVERT: d 83 TYR cc_start: 0.7902 (m-10) cc_final: 0.7468 (m-80) REVERT: d 86 ARG cc_start: 0.7581 (mmp80) cc_final: 0.7122 (mmp80) REVERT: d 100 LEU cc_start: 0.9453 (mt) cc_final: 0.9093 (mt) REVERT: d 101 LEU cc_start: 0.8952 (tp) cc_final: 0.8591 (tt) REVERT: d 105 GLU cc_start: 0.6383 (tp30) cc_final: 0.5930 (tp30) REVERT: d 108 LYS cc_start: 0.8394 (tmtt) cc_final: 0.8107 (tttt) REVERT: g 73 ASN cc_start: 0.8741 (m-40) cc_final: 0.8306 (m110) REVERT: g 76 THR cc_start: 0.8516 (p) cc_final: 0.8200 (t) REVERT: g 101 THR cc_start: 0.8961 (m) cc_final: 0.8450 (p) REVERT: g 111 ILE cc_start: 0.8497 (mt) cc_final: 0.8244 (tt) REVERT: g 114 VAL cc_start: 0.9104 (m) cc_final: 0.8783 (p) REVERT: h 71 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7516 (tp30) REVERT: e 56 LYS cc_start: 0.8693 (ttpp) cc_final: 0.8338 (tttm) outliers start: 31 outliers final: 27 residues processed: 188 average time/residue: 0.0927 time to fit residues: 25.8081 Evaluate side-chains 187 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1686 HIS Chi-restraints excluded: chain O residue 1711 THR Chi-restraints excluded: chain O residue 1740 HIS Chi-restraints excluded: chain O residue 1772 CYS Chi-restraints excluded: chain O residue 1774 THR Chi-restraints excluded: chain O residue 1825 TYR Chi-restraints excluded: chain a residue 41 TYR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain a residue 133 GLU Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain c residue 91 GLU Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain f residue 25 ASN Chi-restraints excluded: chain f residue 45 ARG Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 64 SER Chi-restraints excluded: chain h residue 68 ASP Chi-restraints excluded: chain h residue 71 GLU Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 113 GLU Chi-restraints excluded: chain k residue 936 GLU Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain e residue 124 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 85 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 116 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1686 HIS d 82 HIS ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.074392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.053153 restraints weight = 49411.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.054552 restraints weight = 24307.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055386 restraints weight = 16226.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.055842 restraints weight = 13148.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.056051 restraints weight = 11867.473| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13992 Z= 0.147 Angle : 0.664 9.105 19972 Z= 0.376 Chirality : 0.044 0.285 2237 Planarity : 0.004 0.047 1664 Dihedral : 29.886 166.923 3901 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.07 % Allowed : 16.75 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.27), residues: 983 helix: 2.14 (0.21), residues: 573 sheet: -1.01 (0.67), residues: 41 loop : -1.14 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 29 TYR 0.019 0.002 TYR d 83 PHE 0.011 0.001 PHE e 67 TRP 0.037 0.003 TRP O1699 HIS 0.007 0.001 HIS O1686 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (13992) covalent geometry : angle 0.66383 / 0.38 (19972) hydrogen bonds : bond 0.03962 / 4.54 ( 766) hydrogen bonds : angle 3.29187 / 4.61 ( 1933) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: O 1775 GLN cc_start: 0.7824 (mt0) cc_final: 0.7407 (mt0) REVERT: O 1808 TYR cc_start: 0.6603 (t80) cc_final: 0.6321 (t80) REVERT: b 68 ASP cc_start: 0.8218 (m-30) cc_final: 0.7872 (m-30) REVERT: c 41 GLU cc_start: 0.7764 (tp30) cc_final: 0.7398 (tp30) REVERT: d 83 TYR cc_start: 0.7787 (m-10) cc_final: 0.7382 (m-80) REVERT: d 86 ARG cc_start: 0.7492 (mmp80) cc_final: 0.6916 (mmp80) REVERT: d 100 LEU cc_start: 0.9356 (mt) cc_final: 0.9148 (mt) REVERT: d 101 LEU cc_start: 0.8961 (tp) cc_final: 0.8652 (tt) REVERT: d 105 GLU cc_start: 0.6614 (tp30) cc_final: 0.6266 (tp30) REVERT: d 108 LYS cc_start: 0.8414 (tmtt) cc_final: 0.8028 (tttt) REVERT: g 73 ASN cc_start: 0.8803 (m-40) cc_final: 0.8589 (m110) REVERT: g 76 THR cc_start: 0.8549 (p) cc_final: 0.8230 (t) REVERT: g 101 THR cc_start: 0.8966 (m) cc_final: 0.8443 (p) REVERT: g 111 ILE cc_start: 0.8494 (mt) cc_final: 0.8210 (tt) REVERT: g 114 VAL cc_start: 0.9105 (m) cc_final: 0.8788 (p) REVERT: h 71 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7543 (tp30) REVERT: e 56 LYS cc_start: 0.8653 (ttpp) cc_final: 0.8307 (tttm) outliers start: 26 outliers final: 24 residues processed: 183 average time/residue: 0.0835 time to fit residues: 23.1230 Evaluate side-chains 185 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1651 ILE Chi-restraints excluded: chain O residue 1711 THR Chi-restraints excluded: chain O residue 1740 HIS Chi-restraints excluded: chain O residue 1772 CYS Chi-restraints excluded: chain O residue 1774 THR Chi-restraints excluded: chain O residue 1825 TYR Chi-restraints excluded: chain a residue 41 TYR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain a residue 133 GLU Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain f residue 25 ASN Chi-restraints excluded: chain f residue 45 ARG Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 64 SER Chi-restraints excluded: chain h residue 68 ASP Chi-restraints excluded: chain h residue 71 GLU Chi-restraints excluded: chain h residue 113 GLU Chi-restraints excluded: chain k residue 936 GLU Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 124 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 0.0050 chunk 99 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 82 HIS f 25 ASN ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.074738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053430 restraints weight = 49216.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.054825 restraints weight = 24366.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.055669 restraints weight = 16363.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.056064 restraints weight = 13283.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.056340 restraints weight = 12078.275| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13992 Z= 0.142 Angle : 0.648 9.581 19972 Z= 0.369 Chirality : 0.043 0.289 2237 Planarity : 0.004 0.047 1664 Dihedral : 29.695 166.542 3901 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.83 % Allowed : 17.33 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.27), residues: 983 helix: 2.17 (0.21), residues: 579 sheet: -1.20 (0.65), residues: 39 loop : -1.00 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG g 29 TYR 0.025 0.002 TYR d 83 PHE 0.011 0.001 PHE e 67 TRP 0.046 0.004 TRP O1699 HIS 0.006 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (13992) covalent geometry : angle 0.64808 / 0.37 (19972) hydrogen bonds : bond 0.03842 / 4.40 ( 766) hydrogen bonds : angle 3.24955 / 4.57 ( 1933) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: O 1775 GLN cc_start: 0.7858 (mt0) cc_final: 0.7448 (mt0) REVERT: O 1808 TYR cc_start: 0.6583 (t80) cc_final: 0.6311 (t80) REVERT: c 41 GLU cc_start: 0.7759 (tp30) cc_final: 0.7385 (tp30) REVERT: d 83 TYR cc_start: 0.7862 (m-10) cc_final: 0.7441 (m-80) REVERT: d 86 ARG cc_start: 0.7479 (mmp80) cc_final: 0.7041 (mmp80) REVERT: d 101 LEU cc_start: 0.8946 (tp) cc_final: 0.8656 (tt) REVERT: d 105 GLU cc_start: 0.6569 (tp30) cc_final: 0.6201 (tp30) REVERT: d 108 LYS cc_start: 0.8443 (tmtt) cc_final: 0.8107 (tttt) REVERT: g 73 ASN cc_start: 0.8803 (m-40) cc_final: 0.8348 (m110) REVERT: g 76 THR cc_start: 0.8514 (p) cc_final: 0.8206 (t) REVERT: g 101 THR cc_start: 0.9035 (m) cc_final: 0.8471 (p) REVERT: g 111 ILE cc_start: 0.8523 (mt) cc_final: 0.8234 (tt) REVERT: g 114 VAL cc_start: 0.9109 (m) cc_final: 0.8799 (p) REVERT: h 59 MET cc_start: 0.8478 (tpp) cc_final: 0.8091 (tpp) REVERT: e 56 LYS cc_start: 0.8679 (ttpp) cc_final: 0.8316 (tttm) outliers start: 24 outliers final: 20 residues processed: 181 average time/residue: 0.0905 time to fit residues: 24.6298 Evaluate side-chains 180 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1651 ILE Chi-restraints excluded: chain O residue 1711 THR Chi-restraints excluded: chain O residue 1740 HIS Chi-restraints excluded: chain O residue 1772 CYS Chi-restraints excluded: chain O residue 1774 THR Chi-restraints excluded: chain O residue 1825 TYR Chi-restraints excluded: chain a residue 41 TYR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain a residue 133 GLU Chi-restraints excluded: chain c residue 91 GLU Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain f residue 25 ASN Chi-restraints excluded: chain f residue 45 ARG Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 64 SER Chi-restraints excluded: chain h residue 68 ASP Chi-restraints excluded: chain e residue 71 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 8 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 82 HIS f 25 ASN ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.074386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.053137 restraints weight = 49022.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054514 restraints weight = 24354.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.055337 restraints weight = 16384.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.055785 restraints weight = 13328.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.056045 restraints weight = 12050.580| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13992 Z= 0.162 Angle : 0.662 9.198 19972 Z= 0.373 Chirality : 0.044 0.292 2237 Planarity : 0.004 0.047 1664 Dihedral : 29.712 166.251 3901 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.83 % Allowed : 17.45 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.27), residues: 983 helix: 2.14 (0.21), residues: 578 sheet: -1.31 (0.64), residues: 39 loop : -1.04 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 40 TYR 0.020 0.002 TYR d 83 PHE 0.013 0.001 PHE O1816 TRP 0.039 0.003 TRP O1699 HIS 0.007 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (13992) covalent geometry : angle 0.66209 / 0.37 (19972) hydrogen bonds : bond 0.03959 / 4.52 ( 766) hydrogen bonds : angle 3.26582 / 4.59 ( 1933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1851.96 seconds wall clock time: 32 minutes 37.80 seconds (1957.80 seconds total)