Starting phenix.real_space_refine on Fri Jul 3 08:03:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gui_34274/07_2026/8gui_34274.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gui_34274/07_2026/8gui_34274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gui_34274/07_2026/8gui_34274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gui_34274/07_2026/8gui_34274.map" model { file = "/net/cci-nas-00/data/ceres_data/8gui_34274/07_2026/8gui_34274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gui_34274/07_2026/8gui_34274.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8gui_34274/07_2026/8gui_34274.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gui_34274/07_2026/8gui_34274.cif" } resolution = 2.81 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= 0.001 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 294 5.49 5 S 33 5.16 5 C 7467 2.51 5 N 2505 2.21 5 O 3045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13348 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 854 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 106} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 744 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 862 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 107} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 590 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "L" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 595 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12430 SG CYS K 937 73.393 60.676 79.904 1.00109.17 S ATOM 12608 SG CYS K 957 74.505 58.912 76.711 1.00 98.43 S ATOM 12630 SG CYS K 960 74.436 57.059 79.742 1.00103.47 S ATOM 12316 SG CYS K 922 76.308 64.492 69.411 1.00129.40 S ATOM 12335 SG CYS K 925 77.446 65.863 66.094 1.00128.06 S ATOM 12475 SG CYS K 942 74.286 67.379 67.931 1.00117.74 S ATOM 12501 SG CYS K 945 74.011 64.345 66.214 1.00109.14 S ATOM 13024 SG CYS L 963 70.335 79.725 84.994 1.00140.01 S ATOM 13200 SG CYS L 983 72.002 82.530 86.878 1.00146.88 S ATOM 13222 SG CYS L 986 68.715 83.154 85.107 1.00146.57 S ATOM 12911 SG CYS L 948 81.094 80.332 87.061 1.00158.18 S ATOM 12930 SG CYS L 951 84.728 80.602 87.562 1.00158.61 S ATOM 13069 SG CYS L 968 82.695 77.429 89.070 1.00149.40 S ATOM 13095 SG CYS L 971 82.623 80.423 90.704 1.00149.73 S Time building chain proxies: 2.81, per 1000 atoms: 0.21 Number of scatterers: 13348 At special positions: 0 Unit cell: (115.5, 115.5, 120.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 33 16.00 P 294 15.00 O 3045 8.00 N 2505 7.00 C 7467 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: 1.14 Conformation dependent library (CDL) restraints added in 360.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" ND1 HIS K 939 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 957 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 960 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 937 " pdb=" ZN K1002 " pdb="ZN ZN K1002 " - pdb=" SG CYS K 945 " pdb="ZN ZN K1002 " - pdb=" SG CYS K 942 " pdb="ZN ZN K1002 " - pdb=" SG CYS K 922 " pdb="ZN ZN K1002 " - pdb=" SG CYS K 925 " pdb=" ZN L1101 " pdb="ZN ZN L1101 " - pdb=" ND1 HIS L 965 " pdb="ZN ZN L1101 " - pdb=" SG CYS L 983 " pdb="ZN ZN L1101 " - pdb=" SG CYS L 963 " pdb="ZN ZN L1101 " - pdb=" SG CYS L 986 " pdb=" ZN L1102 " pdb="ZN ZN L1102 " - pdb=" SG CYS L 971 " pdb="ZN ZN L1102 " - pdb=" SG CYS L 948 " pdb="ZN ZN L1102 " - pdb=" SG CYS L 968 " pdb="ZN ZN L1102 " - pdb=" SG CYS L 951 " Number of angles added : 18 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1730 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 12 sheets defined 66.1% alpha, 3.7% beta 147 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.519A 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: 3.602A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.661A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.181A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.645A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.742A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.698A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.234A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 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 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 124 removed outlier: 3.557A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 905 through 920 removed outlier: 3.528A pdb=" N ILE K 913 " --> pdb=" O LEU K 909 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG K 919 " --> pdb=" O ASP K 915 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU K 920 " --> pdb=" O TYR K 916 " (cutoff:3.500A) Processing helix chain 'K' and resid 942 through 952 Processing helix chain 'L' and resid 930 through 946 Processing helix chain 'L' and resid 968 through 978 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.875A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.555A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.257A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.025A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.113A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 940 through 941 Processing sheet with id=AB3, first strand: chain 'L' and resid 966 through 967 removed outlier: 3.550A pdb=" N HIS L 996 " --> pdb=" O VAL L 959 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 1.49 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: 2950 1.33 - 1.45: 4257 1.45 - 1.57: 6342 1.57 - 1.69: 586 1.69 - 1.81: 45 Bond restraints: 14180 Sorted by residual: bond pdb=" C3' DG J 137 " pdb=" C2' DG J 137 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 bond pdb=" C3' DC I 12 " pdb=" C2' DC I 12 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DT J 7 " pdb=" C2' DT J 7 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DA I 52 " pdb=" C2' DA I 52 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 ... (remaining 14175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 18620 1.28 - 2.57: 1552 2.57 - 3.85: 191 3.85 - 5.13: 16 5.13 - 6.42: 7 Bond angle restraints: 20386 Sorted by residual: angle pdb=" O4' DG I 100 " pdb=" C4' DG I 100 " pdb=" C3' DG I 100 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.23e+01 angle pdb=" N3 DT J 17 " pdb=" C4 DT J 17 " pdb=" O4 DT J 17 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT I 117 " pdb=" C4 DT I 117 " pdb=" O4 DT I 117 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J 24 " pdb=" C4 DT J 24 " pdb=" O4 DT J 24 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 20381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 6402 35.66 - 71.33: 1375 71.33 - 106.99: 18 106.99 - 142.66: 1 142.66 - 178.32: 6 Dihedral angle restraints: 7802 sinusoidal: 5126 harmonic: 2676 Sorted by residual: dihedral pdb=" CA ARG L 954 " pdb=" C ARG L 954 " pdb=" N LYS L 955 " pdb=" CA LYS L 955 " ideal model delta harmonic sigma weight residual 180.00 -153.54 -26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" C4' DT I 77 " pdb=" C3' DT I 77 " pdb=" O3' DT I 77 " pdb=" P DC I 78 " ideal model delta sinusoidal sigma weight residual -140.00 38.32 -178.32 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 4 " pdb=" C3' DG J 4 " pdb=" O3' DG J 4 " pdb=" P DG J 5 " ideal model delta sinusoidal sigma weight residual -140.00 33.92 -173.92 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1548 0.040 - 0.081: 554 0.081 - 0.121: 182 0.121 - 0.162: 17 0.162 - 0.202: 4 Chirality restraints: 2305 Sorted by residual: chirality pdb=" C3' DA I 41 " pdb=" C4' DA I 41 " pdb=" O3' DA I 41 " pdb=" C2' DA I 41 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CG LEU F 62 " pdb=" CB LEU F 62 " pdb=" CD1 LEU F 62 " pdb=" CD2 LEU F 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" C3' DA I 131 " pdb=" C4' DA I 131 " pdb=" O3' DA I 131 " pdb=" C2' DA I 131 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 2302 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 954 " 0.176 9.50e-02 1.11e+02 7.91e-02 3.92e+00 pdb=" NE ARG L 954 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG L 954 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG L 954 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG L 954 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.66e+00 pdb=" N PRO H 103 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 40 " -0.011 2.00e-02 2.50e+03 1.05e-02 2.22e+00 pdb=" CG TYR H 40 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR H 40 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR H 40 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR H 40 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR H 40 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR H 40 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 40 " 0.001 2.00e-02 2.50e+03 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 433 2.67 - 3.23: 11700 3.23 - 3.78: 26309 3.78 - 4.34: 33865 4.34 - 4.90: 47480 Nonbonded interactions: 119787 Sorted by model distance: nonbonded pdb=" OH TYR C 50 " pdb=" OE1 GLN D 95 " model vdw 2.109 3.040 nonbonded pdb=" N2 DG I 132 " pdb=" O2 DC J 16 " model vdw 2.182 2.496 nonbonded pdb=" OE2 GLU D 105 " pdb=" OG1 THR K 952 " model vdw 2.232 3.040 nonbonded pdb=" OD2 ASP F 68 " pdb=" NH2 ARG F 92 " model vdw 2.240 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.264 3.120 ... (remaining 119782 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' selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = (chain 'B' and resid 22 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and ((resid 9 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 through 120)) selection = (chain 'G' and (resid 9 through 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB )) or resid 37 through 98 or (resid 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 through 120)) } ncs_group { reference = (chain 'D' and resid 30 through 124) selection = (chain 'H' and (resid 30 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 124)) } ncs_group { reference = (chain 'K' and (resid 906 through 909 or resid 911 through 914 or resid 916 thro \ ugh 926 or resid 928 through 946 or resid 949 through 950 or resid 953 through 9 \ 66 or resid 968 through 974 or resid 1001 through 1002)) selection = (chain 'L' and (resid 932 through 935 or resid 937 through 940 or resid 942 thro \ ugh 952 or resid 954 through 972 or resid 975 through 976 or resid 979 through 9 \ 92 or resid 994 through 1000 or resid 1101 through 1102)) } 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=0.27 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.700 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 14196 Z= 0.495 Angle : 0.758 15.036 20404 Z= 0.638 Chirality : 0.045 0.202 2305 Planarity : 0.004 0.079 1563 Dihedral : 27.518 178.320 6072 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.13 % Allowed : 0.13 % Favored : 99.74 % 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: 1.95 (0.28), residues: 900 helix: 1.94 (0.21), residues: 592 sheet: None (None), residues: 0 loop : 0.11 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.026 0.002 TYR H 40 PHE 0.010 0.001 PHE A 78 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.50 (14180) covalent geometry : angle 0.72922 / 0.64 (20386) hydrogen bonds : bond 0.10628 / 6.98 ( 831) hydrogen bonds : angle 3.72738 / 2.62 ( 2089) metal coordination : bond 0.01096 / 0.72 ( 16) metal coordination : angle 6.94348 / 4.52 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8140 (m-30) cc_final: 0.7825 (m-30) REVERT: C 73 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8668 (t160) REVERT: H 71 GLU cc_start: 0.7765 (tp30) cc_final: 0.7495 (mm-30) REVERT: K 938 PHE cc_start: 0.7614 (m-80) cc_final: 0.7114 (m-80) REVERT: K 943 PHE cc_start: 0.8515 (t80) cc_final: 0.7973 (t80) REVERT: K 955 ARG cc_start: 0.8579 (mtm110) cc_final: 0.8074 (mtm110) outliers start: 1 outliers final: 2 residues processed: 208 average time/residue: 0.8082 time to fit residues: 179.5829 Evaluate side-chains 176 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 173 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain F residue 24 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.113164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.085069 restraints weight = 23064.733| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.37 r_work: 0.3192 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14196 Z= 0.184 Angle : 0.696 17.267 20404 Z= 0.392 Chirality : 0.047 0.352 2305 Planarity : 0.006 0.105 1563 Dihedral : 31.505 176.371 4241 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.35 % Allowed : 13.69 % 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: 1.89 (0.27), residues: 900 helix: 1.93 (0.20), residues: 597 sheet: -2.56 (1.57), residues: 10 loop : 0.05 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 35 TYR 0.026 0.002 TYR L 976 PHE 0.015 0.002 PHE A 78 HIS 0.010 0.001 HIS K 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 (14180) covalent geometry : angle 0.66397 / 0.39 (20386) hydrogen bonds : bond 0.05006 / 3.41 ( 831) hydrogen bonds : angle 3.27523 / 2.32 ( 2089) metal coordination : bond 0.00879 / 0.53 ( 16) metal coordination : angle 7.07847 / 4.71 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: E 81 ASP cc_start: 0.7968 (t0) cc_final: 0.7759 (t0) REVERT: K 943 PHE cc_start: 0.8775 (t80) cc_final: 0.8474 (t80) REVERT: L 982 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7595 (mmmt) REVERT: L 996 HIS cc_start: 0.7448 (t-90) cc_final: 0.7098 (t-90) outliers start: 18 outliers final: 6 residues processed: 195 average time/residue: 0.7898 time to fit residues: 164.5895 Evaluate side-chains 186 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 180 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 60 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 970 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 = 0.3823 r_free = 0.3823 target = 0.113109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.084948 restraints weight = 23196.959| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.39 r_work: 0.3190 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14196 Z= 0.169 Angle : 0.663 13.889 20404 Z= 0.377 Chirality : 0.046 0.353 2305 Planarity : 0.005 0.076 1563 Dihedral : 31.512 174.379 4235 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.96 % Allowed : 15.91 % Favored : 82.14 % 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: 2.05 (0.27), residues: 900 helix: 2.09 (0.20), residues: 599 sheet: -2.36 (1.52), residues: 10 loop : 0.01 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 971 TYR 0.019 0.002 TYR H 40 PHE 0.018 0.002 PHE K 941 HIS 0.005 0.001 HIS K 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.17 (14180) covalent geometry : angle 0.63924 / 0.38 (20386) hydrogen bonds : bond 0.04639 / 3.14 ( 831) hydrogen bonds : angle 3.15989 / 2.25 ( 2089) metal coordination : bond 0.00662 / 0.39 ( 16) metal coordination : angle 5.99059 / 3.81 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.383 Fit side-chains REVERT: E 59 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.7709 (pm20) REVERT: E 81 ASP cc_start: 0.8077 (t0) cc_final: 0.7787 (t0) REVERT: E 120 MET cc_start: 0.8815 (mtp) cc_final: 0.8604 (mtt) REVERT: K 943 PHE cc_start: 0.8848 (t80) cc_final: 0.7521 (t80) REVERT: K 954 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8430 (tp40) REVERT: L 985 LYS cc_start: 0.8716 (mmmm) cc_final: 0.8470 (ttmm) outliers start: 15 outliers final: 7 residues processed: 190 average time/residue: 0.7890 time to fit residues: 160.2673 Evaluate side-chains 189 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 181 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 35 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 93 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 49 HIS D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 970 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.113401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.085204 restraints weight = 23284.050| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.39 r_work: 0.3197 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14196 Z= 0.162 Angle : 0.656 12.835 20404 Z= 0.373 Chirality : 0.045 0.356 2305 Planarity : 0.005 0.064 1563 Dihedral : 31.550 172.714 4235 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.61 % Allowed : 16.95 % Favored : 80.44 % 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: 2.17 (0.27), residues: 900 helix: 2.13 (0.20), residues: 600 sheet: None (None), residues: 0 loop : 0.07 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG K 971 TYR 0.021 0.002 TYR H 40 PHE 0.027 0.002 PHE L 969 HIS 0.007 0.001 HIS L 996 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (14180) covalent geometry : angle 0.63390 / 0.37 (20386) hydrogen bonds : bond 0.04485 / 3.03 ( 831) hydrogen bonds : angle 3.11281 / 2.23 ( 2089) metal coordination : bond 0.00692 / 0.39 ( 16) metal coordination : angle 5.69597 / 3.44 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.9103 (ptmm) cc_final: 0.8756 (ttpt) REVERT: D 99 ARG cc_start: 0.8620 (mtt-85) cc_final: 0.8414 (mtt90) REVERT: E 59 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.7719 (pm20) REVERT: E 81 ASP cc_start: 0.8139 (t0) cc_final: 0.7822 (t0) REVERT: E 122 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8672 (ptpp) REVERT: K 928 ARG cc_start: 0.7443 (pmt100) cc_final: 0.6982 (pmt100) REVERT: K 954 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8444 (tp40) REVERT: L 985 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8431 (ttmm) outliers start: 20 outliers final: 8 residues processed: 196 average time/residue: 0.8011 time to fit residues: 167.6062 Evaluate side-chains 188 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain L residue 945 ARG Chi-restraints excluded: chain L residue 985 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 73 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 49 HIS D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.117819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.089087 restraints weight = 24982.413| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.48 r_work: 0.3191 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14196 Z= 0.156 Angle : 0.658 18.671 20404 Z= 0.370 Chirality : 0.045 0.357 2305 Planarity : 0.005 0.063 1563 Dihedral : 31.561 171.604 4235 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.87 % Allowed : 17.47 % Favored : 79.66 % 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: 2.22 (0.27), residues: 900 helix: 2.19 (0.20), residues: 602 sheet: None (None), residues: 0 loop : 0.02 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 971 TYR 0.021 0.002 TYR H 40 PHE 0.016 0.002 PHE L 969 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.16 (14180) covalent geometry : angle 0.62730 / 0.37 (20386) hydrogen bonds : bond 0.04361 / 2.94 ( 831) hydrogen bonds : angle 3.07009 / 2.20 ( 2089) metal coordination : bond 0.00883 / 0.54 ( 16) metal coordination : angle 6.67508 / 3.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: D 99 ARG cc_start: 0.8590 (mtt-85) cc_final: 0.8366 (mtt90) REVERT: E 59 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.7741 (pm20) REVERT: E 81 ASP cc_start: 0.8083 (t0) cc_final: 0.7747 (t0) REVERT: H 71 GLU cc_start: 0.8512 (tp30) cc_final: 0.8256 (mm-30) REVERT: K 931 ASP cc_start: 0.8937 (p0) cc_final: 0.8637 (p0) REVERT: K 938 PHE cc_start: 0.8253 (m-80) cc_final: 0.7594 (m-80) REVERT: K 954 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8453 (tp40) REVERT: L 985 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8497 (ttmm) REVERT: L 996 HIS cc_start: 0.8055 (t-90) cc_final: 0.7653 (t-90) outliers start: 22 outliers final: 11 residues processed: 194 average time/residue: 0.7950 time to fit residues: 164.6423 Evaluate side-chains 196 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain L residue 945 ARG Chi-restraints excluded: chain L residue 985 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 0.0000 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN C 73 ASN D 49 HIS D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.113075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.084810 restraints weight = 23218.910| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.40 r_work: 0.3183 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14196 Z= 0.164 Angle : 0.653 17.976 20404 Z= 0.369 Chirality : 0.045 0.361 2305 Planarity : 0.005 0.061 1563 Dihedral : 31.586 171.414 4235 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.13 % Allowed : 17.73 % Favored : 79.14 % 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: 2.20 (0.27), residues: 900 helix: 2.17 (0.20), residues: 603 sheet: None (None), residues: 0 loop : 0.01 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 955 TYR 0.023 0.002 TYR H 40 PHE 0.016 0.002 PHE L 969 HIS 0.005 0.001 HIS K 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (14180) covalent geometry : angle 0.62978 / 0.37 (20386) hydrogen bonds : bond 0.04397 / 2.97 ( 831) hydrogen bonds : angle 3.07565 / 2.20 ( 2089) metal coordination : bond 0.00712 / 0.41 ( 16) metal coordination : angle 5.88401 / 3.38 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8201 (pp30) cc_final: 0.7888 (pp30) REVERT: C 95 LYS cc_start: 0.9188 (ptmm) cc_final: 0.8875 (ttpp) REVERT: D 99 ARG cc_start: 0.8600 (mtt-85) cc_final: 0.8371 (mtt90) REVERT: E 59 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.7741 (pm20) REVERT: E 81 ASP cc_start: 0.8143 (t0) cc_final: 0.7801 (t0) REVERT: E 122 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8645 (ptpp) REVERT: H 108 LYS cc_start: 0.8715 (tmtt) cc_final: 0.8447 (ttmm) REVERT: K 938 PHE cc_start: 0.8196 (m-80) cc_final: 0.7728 (m-80) REVERT: K 954 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8416 (tp40) REVERT: L 985 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8434 (ttmm) REVERT: L 996 HIS cc_start: 0.8343 (t-90) cc_final: 0.7997 (t-90) outliers start: 24 outliers final: 14 residues processed: 189 average time/residue: 0.8405 time to fit residues: 169.2112 Evaluate side-chains 197 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 920 LEU Chi-restraints excluded: chain L residue 945 ARG Chi-restraints excluded: chain L residue 985 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 69 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 109 optimal weight: 0.0470 chunk 77 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN C 73 ASN D 49 HIS D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.118019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089495 restraints weight = 24761.941| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.45 r_work: 0.3231 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14196 Z= 0.154 Angle : 0.639 14.980 20404 Z= 0.364 Chirality : 0.045 0.359 2305 Planarity : 0.005 0.061 1563 Dihedral : 31.573 171.875 4235 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.39 % Allowed : 18.25 % Favored : 78.36 % 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: 2.27 (0.27), residues: 900 helix: 2.22 (0.20), residues: 603 sheet: None (None), residues: 0 loop : 0.04 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 955 TYR 0.023 0.002 TYR H 40 PHE 0.013 0.002 PHE L 969 HIS 0.005 0.001 HIS K 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (14180) covalent geometry : angle 0.62006 / 0.36 (20386) hydrogen bonds : bond 0.04257 / 2.87 ( 831) hydrogen bonds : angle 3.04403 / 2.18 ( 2089) metal coordination : bond 0.00628 / 0.34 ( 16) metal coordination : angle 5.18044 / 2.93 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.9163 (ptmm) cc_final: 0.8867 (ttpp) REVERT: D 99 ARG cc_start: 0.8611 (mtt-85) cc_final: 0.8400 (mtt90) REVERT: E 59 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: E 81 ASP cc_start: 0.8119 (t0) cc_final: 0.7786 (t0) REVERT: G 90 ASP cc_start: 0.8558 (t0) cc_final: 0.8347 (t0) REVERT: H 108 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8478 (ttmm) REVERT: K 931 ASP cc_start: 0.8862 (p0) cc_final: 0.8539 (p0) REVERT: K 938 PHE cc_start: 0.8274 (m-80) cc_final: 0.7965 (m-80) REVERT: K 954 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8433 (tp40) REVERT: L 985 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8416 (ttmm) REVERT: L 996 HIS cc_start: 0.8499 (t-90) cc_final: 0.8224 (t-90) outliers start: 26 outliers final: 14 residues processed: 193 average time/residue: 0.8139 time to fit residues: 167.4764 Evaluate side-chains 196 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 920 LEU Chi-restraints excluded: chain L residue 945 ARG Chi-restraints excluded: chain L residue 985 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 104 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 62 optimal weight: 0.0070 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN C 73 ASN D 49 HIS D 84 ASN E 68 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.113372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.084978 restraints weight = 22922.876| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.41 r_work: 0.3224 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14196 Z= 0.167 Angle : 0.648 13.080 20404 Z= 0.369 Chirality : 0.045 0.361 2305 Planarity : 0.005 0.067 1563 Dihedral : 31.577 171.499 4235 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.61 % Allowed : 19.95 % Favored : 77.44 % 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: 2.23 (0.28), residues: 900 helix: 2.19 (0.20), residues: 603 sheet: None (None), residues: 0 loop : 0.04 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 955 TYR 0.026 0.002 TYR H 40 PHE 0.029 0.002 PHE K 969 HIS 0.006 0.001 HIS K 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (14180) covalent geometry : angle 0.63335 / 0.37 (20386) hydrogen bonds : bond 0.04320 / 2.94 ( 831) hydrogen bonds : angle 3.07164 / 2.21 ( 2089) metal coordination : bond 0.00706 / 0.39 ( 16) metal coordination : angle 4.66736 / 2.59 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8088 (pp30) cc_final: 0.7837 (pp30) REVERT: C 95 LYS cc_start: 0.9176 (ptmm) cc_final: 0.8863 (ttpp) REVERT: D 99 ARG cc_start: 0.8631 (mtt-85) cc_final: 0.8407 (mtt90) REVERT: E 59 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.7739 (pm20) REVERT: E 81 ASP cc_start: 0.8159 (t0) cc_final: 0.7815 (t0) REVERT: G 90 ASP cc_start: 0.8633 (t0) cc_final: 0.8402 (t70) REVERT: G 99 LYS cc_start: 0.9232 (mtmt) cc_final: 0.9031 (mmmt) REVERT: K 938 PHE cc_start: 0.8281 (m-80) cc_final: 0.7984 (m-80) REVERT: K 954 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8413 (tp40) REVERT: L 985 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8393 (ttmm) REVERT: L 996 HIS cc_start: 0.8533 (t-90) cc_final: 0.8245 (t-90) outliers start: 20 outliers final: 14 residues processed: 191 average time/residue: 0.8258 time to fit residues: 168.1750 Evaluate side-chains 198 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 920 LEU Chi-restraints excluded: chain L residue 945 ARG Chi-restraints excluded: chain L residue 985 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 65 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 49 HIS D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.113543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.085042 restraints weight = 23315.680| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.42 r_work: 0.3188 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14196 Z= 0.160 Angle : 0.649 12.700 20404 Z= 0.369 Chirality : 0.045 0.361 2305 Planarity : 0.004 0.063 1563 Dihedral : 31.584 171.714 4235 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.87 % Allowed : 20.21 % Favored : 76.92 % 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: 2.24 (0.28), residues: 900 helix: 2.20 (0.20), residues: 602 sheet: None (None), residues: 0 loop : 0.06 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 955 TYR 0.027 0.002 TYR H 40 PHE 0.012 0.002 PHE A 67 HIS 0.006 0.001 HIS K 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (14180) covalent geometry : angle 0.63567 / 0.37 (20386) hydrogen bonds : bond 0.04262 / 2.89 ( 831) hydrogen bonds : angle 3.06068 / 2.20 ( 2089) metal coordination : bond 0.00701 / 0.41 ( 16) metal coordination : angle 4.51116 / 2.49 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8152 (pp30) cc_final: 0.7836 (pp30) REVERT: B 85 ASP cc_start: 0.9192 (m-30) cc_final: 0.8963 (m-30) REVERT: C 73 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8721 (t160) REVERT: C 95 LYS cc_start: 0.9163 (ptmm) cc_final: 0.8864 (ttpp) REVERT: D 57 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8691 (mmtm) REVERT: E 59 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: E 81 ASP cc_start: 0.8158 (t0) cc_final: 0.7863 (t0) REVERT: H 108 LYS cc_start: 0.8718 (tmtt) cc_final: 0.8472 (ttmm) REVERT: K 938 PHE cc_start: 0.8238 (m-80) cc_final: 0.7989 (m-80) REVERT: K 954 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8374 (tp40) REVERT: L 985 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8392 (ttmm) REVERT: L 996 HIS cc_start: 0.8486 (t-90) cc_final: 0.8207 (t-90) outliers start: 22 outliers final: 15 residues processed: 189 average time/residue: 0.8149 time to fit residues: 164.3146 Evaluate side-chains 199 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 920 LEU Chi-restraints excluded: chain L residue 945 ARG Chi-restraints excluded: chain L residue 985 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 20.0000 chunk 42 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 104 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 17 optimal weight: 0.0040 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN C 73 ASN D 49 HIS D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.114241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.085758 restraints weight = 23153.352| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.41 r_work: 0.3242 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14196 Z= 0.146 Angle : 0.652 11.841 20404 Z= 0.370 Chirality : 0.045 0.356 2305 Planarity : 0.005 0.070 1563 Dihedral : 31.562 171.987 4235 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.61 % Allowed : 20.73 % Favored : 76.66 % 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: 2.27 (0.28), residues: 900 helix: 2.22 (0.20), residues: 602 sheet: None (None), residues: 0 loop : 0.06 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 955 TYR 0.029 0.002 TYR H 40 PHE 0.012 0.001 PHE A 67 HIS 0.007 0.001 HIS K 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (14180) covalent geometry : angle 0.63679 / 0.37 (20386) hydrogen bonds : bond 0.04156 / 2.82 ( 831) hydrogen bonds : angle 3.04396 / 2.19 ( 2089) metal coordination : bond 0.00682 / 0.41 ( 16) metal coordination : angle 4.75483 / 2.61 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8169 (pp30) cc_final: 0.7848 (pp30) REVERT: B 85 ASP cc_start: 0.9169 (m-30) cc_final: 0.8921 (m-30) REVERT: C 95 LYS cc_start: 0.9180 (ptmm) cc_final: 0.8867 (ttpp) REVERT: D 57 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8702 (mmtm) REVERT: E 59 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.7736 (pm20) REVERT: E 81 ASP cc_start: 0.8164 (t0) cc_final: 0.7869 (t0) REVERT: H 108 LYS cc_start: 0.8697 (tmtt) cc_final: 0.8439 (ttmm) REVERT: K 938 PHE cc_start: 0.8236 (m-80) cc_final: 0.8034 (m-80) REVERT: K 954 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8367 (tp40) REVERT: L 985 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8413 (ttmm) REVERT: L 996 HIS cc_start: 0.8531 (t-90) cc_final: 0.8234 (t-90) outliers start: 20 outliers final: 15 residues processed: 189 average time/residue: 0.8134 time to fit residues: 163.9858 Evaluate side-chains 195 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 920 LEU Chi-restraints excluded: chain L residue 945 ARG Chi-restraints excluded: chain L residue 985 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 91 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN C 73 ASN D 49 HIS D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.114057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.085557 restraints weight = 23203.455| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.41 r_work: 0.3237 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14196 Z= 0.157 Angle : 0.658 14.331 20404 Z= 0.371 Chirality : 0.045 0.357 2305 Planarity : 0.005 0.070 1563 Dihedral : 31.550 171.725 4235 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.61 % Allowed : 20.86 % Favored : 76.53 % 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: 2.23 (0.28), residues: 900 helix: 2.19 (0.20), residues: 602 sheet: None (None), residues: 0 loop : 0.06 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 973 TYR 0.030 0.002 TYR H 40 PHE 0.012 0.002 PHE A 67 HIS 0.006 0.001 HIS K 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 (14180) covalent geometry : angle 0.64389 / 0.37 (20386) hydrogen bonds : bond 0.04235 / 2.87 ( 831) hydrogen bonds : angle 3.04664 / 2.19 ( 2089) metal coordination : bond 0.00766 / 0.47 ( 16) metal coordination : angle 4.59427 / 2.55 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5305.79 seconds wall clock time: 91 minutes 18.63 seconds (5478.63 seconds total)