Starting phenix.real_space_refine on Fri Mar 6 00:34:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kiz_0695/03_2026/6kiz_0695.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kiz_0695/03_2026/6kiz_0695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kiz_0695/03_2026/6kiz_0695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kiz_0695/03_2026/6kiz_0695.map" model { file = "/net/cci-nas-00/data/ceres_data/6kiz_0695/03_2026/6kiz_0695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kiz_0695/03_2026/6kiz_0695.cif" } resolution = 4.5 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 Anisotropic ADP refinement not supported. Converting 8536 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 290 5.49 5 S 60 5.16 5 C 11641 2.51 5 N 3616 2.21 5 O 4281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19889 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, '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: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 738 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} 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: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "N" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2759 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} Chain breaks: 1 Chain: "K" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1436 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2326 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain: "T" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1399 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 12, 'TRANS': 163} Chain breaks: 1 Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16043 SG CYS K3957 92.948 68.835 21.393 1.00999.99 S ATOM 16057 SG CYS K3959 92.662 72.122 17.786 1.00999.99 S Time building chain proxies: 4.65, per 1000 atoms: 0.23 Number of scatterers: 19889 At special positions: 0 Unit cell: (146.3, 157.3, 140.8, 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 1 29.99 S 60 16.00 P 290 15.00 O 4281 8.00 N 3616 7.00 C 11641 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 674.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K4002 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3959 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3957 " 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 30 sheets defined 33.3% alpha, 14.9% beta 140 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.645A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.757A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.920A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 77 removed outlier: 4.374A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 4.063A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 removed outlier: 3.622A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.041A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.892A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 53 through 81 removed outlier: 3.722A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.616A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.593A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.644A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.757A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.836A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.776A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.691A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 4.188A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.868A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.944A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.706A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.634A pdb=" N TYR H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 4.056A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA H 121 " --> pdb=" O CYS H 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 234 Processing helix chain 'K' and resid 3815 through 3831 removed outlier: 3.520A pdb=" N LYS K3824 " --> pdb=" O PHE K3820 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS K3825 " --> pdb=" O ARG K3821 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS K3828 " --> pdb=" O LYS K3824 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU K3829 " --> pdb=" O LYS K3825 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL K3831 " --> pdb=" O SER K3827 " (cutoff:3.500A) Processing helix chain 'K' and resid 3866 through 3879 removed outlier: 3.562A pdb=" N LYS K3870 " --> pdb=" O ILE K3866 " (cutoff:3.500A) Processing helix chain 'K' and resid 3900 through 3904 Processing helix chain 'T' and resid 499 through 503 removed outlier: 3.539A pdb=" N ASP T 502 " --> pdb=" O PRO T 499 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET T 503 " --> pdb=" O MET T 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 499 through 503' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.906A 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: 6.457A 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: 7.335A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.785A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.223A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'N' and resid 31 through 32 removed outlier: 4.632A pdb=" N LEU N 39 " --> pdb=" O TRP N 51 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP N 51 " --> pdb=" O LEU N 39 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL N 49 " --> pdb=" O VAL N 41 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASP N 52 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE N 58 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 80 through 82 Processing sheet with id=AB1, first strand: chain 'N' and resid 110 through 112 removed outlier: 6.227A pdb=" N LYS N 122 " --> pdb=" O HIS N 116 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 110 through 112 Processing sheet with id=AB3, first strand: chain 'N' and resid 165 through 169 Processing sheet with id=AB4, first strand: chain 'N' and resid 201 through 204 removed outlier: 6.527A pdb=" N ASN N 216 " --> pdb=" O LYS N 202 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE N 204 " --> pdb=" O LEU N 214 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU N 214 " --> pdb=" O ILE N 204 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR N 217 " --> pdb=" O ILE N 221 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE N 221 " --> pdb=" O THR N 217 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN N 243 " --> pdb=" O VAL N 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 254 through 259 removed outlier: 3.589A pdb=" N TYR N 277 " --> pdb=" O ALA N 268 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS N 288 " --> pdb=" O ILE N 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 300 through 303 Processing sheet with id=AB7, first strand: chain 'N' and resid 343 through 344 removed outlier: 6.505A pdb=" N VAL N 343 " --> pdb=" O VAL K3862 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ARG K3864 " --> pdb=" O VAL N 343 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 3833 through 3835 Processing sheet with id=AB9, first strand: chain 'K' and resid 3854 through 3857 removed outlier: 6.990A pdb=" N MET K3854 " --> pdb=" O ALA K3930 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA K3930 " --> pdb=" O MET K3854 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE K3856 " --> pdb=" O ILE K3928 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS K3925 " --> pdb=" O ILE K3918 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE K3918 " --> pdb=" O HIS K3925 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL K3927 " --> pdb=" O ARG K3916 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 36 through 40 removed outlier: 6.629A pdb=" N LEU R 329 " --> pdb=" O LYS R 38 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER R 318 " --> pdb=" O LYS R 328 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP R 330 " --> pdb=" O ILE R 316 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA R 308 " --> pdb=" O ALA R 317 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA R 319 " --> pdb=" O SER R 306 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER R 306 " --> pdb=" O ALA R 319 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 48 through 53 removed outlier: 6.769A pdb=" N SER R 63 " --> pdb=" O SER R 49 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL R 51 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA R 61 " --> pdb=" O VAL R 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 69 through 72 removed outlier: 5.870A pdb=" N ILE R 69 " --> pdb=" O THR R 82 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR R 82 " --> pdb=" O ILE R 69 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE R 71 " --> pdb=" O GLU R 80 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 90 through 95 removed outlier: 3.534A pdb=" N ASP R 92 " --> pdb=" O ALA R 105 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA R 94 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL R 103 " --> pdb=" O ALA R 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 132 through 137 removed outlier: 3.955A pdb=" N ASN R 136 " --> pdb=" O VAL R 145 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL R 145 " --> pdb=" O ASN R 136 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG R 154 " --> pdb=" O SER R 146 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 177 through 179 removed outlier: 3.778A pdb=" N HIS R 178 " --> pdb=" O VAL R 187 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG R 196 " --> pdb=" O SER R 188 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS R 195 " --> pdb=" O LEU R 209 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS R 207 " --> pdb=" O ILE R 197 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASP R 199 " --> pdb=" O CYS R 205 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N CYS R 205 " --> pdb=" O ASP R 199 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 217 through 222 removed outlier: 7.010A pdb=" N ALA R 232 " --> pdb=" O SER R 218 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL R 220 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU R 230 " --> pdb=" O VAL R 220 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE R 222 " --> pdb=" O TYR R 228 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR R 228 " --> pdb=" O PHE R 222 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 273 through 276 removed outlier: 3.712A pdb=" N LEU R 297 " --> pdb=" O VAL R 283 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'T' and resid 299 through 300 removed outlier: 3.562A pdb=" N VAL T 480 " --> pdb=" O VAL T 307 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR T 479 " --> pdb=" O ASP T 334 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP T 334 " --> pdb=" O THR T 479 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'T' and resid 315 through 316 removed outlier: 3.612A pdb=" N SER T 347 " --> pdb=" O PHE T 469 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA T 471 " --> pdb=" O GLY T 345 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY T 345 " --> pdb=" O ALA T 471 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER T 473 " --> pdb=" O ARG T 343 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'T' and resid 373 through 374 Processing sheet with id=AD3, first strand: chain 'T' and resid 447 through 448 removed outlier: 3.925A pdb=" N ILE T 447 " --> pdb=" O TYR T 460 " (cutoff:3.500A) 511 hydrogen bonds defined for protein. 1473 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 361 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 4.51 Time building geometry restraints manager: 2.31 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: 4279 1.33 - 1.45: 5959 1.45 - 1.57: 9973 1.57 - 1.69: 578 1.69 - 1.81: 87 Bond restraints: 20876 Sorted by residual: bond pdb=" C SER N 108 " pdb=" N PRO N 109 " ideal model delta sigma weight residual 1.335 1.360 -0.025 8.70e-03 1.32e+04 8.27e+00 bond pdb=" C2 SAH K4001 " pdb=" N3 SAH K4001 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.19e+00 bond pdb=" C8 SAH K4001 " pdb=" N7 SAH K4001 " ideal model delta sigma weight residual 1.299 1.350 -0.051 2.00e-02 2.50e+03 6.38e+00 bond pdb=" C2 SAH K4001 " pdb=" N1 SAH K4001 " ideal model delta sigma weight residual 1.330 1.378 -0.048 2.00e-02 2.50e+03 5.68e+00 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.08e+00 ... (remaining 20871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 28863 2.46 - 4.92: 546 4.92 - 7.38: 34 7.38 - 9.84: 11 9.84 - 12.30: 3 Bond angle restraints: 29457 Sorted by residual: angle pdb=" C GLN N 323 " pdb=" N ASN N 324 " pdb=" CA ASN N 324 " ideal model delta sigma weight residual 124.82 134.73 -9.91 1.78e+00 3.16e-01 3.10e+01 angle pdb=" N VAL G 27 " pdb=" CA VAL G 27 " pdb=" C VAL G 27 " ideal model delta sigma weight residual 112.96 108.43 4.53 1.00e+00 1.00e+00 2.05e+01 angle pdb=" C ASP B 24 " pdb=" N ASN B 25 " pdb=" CA ASN B 25 " ideal model delta sigma weight residual 124.82 132.47 -7.65 1.78e+00 3.16e-01 1.85e+01 angle pdb=" CG SAH K4001 " pdb=" SD SAH K4001 " pdb=" C5' SAH K4001 " ideal model delta sigma weight residual 101.77 89.47 12.30 3.00e+00 1.11e-01 1.68e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 120.20 125.50 -5.30 1.50e+00 4.44e-01 1.25e+01 ... (remaining 29452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.36: 10220 34.36 - 68.71: 1487 68.71 - 103.07: 39 103.07 - 137.42: 1 137.42 - 171.78: 3 Dihedral angle restraints: 11750 sinusoidal: 6646 harmonic: 5104 Sorted by residual: dihedral pdb=" CA GLY N 194 " pdb=" C GLY N 194 " pdb=" N THR N 195 " pdb=" CA THR N 195 " ideal model delta harmonic sigma weight residual -180.00 -138.83 -41.17 0 5.00e+00 4.00e-02 6.78e+01 dihedral pdb=" CA GLU N 16 " pdb=" C GLU N 16 " pdb=" N ALA N 17 " pdb=" CA ALA N 17 " ideal model delta harmonic sigma weight residual -180.00 -152.68 -27.32 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -153.93 -26.07 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 11747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2133 0.042 - 0.083: 829 0.083 - 0.125: 271 0.125 - 0.166: 66 0.166 - 0.208: 8 Chirality restraints: 3307 Sorted by residual: chirality pdb=" CB ILE T 482 " pdb=" CA ILE T 482 " pdb=" CG1 ILE T 482 " pdb=" CG2 ILE T 482 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1' SAH K4001 " pdb=" C2' SAH K4001 " pdb=" N9 SAH K4001 " pdb=" O4' SAH K4001 " both_signs ideal model delta sigma weight residual False 2.35 2.53 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA LEU A 65 " pdb=" N LEU A 65 " pdb=" C LEU A 65 " pdb=" CB LEU A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.24e-01 ... (remaining 3304 not shown) Planarity restraints: 2724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 121 " 0.036 2.00e-02 2.50e+03 1.54e-02 7.12e+00 pdb=" N9 DG I 121 " -0.034 2.00e-02 2.50e+03 pdb=" C8 DG I 121 " -0.009 2.00e-02 2.50e+03 pdb=" N7 DG I 121 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DG I 121 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DG I 121 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG I 121 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 121 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 121 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DG I 121 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 121 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 100 " -0.034 2.00e-02 2.50e+03 1.45e-02 6.28e+00 pdb=" N9 DG I 100 " 0.033 2.00e-02 2.50e+03 pdb=" C8 DG I 100 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 100 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DG I 100 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 100 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 100 " -0.012 2.00e-02 2.50e+03 pdb=" N1 DG I 100 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DG I 100 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 100 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 100 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DG I 100 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER N 108 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO N 109 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO N 109 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO N 109 " -0.034 5.00e-02 4.00e+02 ... (remaining 2721 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4053 2.78 - 3.31: 17022 3.31 - 3.84: 37097 3.84 - 4.37: 41621 4.37 - 4.90: 63305 Nonbonded interactions: 163098 Sorted by model distance: nonbonded pdb=" OG SER N 91 " pdb=" O GLN N 102 " model vdw 2.253 3.040 nonbonded pdb=" N CYS K3959 " pdb="ZN ZN K4002 " model vdw 2.254 2.310 nonbonded pdb=" OG1 THR N 217 " pdb=" OD1 ASP N 219 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.267 3.040 nonbonded pdb=" O2 DC I 95 " pdb=" N2 DG J 53 " model vdw 2.277 3.120 ... (remaining 163093 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' } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 120) selection = (chain 'H' and resid 28 through 120) } 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: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.420 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.009 0.673 20879 Z= 0.374 Angle : 0.857 12.302 29457 Z= 0.492 Chirality : 0.050 0.208 3307 Planarity : 0.006 0.060 2724 Dihedral : 23.337 171.777 8460 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.09 (0.17), residues: 1729 helix: -0.37 (0.19), residues: 547 sheet: -2.98 (0.33), residues: 194 loop : -2.98 (0.16), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 76 TYR 0.038 0.003 TYR B 88 PHE 0.027 0.002 PHE E 104 TRP 0.019 0.002 TRP T 366 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00740 (20876) covalent geometry : angle 0.85722 (29457) hydrogen bonds : bond 0.15878 ( 870) hydrogen bonds : angle 6.31043 ( 2195) metal coordination : bond 0.50002 ( 2) Misc. bond : bond 0.00067 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8711 (mt-10) REVERT: A 76 GLN cc_start: 0.9116 (tt0) cc_final: 0.8850 (pt0) REVERT: A 90 MET cc_start: 0.9171 (mmt) cc_final: 0.8871 (mmp) REVERT: A 94 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8787 (mm-30) REVERT: A 125 GLN cc_start: 0.9373 (mt0) cc_final: 0.9109 (mt0) REVERT: B 63 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8712 (mt-10) REVERT: B 84 MET cc_start: 0.8852 (mmm) cc_final: 0.8368 (mmm) REVERT: C 56 GLU cc_start: 0.9031 (tt0) cc_final: 0.8735 (tt0) REVERT: C 64 GLU cc_start: 0.9002 (tp30) cc_final: 0.8631 (tp30) REVERT: C 75 LYS cc_start: 0.9597 (mmtp) cc_final: 0.8919 (mmmm) REVERT: C 90 ASP cc_start: 0.8844 (t0) cc_final: 0.8400 (t0) REVERT: C 101 THR cc_start: 0.9061 (m) cc_final: 0.8565 (p) REVERT: C 110 ASN cc_start: 0.9180 (t0) cc_final: 0.8540 (m-40) REVERT: D 73 GLU cc_start: 0.9348 (tp30) cc_final: 0.9034 (tp30) REVERT: D 90 GLU cc_start: 0.8562 (mp0) cc_final: 0.8357 (mp0) REVERT: E 64 LYS cc_start: 0.9371 (mtmm) cc_final: 0.8970 (mtmm) REVERT: E 90 MET cc_start: 0.9179 (mmt) cc_final: 0.8750 (mmp) REVERT: E 107 THR cc_start: 0.9209 (m) cc_final: 0.9006 (p) REVERT: E 125 GLN cc_start: 0.9399 (mt0) cc_final: 0.8939 (mp10) REVERT: F 44 LYS cc_start: 0.9284 (tptm) cc_final: 0.9027 (tppp) REVERT: F 49 LEU cc_start: 0.9693 (mt) cc_final: 0.9440 (mm) REVERT: F 59 LYS cc_start: 0.9048 (tttp) cc_final: 0.8705 (ttpp) REVERT: F 63 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8632 (mt-10) REVERT: F 84 MET cc_start: 0.8918 (mmm) cc_final: 0.8345 (tpp) REVERT: G 56 GLU cc_start: 0.9086 (tt0) cc_final: 0.8702 (tt0) REVERT: G 61 GLU cc_start: 0.9240 (tp30) cc_final: 0.8916 (tp30) REVERT: G 90 ASP cc_start: 0.8832 (t0) cc_final: 0.8481 (t0) REVERT: G 92 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8109 (tt0) REVERT: G 101 THR cc_start: 0.8787 (m) cc_final: 0.8365 (p) REVERT: H 80 TYR cc_start: 0.8635 (m-10) cc_final: 0.7935 (m-10) REVERT: H 83 ARG cc_start: 0.8505 (mtp-110) cc_final: 0.8165 (mtp-110) REVERT: N 128 MET cc_start: 0.9073 (tpt) cc_final: 0.8605 (tpt) REVERT: N 197 ASN cc_start: 0.8222 (t0) cc_final: 0.7981 (t0) REVERT: N 243 GLN cc_start: 0.9476 (tp-100) cc_final: 0.8989 (tm-30) REVERT: N 256 LYS cc_start: 0.9299 (tptm) cc_final: 0.9080 (mmmt) REVERT: K 3884 MET cc_start: 0.5800 (mtt) cc_final: 0.5553 (mtt) REVERT: K 3927 VAL cc_start: 0.2113 (t) cc_final: 0.1756 (m) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.2375 time to fit residues: 103.8698 Evaluate side-chains 186 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS C 31 HIS C 104 GLN E 39 HIS F 25 ASN G 31 HIS ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3861 ASN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 320 HIS T 354 GLN T 381 HIS ** T 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.062047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.032801 restraints weight = 140636.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.034012 restraints weight = 68557.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.034751 restraints weight = 43401.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.035190 restraints weight = 32574.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.035430 restraints weight = 27359.747| |-----------------------------------------------------------------------------| r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20879 Z= 0.197 Angle : 0.617 6.958 29457 Z= 0.358 Chirality : 0.041 0.198 3307 Planarity : 0.005 0.041 2724 Dihedral : 28.312 171.666 5095 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.88 (0.19), residues: 1729 helix: 1.54 (0.22), residues: 552 sheet: -2.77 (0.33), residues: 213 loop : -2.73 (0.17), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 367 TYR 0.023 0.002 TYR K3874 PHE 0.011 0.001 PHE T 464 TRP 0.017 0.001 TRP R 95 HIS 0.011 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00425 (20876) covalent geometry : angle 0.61730 (29457) hydrogen bonds : bond 0.06401 ( 870) hydrogen bonds : angle 4.65379 ( 2195) metal coordination : bond 0.01987 ( 2) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8646 (mt-10) REVERT: A 64 LYS cc_start: 0.9366 (mtmm) cc_final: 0.8991 (mttp) REVERT: A 97 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8129 (mt-10) REVERT: B 25 ASN cc_start: 0.8807 (m110) cc_final: 0.8453 (m110) REVERT: B 68 ASP cc_start: 0.8706 (m-30) cc_final: 0.8492 (m-30) REVERT: B 84 MET cc_start: 0.8523 (mmm) cc_final: 0.8137 (mmm) REVERT: C 64 GLU cc_start: 0.8887 (tp30) cc_final: 0.8646 (tp30) REVERT: C 68 ASN cc_start: 0.8723 (m-40) cc_final: 0.8490 (m-40) REVERT: C 75 LYS cc_start: 0.9639 (mmtp) cc_final: 0.9034 (mmmm) REVERT: C 110 ASN cc_start: 0.9181 (t0) cc_final: 0.8596 (m-40) REVERT: D 27 ARG cc_start: 0.6916 (tmt170) cc_final: 0.6678 (tmt170) REVERT: D 90 GLU cc_start: 0.8645 (mp0) cc_final: 0.8386 (mp0) REVERT: E 64 LYS cc_start: 0.9249 (mtmm) cc_final: 0.9037 (mtmm) REVERT: E 89 VAL cc_start: 0.9310 (t) cc_final: 0.9062 (p) REVERT: E 90 MET cc_start: 0.9034 (mmt) cc_final: 0.8740 (mmm) REVERT: E 125 GLN cc_start: 0.9272 (mt0) cc_final: 0.9020 (mp10) REVERT: F 49 LEU cc_start: 0.9537 (mt) cc_final: 0.8396 (mm) REVERT: F 52 GLU cc_start: 0.8938 (pm20) cc_final: 0.8506 (pm20) REVERT: F 84 MET cc_start: 0.8744 (mmm) cc_final: 0.8123 (tpp) REVERT: G 59 THR cc_start: 0.9525 (m) cc_final: 0.9308 (p) REVERT: G 73 ASN cc_start: 0.9434 (t0) cc_final: 0.9188 (t0) REVERT: G 75 LYS cc_start: 0.9540 (mmtt) cc_final: 0.9201 (mmmm) REVERT: G 90 ASP cc_start: 0.9006 (t0) cc_final: 0.8531 (t0) REVERT: G 93 LEU cc_start: 0.9551 (mt) cc_final: 0.9317 (mt) REVERT: G 101 THR cc_start: 0.8803 (m) cc_final: 0.8575 (p) REVERT: N 115 TYR cc_start: 0.7793 (m-80) cc_final: 0.6884 (m-80) REVERT: N 167 TYR cc_start: 0.9037 (m-10) cc_final: 0.8548 (m-80) REVERT: N 246 GLN cc_start: 0.8758 (pm20) cc_final: 0.8517 (pm20) REVERT: K 3868 THR cc_start: 0.5105 (p) cc_final: 0.4476 (p) REVERT: T 336 MET cc_start: 0.5291 (ttm) cc_final: 0.4539 (tpp) REVERT: T 503 MET cc_start: 0.5445 (mmm) cc_final: 0.5227 (tpp) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1721 time to fit residues: 60.2645 Evaluate side-chains 183 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 87 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 169 optimal weight: 50.0000 chunk 129 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 194 optimal weight: 50.0000 chunk 196 optimal weight: 50.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 46 HIS F 25 ASN N 274 HIS ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 456 GLN ** 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 = 0.3455 r_free = 0.3455 target = 0.060854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.031863 restraints weight = 142820.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.033018 restraints weight = 71030.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.033756 restraints weight = 45241.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.034139 restraints weight = 33838.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.034445 restraints weight = 28462.247| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 20879 Z= 0.293 Angle : 0.662 9.032 29457 Z= 0.377 Chirality : 0.042 0.198 3307 Planarity : 0.004 0.042 2724 Dihedral : 28.082 166.961 5095 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.07 % Allowed : 2.00 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.61 (0.20), residues: 1729 helix: 1.83 (0.22), residues: 553 sheet: -2.78 (0.31), residues: 226 loop : -2.55 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG T 367 TYR 0.017 0.002 TYR T 364 PHE 0.010 0.002 PHE T 464 TRP 0.009 0.001 TRP N 279 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00649 (20876) covalent geometry : angle 0.66181 (29457) hydrogen bonds : bond 0.07745 ( 870) hydrogen bonds : angle 4.65621 ( 2195) metal coordination : bond 0.00158 ( 2) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8741 (mt-10) REVERT: A 120 MET cc_start: 0.8787 (mtt) cc_final: 0.7993 (mtm) REVERT: B 25 ASN cc_start: 0.8686 (m110) cc_final: 0.8359 (m110) REVERT: B 84 MET cc_start: 0.8529 (mmm) cc_final: 0.8091 (mmm) REVERT: C 64 GLU cc_start: 0.8874 (tp30) cc_final: 0.8590 (tp30) REVERT: C 68 ASN cc_start: 0.8777 (m-40) cc_final: 0.8530 (m-40) REVERT: C 75 LYS cc_start: 0.9674 (mmtp) cc_final: 0.9061 (mmmm) REVERT: C 110 ASN cc_start: 0.9060 (t0) cc_final: 0.8629 (m-40) REVERT: D 27 ARG cc_start: 0.6843 (tmt170) cc_final: 0.6602 (tmt170) REVERT: D 90 GLU cc_start: 0.8530 (mp0) cc_final: 0.8141 (mp0) REVERT: E 89 VAL cc_start: 0.9476 (t) cc_final: 0.9229 (p) REVERT: E 90 MET cc_start: 0.8926 (mmt) cc_final: 0.8703 (mmm) REVERT: E 106 ASP cc_start: 0.8937 (m-30) cc_final: 0.8715 (m-30) REVERT: E 125 GLN cc_start: 0.9290 (mt0) cc_final: 0.9089 (mt0) REVERT: F 49 LEU cc_start: 0.9353 (mt) cc_final: 0.9109 (mm) REVERT: F 84 MET cc_start: 0.8774 (mmm) cc_final: 0.8396 (tpp) REVERT: G 90 ASP cc_start: 0.9155 (t0) cc_final: 0.8841 (t0) REVERT: G 92 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8092 (tp30) REVERT: H 102 GLU cc_start: 0.8333 (pp20) cc_final: 0.8030 (pp20) REVERT: N 167 TYR cc_start: 0.9092 (m-10) cc_final: 0.8612 (m-80) REVERT: T 315 MET cc_start: -0.0517 (mmp) cc_final: -0.1497 (tpp) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.1749 time to fit residues: 52.9479 Evaluate side-chains 158 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 87 optimal weight: 8.9990 chunk 196 optimal weight: 50.0000 chunk 96 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 159 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 chunk 150 optimal weight: 40.0000 chunk 35 optimal weight: 3.9990 chunk 176 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 46 HIS ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 456 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.061382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.032335 restraints weight = 142089.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.033512 restraints weight = 69525.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.034253 restraints weight = 43842.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.034669 restraints weight = 32772.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.034956 restraints weight = 27574.756| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20879 Z= 0.234 Angle : 0.612 8.243 29457 Z= 0.351 Chirality : 0.040 0.147 3307 Planarity : 0.004 0.042 2724 Dihedral : 27.955 168.855 5095 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.20), residues: 1729 helix: 1.99 (0.21), residues: 553 sheet: -2.48 (0.32), residues: 233 loop : -2.48 (0.18), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 367 TYR 0.016 0.002 TYR K3935 PHE 0.016 0.001 PHE K3844 TRP 0.011 0.001 TRP T 327 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00516 (20876) covalent geometry : angle 0.61162 (29457) hydrogen bonds : bond 0.06464 ( 870) hydrogen bonds : angle 4.35480 ( 2195) metal coordination : bond 0.00063 ( 2) Misc. bond : bond 0.00064 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.9227 (t) cc_final: 0.9015 (t) REVERT: A 50 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8702 (mt-10) REVERT: B 25 ASN cc_start: 0.8657 (m110) cc_final: 0.8321 (m110) REVERT: B 63 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8545 (mt-10) REVERT: B 84 MET cc_start: 0.8535 (mmm) cc_final: 0.8094 (mmm) REVERT: C 62 ILE cc_start: 0.9488 (tp) cc_final: 0.9281 (tp) REVERT: C 110 ASN cc_start: 0.9075 (t0) cc_final: 0.8637 (m-40) REVERT: D 90 GLU cc_start: 0.8561 (mp0) cc_final: 0.8142 (mp0) REVERT: E 73 GLU cc_start: 0.8640 (pt0) cc_final: 0.8183 (pt0) REVERT: E 89 VAL cc_start: 0.9460 (t) cc_final: 0.9195 (p) REVERT: E 90 MET cc_start: 0.8880 (mmt) cc_final: 0.8659 (mmm) REVERT: E 125 GLN cc_start: 0.9309 (mt0) cc_final: 0.9093 (mp10) REVERT: F 84 MET cc_start: 0.8698 (mmm) cc_final: 0.8020 (tpp) REVERT: G 56 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8490 (mm-30) REVERT: G 61 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8384 (tm-30) REVERT: G 75 LYS cc_start: 0.9583 (mmtt) cc_final: 0.9274 (mmmm) REVERT: G 90 ASP cc_start: 0.9158 (t0) cc_final: 0.8701 (t70) REVERT: G 93 LEU cc_start: 0.9593 (mm) cc_final: 0.9208 (mm) REVERT: N 167 TYR cc_start: 0.9155 (m-10) cc_final: 0.8683 (m-80) REVERT: K 3816 MET cc_start: 0.4986 (ttt) cc_final: 0.4289 (mtt) REVERT: T 315 MET cc_start: 0.0007 (mmp) cc_final: -0.0681 (tpp) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1719 time to fit residues: 51.9412 Evaluate side-chains 166 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 124 optimal weight: 30.0000 chunk 67 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 161 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 46 HIS G 73 ASN N 79 HIS ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 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 = 0.3455 r_free = 0.3455 target = 0.061037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.032048 restraints weight = 141582.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.033271 restraints weight = 69595.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.034014 restraints weight = 43969.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.034457 restraints weight = 32946.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.034708 restraints weight = 27577.299| |-----------------------------------------------------------------------------| r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 20879 Z= 0.255 Angle : 0.623 8.453 29457 Z= 0.356 Chirality : 0.041 0.178 3307 Planarity : 0.004 0.044 2724 Dihedral : 27.868 169.104 5095 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.48 (0.20), residues: 1729 helix: 1.90 (0.21), residues: 554 sheet: -2.73 (0.30), residues: 257 loop : -2.40 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K3765 TYR 0.015 0.002 TYR T 364 PHE 0.009 0.001 PHE N 159 TRP 0.009 0.001 TRP T 327 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00564 (20876) covalent geometry : angle 0.62265 (29457) hydrogen bonds : bond 0.06929 ( 870) hydrogen bonds : angle 4.28238 ( 2195) metal coordination : bond 0.00074 ( 2) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.9241 (t) cc_final: 0.9017 (t) REVERT: A 50 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8733 (mt-10) REVERT: A 97 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8471 (mt-10) REVERT: B 25 ASN cc_start: 0.8717 (m110) cc_final: 0.8391 (m110) REVERT: B 84 MET cc_start: 0.8482 (mmm) cc_final: 0.8133 (mmm) REVERT: C 62 ILE cc_start: 0.9466 (tp) cc_final: 0.9257 (tp) REVERT: C 64 GLU cc_start: 0.8946 (tp30) cc_final: 0.8685 (tp30) REVERT: D 68 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8674 (tm-30) REVERT: D 90 GLU cc_start: 0.8688 (mp0) cc_final: 0.8483 (mp0) REVERT: E 73 GLU cc_start: 0.8634 (pt0) cc_final: 0.8205 (pt0) REVERT: E 89 VAL cc_start: 0.9457 (t) cc_final: 0.9205 (p) REVERT: E 90 MET cc_start: 0.8868 (mmt) cc_final: 0.8604 (mmm) REVERT: E 125 GLN cc_start: 0.9310 (mt0) cc_final: 0.9100 (mp10) REVERT: F 84 MET cc_start: 0.8816 (mmm) cc_final: 0.8235 (tpp) REVERT: G 61 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8468 (tm-30) REVERT: G 75 LYS cc_start: 0.9560 (mmtt) cc_final: 0.9174 (mmmm) REVERT: G 90 ASP cc_start: 0.9143 (t0) cc_final: 0.8865 (t0) REVERT: G 92 GLU cc_start: 0.8156 (tp30) cc_final: 0.7660 (mm-30) REVERT: N 115 TYR cc_start: 0.7671 (m-80) cc_final: 0.6809 (m-80) REVERT: N 167 TYR cc_start: 0.9166 (m-10) cc_final: 0.8722 (m-80) REVERT: K 3816 MET cc_start: 0.4879 (ttt) cc_final: 0.4105 (mtt) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1818 time to fit residues: 50.4382 Evaluate side-chains 153 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 139 optimal weight: 40.0000 chunk 113 optimal weight: 7.9990 chunk 158 optimal weight: 50.0000 chunk 197 optimal weight: 40.0000 chunk 33 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 100 optimal weight: 0.0670 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 354 GLN T 375 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.061753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.032850 restraints weight = 139907.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.034043 restraints weight = 68263.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.034803 restraints weight = 43235.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.035245 restraints weight = 32215.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.035482 restraints weight = 26918.659| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20879 Z= 0.191 Angle : 0.574 7.627 29457 Z= 0.331 Chirality : 0.039 0.142 3307 Planarity : 0.004 0.046 2724 Dihedral : 27.766 171.487 5095 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.22 (0.20), residues: 1729 helix: 2.13 (0.21), residues: 561 sheet: -2.55 (0.31), residues: 252 loop : -2.32 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K3765 TYR 0.019 0.001 TYR K3935 PHE 0.008 0.001 PHE R 137 TRP 0.018 0.001 TRP R 241 HIS 0.006 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00417 (20876) covalent geometry : angle 0.57443 (29457) hydrogen bonds : bond 0.05623 ( 870) hydrogen bonds : angle 3.95512 ( 2195) metal coordination : bond 0.00068 ( 2) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.9192 (t) cc_final: 0.8962 (t) REVERT: A 50 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8637 (mt-10) REVERT: A 97 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8317 (mt-10) REVERT: A 120 MET cc_start: 0.8887 (mtt) cc_final: 0.8583 (mtp) REVERT: B 25 ASN cc_start: 0.8555 (m110) cc_final: 0.8191 (m110) REVERT: B 63 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8514 (mt-10) REVERT: B 84 MET cc_start: 0.8491 (mmm) cc_final: 0.8127 (mmm) REVERT: C 62 ILE cc_start: 0.9467 (tp) cc_final: 0.9249 (tp) REVERT: C 64 GLU cc_start: 0.8922 (tp30) cc_final: 0.8676 (tp30) REVERT: D 90 GLU cc_start: 0.8707 (mp0) cc_final: 0.8483 (mp0) REVERT: E 73 GLU cc_start: 0.8680 (pt0) cc_final: 0.8188 (pt0) REVERT: E 89 VAL cc_start: 0.9436 (t) cc_final: 0.9175 (p) REVERT: E 90 MET cc_start: 0.8848 (mmt) cc_final: 0.8593 (mmm) REVERT: E 125 GLN cc_start: 0.9308 (mt0) cc_final: 0.9108 (mp10) REVERT: F 53 GLU cc_start: 0.8931 (mp0) cc_final: 0.8471 (mp0) REVERT: F 84 MET cc_start: 0.8746 (mmm) cc_final: 0.8507 (tpp) REVERT: G 61 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8491 (tm-30) REVERT: G 75 LYS cc_start: 0.9504 (mmtt) cc_final: 0.9212 (mmmm) REVERT: G 90 ASP cc_start: 0.9105 (t0) cc_final: 0.8899 (t0) REVERT: G 92 GLU cc_start: 0.8070 (tp30) cc_final: 0.7670 (mm-30) REVERT: N 115 TYR cc_start: 0.7638 (m-80) cc_final: 0.6786 (m-80) REVERT: N 167 TYR cc_start: 0.9175 (m-10) cc_final: 0.8844 (m-80) REVERT: K 3816 MET cc_start: 0.4919 (ttt) cc_final: 0.4233 (mtt) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1776 time to fit residues: 51.5533 Evaluate side-chains 159 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 71 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 152 optimal weight: 50.0000 chunk 66 optimal weight: 2.9990 chunk 147 optimal weight: 20.0000 chunk 156 optimal weight: 40.0000 chunk 155 optimal weight: 50.0000 chunk 194 optimal weight: 40.0000 chunk 73 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 46 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.060874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.031993 restraints weight = 142425.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.033142 restraints weight = 70263.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.033878 restraints weight = 44724.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.034300 restraints weight = 33457.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.034548 restraints weight = 28101.571| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 20879 Z= 0.262 Angle : 0.623 7.505 29457 Z= 0.355 Chirality : 0.041 0.145 3307 Planarity : 0.004 0.068 2724 Dihedral : 27.765 169.792 5095 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.27 (0.20), residues: 1729 helix: 1.98 (0.21), residues: 562 sheet: -2.43 (0.31), residues: 257 loop : -2.31 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 181 TYR 0.013 0.002 TYR N 13 PHE 0.009 0.001 PHE N 159 TRP 0.017 0.001 TRP R 241 HIS 0.009 0.002 HIS R 128 Details of bonding type rmsd covalent geometry : bond 0.00580 (20876) covalent geometry : angle 0.62294 (29457) hydrogen bonds : bond 0.06875 ( 870) hydrogen bonds : angle 4.14128 ( 2195) metal coordination : bond 0.00049 ( 2) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.9244 (t) cc_final: 0.9028 (t) REVERT: A 50 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8730 (mt-10) REVERT: A 97 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8332 (mt-10) REVERT: A 120 MET cc_start: 0.8998 (mtt) cc_final: 0.8618 (mtp) REVERT: B 25 ASN cc_start: 0.8536 (m110) cc_final: 0.8241 (m110) REVERT: B 59 LYS cc_start: 0.9398 (ttpp) cc_final: 0.9195 (ttpp) REVERT: B 63 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8455 (mt-10) REVERT: B 68 ASP cc_start: 0.8819 (m-30) cc_final: 0.8612 (m-30) REVERT: B 84 MET cc_start: 0.8491 (mmm) cc_final: 0.8076 (mmm) REVERT: C 62 ILE cc_start: 0.9470 (tp) cc_final: 0.9239 (tp) REVERT: C 64 GLU cc_start: 0.8911 (tp30) cc_final: 0.8606 (tp30) REVERT: D 68 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8631 (tm-30) REVERT: E 50 GLU cc_start: 0.9116 (tt0) cc_final: 0.8852 (tm-30) REVERT: E 51 ILE cc_start: 0.9219 (mt) cc_final: 0.8961 (mt) REVERT: E 79 LYS cc_start: 0.9124 (tptp) cc_final: 0.8904 (tptp) REVERT: E 81 ASP cc_start: 0.8240 (p0) cc_final: 0.7986 (p0) REVERT: E 89 VAL cc_start: 0.9470 (t) cc_final: 0.9215 (p) REVERT: E 90 MET cc_start: 0.8842 (mmt) cc_final: 0.8626 (mmm) REVERT: E 125 GLN cc_start: 0.9314 (mt0) cc_final: 0.9086 (mp10) REVERT: F 84 MET cc_start: 0.8711 (mmm) cc_final: 0.7744 (tpp) REVERT: G 61 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8490 (tm-30) REVERT: G 75 LYS cc_start: 0.9490 (mmtt) cc_final: 0.9218 (mmmm) REVERT: G 92 GLU cc_start: 0.8130 (tp30) cc_final: 0.7385 (mm-30) REVERT: N 115 TYR cc_start: 0.7589 (m-80) cc_final: 0.6765 (m-80) REVERT: N 167 TYR cc_start: 0.9199 (m-10) cc_final: 0.8876 (m-80) REVERT: K 3816 MET cc_start: 0.4978 (ttt) cc_final: 0.4299 (mtt) REVERT: K 3931 MET cc_start: 0.6649 (mtt) cc_final: 0.6389 (mtp) REVERT: T 315 MET cc_start: -0.0729 (mmp) cc_final: -0.1223 (tpp) REVERT: T 500 MET cc_start: 0.4303 (mtt) cc_final: 0.3947 (mtt) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1733 time to fit residues: 49.9108 Evaluate side-chains 157 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 8.9990 chunk 112 optimal weight: 40.0000 chunk 30 optimal weight: 0.9980 chunk 145 optimal weight: 40.0000 chunk 87 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 194 optimal weight: 40.0000 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.061695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.032824 restraints weight = 141661.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.033942 restraints weight = 69108.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.034680 restraints weight = 43644.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.035075 restraints weight = 32598.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.035403 restraints weight = 27416.381| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20879 Z= 0.190 Angle : 0.584 8.569 29457 Z= 0.335 Chirality : 0.039 0.145 3307 Planarity : 0.004 0.107 2724 Dihedral : 27.709 171.333 5095 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.12 (0.20), residues: 1729 helix: 2.19 (0.21), residues: 562 sheet: -2.34 (0.32), residues: 257 loop : -2.28 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 181 TYR 0.021 0.001 TYR H 80 PHE 0.007 0.001 PHE N 159 TRP 0.018 0.001 TRP R 241 HIS 0.008 0.001 HIS R 128 Details of bonding type rmsd covalent geometry : bond 0.00417 (20876) covalent geometry : angle 0.58369 (29457) hydrogen bonds : bond 0.05610 ( 870) hydrogen bonds : angle 3.85486 ( 2195) metal coordination : bond 0.00055 ( 2) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.9150 (t) cc_final: 0.8946 (t) REVERT: A 50 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8670 (mt-10) REVERT: A 97 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8293 (mt-10) REVERT: A 120 MET cc_start: 0.8850 (mtt) cc_final: 0.8483 (mtp) REVERT: B 25 ASN cc_start: 0.8460 (m110) cc_final: 0.8167 (m110) REVERT: B 63 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8419 (mt-10) REVERT: B 68 ASP cc_start: 0.8767 (m-30) cc_final: 0.8555 (m-30) REVERT: B 84 MET cc_start: 0.8448 (mmm) cc_final: 0.8092 (mmm) REVERT: C 64 GLU cc_start: 0.8914 (tp30) cc_final: 0.8650 (tp30) REVERT: D 27 ARG cc_start: 0.6556 (tmt170) cc_final: 0.4748 (ptm160) REVERT: D 90 GLU cc_start: 0.8688 (mp0) cc_final: 0.8466 (mp0) REVERT: E 79 LYS cc_start: 0.9113 (tptp) cc_final: 0.8813 (tptp) REVERT: E 81 ASP cc_start: 0.8142 (p0) cc_final: 0.7886 (p0) REVERT: E 89 VAL cc_start: 0.9453 (t) cc_final: 0.9188 (p) REVERT: E 90 MET cc_start: 0.8828 (mmt) cc_final: 0.8624 (mmm) REVERT: E 125 GLN cc_start: 0.9309 (mt0) cc_final: 0.9088 (mp10) REVERT: F 53 GLU cc_start: 0.8899 (mp0) cc_final: 0.8621 (mp0) REVERT: F 84 MET cc_start: 0.8626 (mmm) cc_final: 0.8064 (tpp) REVERT: G 61 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8484 (tm-30) REVERT: G 75 LYS cc_start: 0.9437 (mmtt) cc_final: 0.9154 (mmmm) REVERT: G 92 GLU cc_start: 0.8083 (tp30) cc_final: 0.7690 (mm-30) REVERT: N 167 TYR cc_start: 0.9214 (m-10) cc_final: 0.8959 (m-80) REVERT: N 276 LEU cc_start: 0.9154 (mp) cc_final: 0.8664 (mt) REVERT: K 3816 MET cc_start: 0.4977 (ttt) cc_final: 0.4340 (mtt) REVERT: T 315 MET cc_start: -0.0082 (mmp) cc_final: -0.0923 (tpp) REVERT: T 500 MET cc_start: 0.4900 (mtt) cc_final: 0.4472 (mtt) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1659 time to fit residues: 47.2092 Evaluate side-chains 156 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 141 optimal weight: 30.0000 chunk 173 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 152 optimal weight: 50.0000 chunk 66 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 46 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3906 ASN R 86 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.060329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.031509 restraints weight = 142979.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.032619 restraints weight = 70621.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.033335 restraints weight = 45041.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.033768 restraints weight = 33878.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.033984 restraints weight = 28511.581| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 20879 Z= 0.315 Angle : 0.669 9.158 29457 Z= 0.378 Chirality : 0.042 0.147 3307 Planarity : 0.004 0.053 2724 Dihedral : 27.799 168.184 5095 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.07 % Allowed : 0.33 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.31 (0.20), residues: 1729 helix: 1.80 (0.21), residues: 562 sheet: -2.29 (0.33), residues: 251 loop : -2.29 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 181 TYR 0.017 0.002 TYR R 228 PHE 0.010 0.001 PHE N 159 TRP 0.024 0.002 TRP R 241 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00699 (20876) covalent geometry : angle 0.66913 (29457) hydrogen bonds : bond 0.07736 ( 870) hydrogen bonds : angle 4.34282 ( 2195) metal coordination : bond 0.00042 ( 2) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.9276 (t) cc_final: 0.9064 (t) REVERT: A 50 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8713 (mt-10) REVERT: A 97 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8349 (mt-10) REVERT: A 120 MET cc_start: 0.8974 (mtt) cc_final: 0.8554 (mtp) REVERT: B 25 ASN cc_start: 0.8550 (m110) cc_final: 0.8274 (m110) REVERT: B 59 LYS cc_start: 0.9403 (ttpp) cc_final: 0.9170 (ttpp) REVERT: B 63 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8410 (mt-10) REVERT: B 84 MET cc_start: 0.8504 (mmm) cc_final: 0.8117 (mmm) REVERT: C 64 GLU cc_start: 0.8876 (tp30) cc_final: 0.8644 (tp30) REVERT: D 27 ARG cc_start: 0.6614 (tmt170) cc_final: 0.4774 (ptm160) REVERT: E 73 GLU cc_start: 0.8642 (pt0) cc_final: 0.8298 (pt0) REVERT: E 79 LYS cc_start: 0.9152 (tptp) cc_final: 0.8857 (tptp) REVERT: E 81 ASP cc_start: 0.8297 (p0) cc_final: 0.7990 (p0) REVERT: E 89 VAL cc_start: 0.9476 (t) cc_final: 0.9231 (p) REVERT: E 125 GLN cc_start: 0.9321 (mt0) cc_final: 0.9097 (mp10) REVERT: F 84 MET cc_start: 0.8703 (mmm) cc_final: 0.8182 (tpp) REVERT: G 61 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8458 (tm-30) REVERT: G 75 LYS cc_start: 0.9543 (mmtt) cc_final: 0.9301 (mmmt) REVERT: G 92 GLU cc_start: 0.8149 (tp30) cc_final: 0.7764 (mm-30) REVERT: N 167 TYR cc_start: 0.9231 (m-10) cc_final: 0.8940 (m-80) REVERT: N 276 LEU cc_start: 0.9251 (mp) cc_final: 0.8809 (mt) REVERT: K 3816 MET cc_start: 0.4858 (ttt) cc_final: 0.4125 (mtt) REVERT: K 3941 THR cc_start: 0.2896 (p) cc_final: 0.2467 (p) REVERT: T 500 MET cc_start: 0.5275 (mtt) cc_final: 0.4744 (mtt) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1707 time to fit residues: 45.9937 Evaluate side-chains 151 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 131 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 145 optimal weight: 50.0000 chunk 71 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3907 HIS R 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.062399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.033672 restraints weight = 137913.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.034849 restraints weight = 67615.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.035593 restraints weight = 42918.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.036012 restraints weight = 32063.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.036295 restraints weight = 27014.367| |-----------------------------------------------------------------------------| r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20879 Z= 0.155 Angle : 0.586 11.545 29457 Z= 0.332 Chirality : 0.039 0.148 3307 Planarity : 0.004 0.046 2724 Dihedral : 27.617 173.525 5095 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.21), residues: 1729 helix: 2.23 (0.22), residues: 562 sheet: -2.03 (0.33), residues: 250 loop : -2.24 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 76 TYR 0.019 0.001 TYR D 80 PHE 0.009 0.001 PHE K3820 TRP 0.023 0.001 TRP R 241 HIS 0.013 0.001 HIS K3822 Details of bonding type rmsd covalent geometry : bond 0.00338 (20876) covalent geometry : angle 0.58574 (29457) hydrogen bonds : bond 0.04887 ( 870) hydrogen bonds : angle 3.68672 ( 2195) metal coordination : bond 0.00144 ( 2) Misc. bond : bond 0.00076 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.9122 (t) cc_final: 0.8895 (t) REVERT: A 50 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8599 (mt-10) REVERT: A 97 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8416 (mt-10) REVERT: A 120 MET cc_start: 0.8799 (mtt) cc_final: 0.8009 (mtm) REVERT: B 25 ASN cc_start: 0.8389 (m110) cc_final: 0.8157 (m110) REVERT: B 59 LYS cc_start: 0.9372 (ttpp) cc_final: 0.9138 (ttpp) REVERT: B 63 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8370 (mt-10) REVERT: B 84 MET cc_start: 0.8433 (mmm) cc_final: 0.8168 (mmm) REVERT: C 64 GLU cc_start: 0.8838 (tp30) cc_final: 0.8573 (tp30) REVERT: D 27 ARG cc_start: 0.6452 (tmt170) cc_final: 0.4725 (ptm160) REVERT: D 90 GLU cc_start: 0.8729 (mp0) cc_final: 0.8303 (mp0) REVERT: E 73 GLU cc_start: 0.8420 (pt0) cc_final: 0.8148 (pt0) REVERT: E 106 ASP cc_start: 0.8794 (m-30) cc_final: 0.8504 (m-30) REVERT: E 125 GLN cc_start: 0.9277 (mt0) cc_final: 0.9033 (mp10) REVERT: G 61 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8487 (tm-30) REVERT: G 75 LYS cc_start: 0.9518 (mmtt) cc_final: 0.9199 (mmmm) REVERT: G 90 ASP cc_start: 0.9085 (t0) cc_final: 0.8875 (t0) REVERT: G 92 GLU cc_start: 0.7976 (tp30) cc_final: 0.7589 (mm-30) REVERT: N 167 TYR cc_start: 0.9251 (m-10) cc_final: 0.8934 (m-80) REVERT: N 276 LEU cc_start: 0.9212 (mp) cc_final: 0.8778 (mt) REVERT: K 3816 MET cc_start: 0.4894 (ttt) cc_final: 0.4063 (mtt) REVERT: T 315 MET cc_start: -0.0611 (mmp) cc_final: -0.1216 (tpp) REVERT: T 500 MET cc_start: 0.4758 (mtt) cc_final: 0.4222 (mtt) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1625 time to fit residues: 46.7782 Evaluate side-chains 150 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 89 optimal weight: 8.9990 chunk 195 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 174 optimal weight: 30.0000 chunk 134 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.062861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.034071 restraints weight = 139230.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.035298 restraints weight = 68684.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.036029 restraints weight = 43597.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.036520 restraints weight = 32693.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.036779 restraints weight = 27462.251| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20879 Z= 0.140 Angle : 0.573 11.923 29457 Z= 0.325 Chirality : 0.039 0.199 3307 Planarity : 0.004 0.044 2724 Dihedral : 27.501 174.726 5095 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.88 (0.21), residues: 1729 helix: 2.34 (0.22), residues: 564 sheet: -1.90 (0.33), residues: 252 loop : -2.23 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 76 TYR 0.015 0.001 TYR H 80 PHE 0.009 0.001 PHE K3844 TRP 0.023 0.001 TRP R 241 HIS 0.007 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00303 (20876) covalent geometry : angle 0.57327 (29457) hydrogen bonds : bond 0.04519 ( 870) hydrogen bonds : angle 3.57289 ( 2195) metal coordination : bond 0.00026 ( 2) Misc. bond : bond 0.00034 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4850.84 seconds wall clock time: 83 minutes 46.27 seconds (5026.27 seconds total)