Starting phenix.real_space_refine on Sun Sep 13 23:56:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kiz_0695/09_2026/6kiz_0695.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kiz_0695/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6kiz_0695/09_2026/6kiz_0695.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kiz_0695/09_2026/6kiz_0695.cif" model { file = "/net/cci-nas-00/data/ceres_data/6kiz_0695/09_2026/6kiz_0695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kiz_0695/09_2026/6kiz_0695.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kiz_0695/09_2026/6kiz_0695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kiz_0695/09_2026/6kiz_0695.map" } 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-2.2.1-6174/lib/python3.11/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: 3.13, per 1000 atoms: 0.16 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: 1.62 Conformation dependent library (CDL) restraints added in 438.4 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: 2.20 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: 3.30 Time building geometry restraints manager: 2.00 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=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.435 1.483 -0.048 1.30e-02 5.92e+03 1.34e+01 bond pdb=" C5' DG I 100 " pdb=" C4' DG I 100 " ideal model delta sigma weight residual 1.512 1.537 -0.025 7.00e-03 2.04e+04 1.25e+01 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.23e+01 bond pdb=" C5' DA I 69 " pdb=" C4' DA I 69 " ideal model delta sigma weight residual 1.512 1.537 -0.025 7.00e-03 2.04e+04 1.23e+01 bond pdb=" N9 DA J 117 " pdb=" C4 DA J 117 " ideal model delta sigma weight residual 1.374 1.354 0.020 6.00e-03 2.78e+04 1.11e+01 ... (remaining 20871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 28598 2.46 - 4.92: 807 4.92 - 7.38: 38 7.38 - 9.84: 11 9.84 - 12.30: 3 Bond angle restraints: 29457 Sorted by residual: angle pdb=" O4' DA J 117 " pdb=" C4' DA J 117 " pdb=" C3' DA J 117 " ideal model delta sigma weight residual 106.00 102.24 3.76 6.00e-01 2.78e+00 3.93e+01 angle pdb=" O4' DA I 49 " pdb=" C4' DA I 49 " pdb=" C3' DA I 49 " ideal model delta sigma weight residual 106.00 102.51 3.49 6.00e-01 2.78e+00 3.39e+01 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=" O4' DC I 111 " pdb=" C4' DC I 111 " pdb=" C3' DC I 111 " ideal model delta sigma weight residual 106.00 102.74 3.26 6.00e-01 2.78e+00 2.95e+01 angle pdb=" O4' DG J 106 " pdb=" C4' DG J 106 " pdb=" C3' DG J 106 " ideal model delta sigma weight residual 106.00 102.77 3.23 6.00e-01 2.78e+00 2.90e+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 - 0.048: 2226 0.048 - 0.095: 798 0.095 - 0.143: 247 0.143 - 0.191: 33 0.191 - 0.239: 3 Chirality restraints: 3307 Sorted by residual: chirality pdb=" C3' DC J 126 " pdb=" C4' DC J 126 " pdb=" O3' DC J 126 " pdb=" C2' DC J 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C3' DT J 15 " pdb=" C4' DT J 15 " pdb=" O3' DT J 15 " pdb=" C2' DT J 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.23e+00 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 ... (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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.460 Find NCS groups from input model: 0.170 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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= 0.653 Angle : 0.944 12.302 29457 Z= 0.719 Chirality : 0.053 0.239 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/Z covalent geometry : bond 0.00772 / 0.63 (20876) covalent geometry : angle 0.94383 / 0.72 (29457) hydrogen bonds : bond 0.15878 / 10.85 ( 870) hydrogen bonds : angle 6.31043 / 4.50 ( 2195) metal coordination : bond 0.50002 / 33.57 ( 2) Misc. bond : bond 0.00067 / 0.04 ( 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 : 0.683 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: A 50 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8712 (mt-10) REVERT: A 64 LYS cc_start: 0.9372 (mtmm) cc_final: 0.9094 (mttp) REVERT: A 68 GLN cc_start: 0.9039 (tt0) cc_final: 0.8817 (pt0) REVERT: A 76 GLN cc_start: 0.9116 (tt0) cc_final: 0.8856 (pt0) REVERT: A 90 MET cc_start: 0.9171 (mmt) cc_final: 0.8886 (mmp) REVERT: A 94 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8851 (mm-30) REVERT: A 125 GLN cc_start: 0.9373 (mt0) cc_final: 0.9122 (mt0) REVERT: B 63 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8713 (mt-10) REVERT: B 84 MET cc_start: 0.8852 (mmm) cc_final: 0.8375 (mmm) REVERT: C 56 GLU cc_start: 0.9031 (tt0) cc_final: 0.8737 (tt0) REVERT: C 64 GLU cc_start: 0.9002 (tp30) cc_final: 0.8627 (tp30) REVERT: C 75 LYS cc_start: 0.9597 (mmtp) cc_final: 0.8916 (mmmm) REVERT: C 90 ASP cc_start: 0.8844 (t0) cc_final: 0.8521 (t70) REVERT: C 101 THR cc_start: 0.9061 (m) cc_final: 0.8566 (p) REVERT: C 110 ASN cc_start: 0.9180 (t0) cc_final: 0.8542 (m-40) REVERT: D 27 ARG cc_start: 0.6779 (tmt170) cc_final: 0.6038 (ptm160) REVERT: D 73 GLU cc_start: 0.9348 (tp30) cc_final: 0.9036 (tp30) REVERT: D 90 GLU cc_start: 0.8562 (mp0) cc_final: 0.8356 (mp0) REVERT: E 64 LYS cc_start: 0.9371 (mtmm) cc_final: 0.9023 (mtmm) REVERT: E 90 MET cc_start: 0.9179 (mmt) cc_final: 0.8754 (mmp) REVERT: E 125 GLN cc_start: 0.9399 (mt0) cc_final: 0.8934 (mp10) REVERT: F 44 LYS cc_start: 0.9284 (tptm) cc_final: 0.9026 (tppp) REVERT: F 49 LEU cc_start: 0.9693 (mt) cc_final: 0.9439 (mm) REVERT: F 59 LYS cc_start: 0.9048 (tttp) cc_final: 0.8711 (ttpp) REVERT: F 63 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8633 (mt-10) REVERT: F 84 MET cc_start: 0.8918 (mmm) cc_final: 0.8344 (tpp) REVERT: G 56 GLU cc_start: 0.9086 (tt0) cc_final: 0.8705 (tt0) REVERT: G 61 GLU cc_start: 0.9240 (tp30) cc_final: 0.8921 (tp30) REVERT: G 90 ASP cc_start: 0.8832 (t0) cc_final: 0.8530 (t70) REVERT: G 92 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8512 (mt-10) REVERT: G 101 THR cc_start: 0.8787 (m) cc_final: 0.8367 (p) REVERT: H 80 TYR cc_start: 0.8635 (m-10) cc_final: 0.7931 (m-10) REVERT: N 128 MET cc_start: 0.9073 (tpt) cc_final: 0.8604 (tpt) REVERT: N 197 ASN cc_start: 0.8222 (t0) cc_final: 0.7972 (t0) REVERT: N 243 GLN cc_start: 0.9476 (tp-100) cc_final: 0.8988 (tm-30) REVERT: N 256 LYS cc_start: 0.9299 (tptm) cc_final: 0.9083 (mmmt) REVERT: K 3884 MET cc_start: 0.5800 (mtt) cc_final: 0.5558 (mtt) REVERT: K 3927 VAL cc_start: 0.2113 (t) cc_final: 0.1762 (m) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.2179 time to fit residues: 96.8365 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 : 0.639 ------------------------------------------------------------------------------- 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: 20.0000 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 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: 20.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS C 31 HIS C 104 GLN E 39 HIS E 68 GLN F 25 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3906 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 = 0.3478 r_free = 0.3478 target = 0.061855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.032673 restraints weight = 140506.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.033886 restraints weight = 68792.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.034622 restraints weight = 43547.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.035038 restraints weight = 32558.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.035314 restraints weight = 27394.498| |-----------------------------------------------------------------------------| r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20879 Z= 0.190 Angle : 0.695 8.085 29457 Z= 0.398 Chirality : 0.049 0.365 3307 Planarity : 0.005 0.054 2724 Dihedral : 28.847 169.061 5095 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.73 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: -2.02 (0.19), residues: 1729 helix: 1.41 (0.22), residues: 552 sheet: -2.86 (0.32), residues: 217 loop : -2.80 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG T 367 TYR 0.023 0.002 TYR K3874 PHE 0.016 0.001 PHE T 464 TRP 0.015 0.002 TRP N 279 HIS 0.013 0.001 HIS R 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.19 (20876) covalent geometry : angle 0.69542 / 0.40 (29457) hydrogen bonds : bond 0.07216 / 4.95 ( 870) hydrogen bonds : angle 5.01489 / 3.54 ( 2195) metal coordination : bond 0.01475 / 1.04 ( 2) Misc. bond : bond 0.00050 / 0.03 ( 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 235 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.655 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: A 50 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8564 (mt-10) REVERT: B 25 ASN cc_start: 0.8778 (m110) cc_final: 0.8488 (m110) REVERT: B 84 MET cc_start: 0.8566 (mmm) cc_final: 0.8216 (mmm) REVERT: C 64 GLU cc_start: 0.8872 (tp30) cc_final: 0.8660 (tp30) REVERT: C 75 LYS cc_start: 0.9634 (mmtp) cc_final: 0.9027 (mmmm) REVERT: C 110 ASN cc_start: 0.9171 (t0) cc_final: 0.8564 (m-40) REVERT: D 27 ARG cc_start: 0.6697 (tmt170) cc_final: 0.5331 (ptm160) REVERT: D 76 ARG cc_start: 0.9041 (ttm110) cc_final: 0.8821 (ttp-110) REVERT: D 90 GLU cc_start: 0.8635 (mp0) cc_final: 0.8353 (mp0) REVERT: E 89 VAL cc_start: 0.9283 (t) cc_final: 0.9025 (p) REVERT: E 90 MET cc_start: 0.9039 (mmt) cc_final: 0.8800 (mmm) REVERT: F 49 LEU cc_start: 0.9530 (mt) cc_final: 0.9330 (mm) REVERT: G 73 ASN cc_start: 0.9448 (t0) cc_final: 0.9243 (t0) REVERT: G 99 ARG cc_start: 0.8504 (ptp-170) cc_final: 0.8241 (mpp80) REVERT: G 101 THR cc_start: 0.8784 (m) cc_final: 0.8575 (p) REVERT: H 83 ARG cc_start: 0.8455 (mtp-110) cc_final: 0.8242 (mtp85) REVERT: N 115 TYR cc_start: 0.7688 (m-80) cc_final: 0.6934 (m-80) REVERT: N 128 MET cc_start: 0.9273 (tpt) cc_final: 0.8780 (tpt) REVERT: N 167 TYR cc_start: 0.8997 (m-10) cc_final: 0.8452 (m-80) REVERT: N 246 GLN cc_start: 0.8643 (pm20) cc_final: 0.8387 (pm20) REVERT: T 336 MET cc_start: 0.5363 (ttm) cc_final: 0.4629 (tpp) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1620 time to fit residues: 56.4156 Evaluate side-chains 177 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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: 30.0000 chunk 90 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 169 optimal weight: 50.0000 chunk 129 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 194 optimal weight: 40.0000 chunk 196 optimal weight: 50.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3906 ASN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.061677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.032409 restraints weight = 142078.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.033634 restraints weight = 69821.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.034397 restraints weight = 44223.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.034794 restraints weight = 33065.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.035108 restraints weight = 27844.219| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20879 Z= 0.195 Angle : 0.659 13.204 29457 Z= 0.377 Chirality : 0.047 0.350 3307 Planarity : 0.004 0.038 2724 Dihedral : 28.603 170.141 5095 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: -1.62 (0.20), residues: 1729 helix: 1.90 (0.22), residues: 554 sheet: -2.88 (0.30), residues: 227 loop : -2.59 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG T 367 TYR 0.029 0.002 TYR H 80 PHE 0.018 0.001 PHE K3844 TRP 0.013 0.001 TRP N 279 HIS 0.007 0.001 HIS R 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.20 (20876) covalent geometry : angle 0.65933 / 0.38 (29457) hydrogen bonds : bond 0.07271 / 4.99 ( 870) hydrogen bonds : angle 4.71552 / 3.32 ( 2195) metal coordination : bond 0.00526 / 0.36 ( 2) Misc. bond : bond 0.00012 / 0.01 ( 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 222 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.655 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: A 46 VAL cc_start: 0.9247 (t) cc_final: 0.9019 (t) REVERT: A 50 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8581 (mt-10) REVERT: B 25 ASN cc_start: 0.8726 (m110) cc_final: 0.8393 (m110) REVERT: B 84 MET cc_start: 0.8518 (mmm) cc_final: 0.8081 (mmm) REVERT: C 64 GLU cc_start: 0.8890 (tp30) cc_final: 0.8611 (tp30) REVERT: C 75 LYS cc_start: 0.9642 (mmtp) cc_final: 0.9009 (mmmm) REVERT: C 92 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7995 (pm20) REVERT: C 110 ASN cc_start: 0.9188 (t0) cc_final: 0.8610 (m-40) REVERT: D 27 ARG cc_start: 0.6704 (tmt170) cc_final: 0.5338 (ptm160) REVERT: D 90 GLU cc_start: 0.8602 (mp0) cc_final: 0.8211 (mp0) REVERT: E 89 VAL cc_start: 0.9441 (t) cc_final: 0.9161 (p) REVERT: F 49 LEU cc_start: 0.9561 (mt) cc_final: 0.8493 (mm) REVERT: F 52 GLU cc_start: 0.9012 (pm20) cc_final: 0.8656 (pm20) REVERT: F 84 MET cc_start: 0.8572 (tpp) cc_final: 0.8116 (tpp) REVERT: G 73 ASN cc_start: 0.9435 (t0) cc_final: 0.9189 (t0) REVERT: G 101 THR cc_start: 0.8812 (m) cc_final: 0.8594 (p) REVERT: H 76 ARG cc_start: 0.9032 (ttm-80) cc_final: 0.8691 (ttm110) REVERT: H 83 ARG cc_start: 0.8601 (mtp-110) cc_final: 0.8311 (mtp85) REVERT: N 115 TYR cc_start: 0.7871 (m-80) cc_final: 0.7002 (m-80) REVERT: N 128 MET cc_start: 0.9215 (tpt) cc_final: 0.8707 (tpt) REVERT: N 167 TYR cc_start: 0.9056 (m-10) cc_final: 0.8583 (m-80) REVERT: K 3868 THR cc_start: 0.4787 (p) cc_final: 0.4543 (p) REVERT: T 315 MET cc_start: -0.1395 (mmt) cc_final: -0.1605 (mmt) REVERT: T 336 MET cc_start: 0.5468 (ttm) cc_final: 0.5213 (ttm) REVERT: T 503 MET cc_start: 0.5517 (mmm) cc_final: 0.5290 (tpp) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1716 time to fit residues: 55.7465 Evaluate side-chains 172 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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: 30.0000 chunk 196 optimal weight: 10.0000 chunk 96 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 159 optimal weight: 50.0000 chunk 169 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 176 optimal weight: 30.0000 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 46 HIS D 106 HIS E 68 GLN F 25 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.061012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.032278 restraints weight = 141926.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.033408 restraints weight = 70771.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.034135 restraints weight = 45244.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.034517 restraints weight = 33963.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.034833 restraints weight = 28678.177| |-----------------------------------------------------------------------------| r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20879 Z= 0.232 Angle : 0.672 8.253 29457 Z= 0.381 Chirality : 0.047 0.335 3307 Planarity : 0.004 0.040 2724 Dihedral : 28.503 169.782 5095 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % 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: -1.52 (0.20), residues: 1729 helix: 1.89 (0.22), residues: 555 sheet: -2.70 (0.32), residues: 223 loop : -2.52 (0.18), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 92 TYR 0.014 0.002 TYR N 165 PHE 0.009 0.001 PHE K3844 TRP 0.039 0.002 TRP R 241 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.23 (20876) covalent geometry : angle 0.67206 / 0.38 (29457) hydrogen bonds : bond 0.07544 / 5.16 ( 870) hydrogen bonds : angle 4.71750 / 3.33 ( 2195) metal coordination : bond 0.00007 / 0.00 ( 2) Misc. bond : bond 0.00026 / 0.02 ( 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 204 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 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: symmetry clash REVERT: A 50 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8670 (mt-10) REVERT: A 97 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8326 (mt-10) REVERT: A 120 MET cc_start: 0.8661 (mtt) cc_final: 0.8400 (mtp) REVERT: B 25 ASN cc_start: 0.8650 (m110) cc_final: 0.8372 (m110) REVERT: B 59 LYS cc_start: 0.9365 (ttpp) cc_final: 0.9066 (ttpp) REVERT: B 63 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8429 (mp0) REVERT: B 84 MET cc_start: 0.8609 (mmm) cc_final: 0.8174 (mmm) REVERT: C 64 GLU cc_start: 0.8894 (tp30) cc_final: 0.8599 (tp30) REVERT: C 75 LYS cc_start: 0.9659 (mmtp) cc_final: 0.9062 (mmmm) REVERT: C 92 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7753 (pm20) REVERT: D 27 ARG cc_start: 0.6721 (tmt170) cc_final: 0.5261 (ptm160) REVERT: D 90 GLU cc_start: 0.8551 (mp0) cc_final: 0.8350 (mp0) REVERT: E 89 VAL cc_start: 0.9443 (t) cc_final: 0.9241 (p) REVERT: E 106 ASP cc_start: 0.8932 (m-30) cc_final: 0.8659 (m-30) REVERT: F 84 MET cc_start: 0.8626 (tpp) cc_final: 0.8162 (tpp) REVERT: G 73 ASN cc_start: 0.9420 (t0) cc_final: 0.9215 (t0) REVERT: G 93 LEU cc_start: 0.9495 (mm) cc_final: 0.9185 (mm) REVERT: N 115 TYR cc_start: 0.7812 (m-80) cc_final: 0.6786 (m-80) REVERT: N 128 MET cc_start: 0.9204 (tpt) cc_final: 0.8719 (tpt) REVERT: N 167 TYR cc_start: 0.9094 (m-10) cc_final: 0.8623 (m-80) REVERT: N 243 GLN cc_start: 0.8589 (mt0) cc_final: 0.8388 (mt0) REVERT: N 246 GLN cc_start: 0.8832 (pm20) cc_final: 0.8573 (pm20) REVERT: T 336 MET cc_start: 0.4744 (ttm) cc_final: 0.4478 (ttm) REVERT: T 503 MET cc_start: 0.5142 (mmm) cc_final: 0.4921 (tpp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1661 time to fit residues: 50.1521 Evaluate side-chains 162 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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: 5.9990 chunk 67 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 80 optimal weight: 30.0000 chunk 138 optimal weight: 8.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 46 HIS D 106 HIS F 25 ASN ** 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 = 0.3465 r_free = 0.3465 target = 0.061329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.032423 restraints weight = 142538.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.033597 restraints weight = 70730.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.034337 restraints weight = 45351.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.034782 restraints weight = 34223.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.035041 restraints weight = 28897.804| |-----------------------------------------------------------------------------| r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20879 Z= 0.208 Angle : 0.653 10.289 29457 Z= 0.371 Chirality : 0.047 0.327 3307 Planarity : 0.004 0.041 2724 Dihedral : 28.404 170.708 5095 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % 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: 2.03 (0.22), residues: 555 sheet: -2.62 (0.31), residues: 230 loop : -2.47 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 83 TYR 0.017 0.002 TYR K3883 PHE 0.008 0.001 PHE N 159 TRP 0.018 0.001 TRP R 241 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.21 (20876) covalent geometry : angle 0.65290 / 0.37 (29457) hydrogen bonds : bond 0.07061 / 4.82 ( 870) hydrogen bonds : angle 4.54895 / 3.22 ( 2195) metal coordination : bond 0.00077 / 0.05 ( 2) Misc. bond : bond 0.00026 / 0.02 ( 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 205 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.9274 (t) cc_final: 0.9000 (t) REVERT: A 50 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8713 (mt-10) REVERT: A 97 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8328 (mt-10) REVERT: B 25 ASN cc_start: 0.8650 (m110) cc_final: 0.8325 (m110) REVERT: B 59 LYS cc_start: 0.9350 (ttpp) cc_final: 0.9143 (ttpp) REVERT: B 63 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8389 (mt-10) REVERT: B 84 MET cc_start: 0.8550 (mmm) cc_final: 0.8112 (mmm) REVERT: C 64 GLU cc_start: 0.8820 (tp30) cc_final: 0.8510 (tp30) REVERT: C 75 LYS cc_start: 0.9661 (mmtp) cc_final: 0.9070 (mmmm) REVERT: C 92 GLU cc_start: 0.7909 (mt-10) cc_final: 0.6831 (mt-10) REVERT: D 27 ARG cc_start: 0.6734 (tmt170) cc_final: 0.5411 (ptm160) REVERT: E 106 ASP cc_start: 0.8917 (m-30) cc_final: 0.8600 (m-30) REVERT: F 84 MET cc_start: 0.8517 (tpp) cc_final: 0.8021 (tpp) REVERT: G 92 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7181 (tt0) REVERT: N 115 TYR cc_start: 0.7777 (m-80) cc_final: 0.6792 (m-80) REVERT: N 128 MET cc_start: 0.9192 (tpt) cc_final: 0.8795 (tpt) REVERT: N 167 TYR cc_start: 0.9087 (m-10) cc_final: 0.8641 (m-80) REVERT: N 246 GLN cc_start: 0.8871 (pm20) cc_final: 0.8588 (pm20) REVERT: T 503 MET cc_start: 0.5201 (mmm) cc_final: 0.4978 (tpp) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1630 time to fit residues: 49.5545 Evaluate side-chains 160 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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: 20.0000 chunk 113 optimal weight: 20.0000 chunk 158 optimal weight: 50.0000 chunk 197 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 171 optimal weight: 40.0000 chunk 163 optimal weight: 30.0000 chunk 71 optimal weight: 40.0000 chunk 100 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 46 HIS F 25 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.061353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.032450 restraints weight = 140380.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.033589 restraints weight = 68674.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.034333 restraints weight = 43500.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.034783 restraints weight = 32571.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.035016 restraints weight = 27342.335| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20879 Z= 0.205 Angle : 0.644 8.463 29457 Z= 0.366 Chirality : 0.046 0.320 3307 Planarity : 0.004 0.060 2724 Dihedral : 28.341 171.622 5095 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: -1.40 (0.20), residues: 1729 helix: 2.01 (0.22), residues: 556 sheet: -2.63 (0.31), residues: 237 loop : -2.45 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K3808 TYR 0.014 0.001 TYR N 165 PHE 0.013 0.001 PHE C 25 TRP 0.008 0.001 TRP N 279 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.21 (20876) covalent geometry : angle 0.64375 / 0.37 (29457) hydrogen bonds : bond 0.06991 / 4.77 ( 870) hydrogen bonds : angle 4.45550 / 3.15 ( 2195) metal coordination : bond 0.00070 / 0.05 ( 2) Misc. bond : bond 0.00045 / 0.03 ( 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 : 0.737 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: 0.9247 (t) cc_final: 0.9006 (t) REVERT: A 50 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8727 (mt-10) REVERT: A 97 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8316 (mt-10) REVERT: A 120 MET cc_start: 0.8895 (mtt) cc_final: 0.8139 (mtm) REVERT: B 25 ASN cc_start: 0.8583 (m110) cc_final: 0.8259 (m110) REVERT: B 59 LYS cc_start: 0.9394 (ttpp) cc_final: 0.9145 (ttpp) REVERT: B 63 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8407 (mt-10) REVERT: B 84 MET cc_start: 0.8518 (mmm) cc_final: 0.8116 (mmm) REVERT: C 64 GLU cc_start: 0.8844 (tp30) cc_final: 0.8533 (tp30) REVERT: C 92 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7130 (mt-10) REVERT: D 27 ARG cc_start: 0.6696 (tmt170) cc_final: 0.5254 (ptm160) REVERT: D 102 GLU cc_start: 0.8576 (pm20) cc_final: 0.8366 (pm20) REVERT: E 106 ASP cc_start: 0.8898 (m-30) cc_final: 0.8558 (m-30) REVERT: F 84 MET cc_start: 0.8530 (tpp) cc_final: 0.8044 (tpp) REVERT: G 90 ASP cc_start: 0.8987 (t0) cc_final: 0.8727 (t70) REVERT: G 91 GLU cc_start: 0.9045 (pp20) cc_final: 0.8350 (pp20) REVERT: N 115 TYR cc_start: 0.7799 (m-80) cc_final: 0.6848 (m-80) REVERT: N 128 MET cc_start: 0.9228 (tpt) cc_final: 0.8731 (tpt) REVERT: N 167 TYR cc_start: 0.9131 (m-10) cc_final: 0.8666 (m-80) REVERT: N 246 GLN cc_start: 0.8893 (pm20) cc_final: 0.8576 (pm20) REVERT: K 3816 MET cc_start: 0.5192 (ttt) cc_final: 0.4528 (mtt) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1657 time to fit residues: 48.0870 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 : 0.423 ------------------------------------------------------------------------------- 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: 40.0000 chunk 159 optimal weight: 30.0000 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 152 optimal weight: 50.0000 chunk 66 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 156 optimal weight: 50.0000 chunk 155 optimal weight: 9.9990 chunk 194 optimal weight: 30.0000 chunk 73 optimal weight: 40.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 46 HIS F 25 ASN F 75 HIS G 73 ASN N 79 HIS N 274 HIS ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS ** T 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.059964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.031021 restraints weight = 143300.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.032153 restraints weight = 71063.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.032866 restraints weight = 45524.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.033284 restraints weight = 34278.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.033494 restraints weight = 28858.587| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 20879 Z= 0.358 Angle : 0.791 9.338 29457 Z= 0.433 Chirality : 0.050 0.288 3307 Planarity : 0.006 0.075 2724 Dihedral : 28.433 168.569 5095 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.07 % Allowed : 1.20 % 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: -1.84 (0.19), residues: 1729 helix: 1.28 (0.21), residues: 555 sheet: -2.79 (0.32), residues: 234 loop : -2.48 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 42 TYR 0.028 0.002 TYR D 80 PHE 0.018 0.002 PHE C 25 TRP 0.032 0.002 TRP R 241 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.36 (20876) covalent geometry : angle 0.79126 / 0.43 (29457) hydrogen bonds : bond 0.09989 / 6.79 ( 870) hydrogen bonds : angle 5.08264 / 3.61 ( 2195) metal coordination : bond 0.00043 / 0.03 ( 2) Misc. bond : bond 0.00042 / 0.03 ( 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 172 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.623 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: 0.8973 (mt-10) cc_final: 0.8708 (mt-10) REVERT: A 97 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8349 (mt-10) REVERT: B 25 ASN cc_start: 0.8646 (m110) cc_final: 0.8349 (m110) REVERT: B 84 MET cc_start: 0.8555 (mmm) cc_final: 0.8185 (mmm) REVERT: C 64 GLU cc_start: 0.8849 (tp30) cc_final: 0.8617 (tp30) REVERT: D 27 ARG cc_start: 0.6817 (tmt170) cc_final: 0.5141 (ptm160) REVERT: D 90 GLU cc_start: 0.8579 (mp0) cc_final: 0.8344 (mp0) REVERT: E 106 ASP cc_start: 0.8927 (m-30) cc_final: 0.8676 (m-30) REVERT: F 84 MET cc_start: 0.8655 (tpp) cc_final: 0.8197 (tpp) REVERT: G 61 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8378 (tm-30) REVERT: N 115 TYR cc_start: 0.7959 (m-80) cc_final: 0.7163 (m-80) REVERT: N 128 MET cc_start: 0.9231 (tpt) cc_final: 0.8776 (tpt) REVERT: N 167 TYR cc_start: 0.9125 (m-10) cc_final: 0.8677 (m-80) REVERT: K 3816 MET cc_start: 0.5509 (ttt) cc_final: 0.4912 (mtt) REVERT: T 503 MET cc_start: 0.5532 (tpp) cc_final: 0.5129 (tpp) outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.1637 time to fit residues: 41.6267 Evaluate side-chains 142 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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: 30.0000 chunk 112 optimal weight: 40.0000 chunk 30 optimal weight: 1.9990 chunk 145 optimal weight: 50.0000 chunk 87 optimal weight: 30.0000 chunk 168 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 194 optimal weight: 40.0000 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 46 HIS F 25 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.061554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.032478 restraints weight = 141561.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.033586 restraints weight = 68814.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.034318 restraints weight = 43449.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.034756 restraints weight = 32465.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.034995 restraints weight = 27265.236| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3365 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= 0.174 Angle : 0.648 8.801 29457 Z= 0.368 Chirality : 0.047 0.315 3307 Planarity : 0.004 0.048 2724 Dihedral : 28.355 171.067 5095 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -1.50 (0.20), residues: 1729 helix: 1.84 (0.22), residues: 559 sheet: -2.71 (0.31), residues: 236 loop : -2.45 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 76 TYR 0.017 0.001 TYR H 118 PHE 0.014 0.001 PHE K3844 TRP 0.025 0.002 TRP R 241 HIS 0.009 0.001 HIS R 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (20876) covalent geometry : angle 0.64783 / 0.37 (29457) hydrogen bonds : bond 0.06961 / 4.72 ( 870) hydrogen bonds : angle 4.54542 / 3.22 ( 2195) metal coordination : bond 0.00086 / 0.06 ( 2) Misc. bond : bond 0.00033 / 0.02 ( 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 195 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.600 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: 0.8945 (mt-10) cc_final: 0.8705 (mt-10) REVERT: A 97 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8368 (mt-10) REVERT: B 25 ASN cc_start: 0.8629 (m110) cc_final: 0.8274 (m110) REVERT: B 63 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8466 (mp0) REVERT: B 84 MET cc_start: 0.8441 (mmm) cc_final: 0.8019 (mmm) REVERT: C 64 GLU cc_start: 0.8801 (tp30) cc_final: 0.8523 (tp30) REVERT: D 27 ARG cc_start: 0.6875 (tmt170) cc_final: 0.5145 (ptm160) REVERT: D 90 GLU cc_start: 0.8719 (mp0) cc_final: 0.8506 (mp0) REVERT: E 50 GLU cc_start: 0.9050 (tt0) cc_final: 0.8742 (tm-30) REVERT: E 51 ILE cc_start: 0.9255 (mt) cc_final: 0.9017 (mt) REVERT: E 54 TYR cc_start: 0.8860 (m-80) cc_final: 0.8608 (m-10) REVERT: E 106 ASP cc_start: 0.8900 (m-30) cc_final: 0.8585 (m-30) REVERT: F 53 GLU cc_start: 0.8988 (mp0) cc_final: 0.8273 (mp0) REVERT: F 84 MET cc_start: 0.8577 (tpp) cc_final: 0.8105 (tpp) REVERT: G 75 LYS cc_start: 0.9477 (mmtt) cc_final: 0.9237 (mmmm) REVERT: N 115 TYR cc_start: 0.7742 (m-80) cc_final: 0.6867 (m-80) REVERT: N 128 MET cc_start: 0.9253 (tpt) cc_final: 0.8784 (tpt) REVERT: N 167 TYR cc_start: 0.9154 (m-10) cc_final: 0.8691 (m-80) REVERT: K 3816 MET cc_start: 0.5332 (ttt) cc_final: 0.4716 (mtt) REVERT: T 500 MET cc_start: 0.5216 (mtt) cc_final: 0.4792 (mtp) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1664 time to fit residues: 48.1078 Evaluate side-chains 155 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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: 8.9990 chunk 173 optimal weight: 40.0000 chunk 78 optimal weight: 30.0000 chunk 98 optimal weight: 30.0000 chunk 152 optimal weight: 50.0000 chunk 66 optimal weight: 7.9990 chunk 75 optimal weight: 30.0000 chunk 36 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 overall best weight: 5.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 46 HIS D 106 HIS F 25 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.061015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.032103 restraints weight = 140967.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.033281 restraints weight = 68680.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.034008 restraints weight = 43267.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.034434 restraints weight = 32313.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.034654 restraints weight = 27126.144| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20879 Z= 0.223 Angle : 0.672 8.672 29457 Z= 0.377 Chirality : 0.047 0.309 3307 Planarity : 0.005 0.061 2724 Dihedral : 28.299 171.744 5095 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -1.50 (0.20), residues: 1729 helix: 1.80 (0.21), residues: 561 sheet: -2.73 (0.31), residues: 242 loop : -2.41 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 317 TYR 0.021 0.002 TYR H 80 PHE 0.010 0.001 PHE N 159 TRP 0.033 0.002 TRP R 95 HIS 0.007 0.002 HIS R 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.22 (20876) covalent geometry : angle 0.67158 / 0.38 (29457) hydrogen bonds : bond 0.07537 / 5.13 ( 870) hydrogen bonds : angle 4.57590 / 3.24 ( 2195) metal coordination : bond 0.00065 / 0.05 ( 2) Misc. bond : bond 0.00054 / 0.04 ( 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 182 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.565 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: 0.9262 (t) cc_final: 0.9005 (t) REVERT: A 50 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8729 (mt-10) REVERT: A 97 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8340 (mt-10) REVERT: B 25 ASN cc_start: 0.8585 (m110) cc_final: 0.8275 (m110) REVERT: B 63 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8464 (mt-10) REVERT: B 84 MET cc_start: 0.8522 (mmm) cc_final: 0.8131 (mmm) REVERT: C 64 GLU cc_start: 0.8830 (tp30) cc_final: 0.8535 (tp30) REVERT: D 27 ARG cc_start: 0.6547 (tmt170) cc_final: 0.4736 (ptm160) REVERT: D 90 GLU cc_start: 0.8671 (mp0) cc_final: 0.8447 (mp0) REVERT: D 102 GLU cc_start: 0.8577 (pp20) cc_final: 0.7915 (pp20) REVERT: E 106 ASP cc_start: 0.8883 (m-30) cc_final: 0.8613 (m-30) REVERT: F 84 MET cc_start: 0.8490 (tpp) cc_final: 0.7971 (tpp) REVERT: H 76 ARG cc_start: 0.9091 (ttm-80) cc_final: 0.8882 (ttm110) REVERT: N 115 TYR cc_start: 0.7752 (m-80) cc_final: 0.6898 (m-80) REVERT: N 128 MET cc_start: 0.9226 (tpt) cc_final: 0.8770 (tpt) REVERT: N 167 TYR cc_start: 0.9167 (m-10) cc_final: 0.8704 (m-80) REVERT: K 3816 MET cc_start: 0.5368 (ttt) cc_final: 0.4748 (mtt) REVERT: R 131 TYR cc_start: 0.9486 (m-80) cc_final: 0.9280 (m-80) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1661 time to fit residues: 45.1108 Evaluate side-chains 147 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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: 20.0000 chunk 67 optimal weight: 8.9990 chunk 145 optimal weight: 0.0770 chunk 71 optimal weight: 40.0000 chunk 48 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 164 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS F 25 ASN ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3861 ASN ** 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 = 0.3489 r_free = 0.3489 target = 0.062559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.033656 restraints weight = 139676.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.034824 restraints weight = 67814.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.035594 restraints weight = 42617.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.036045 restraints weight = 31676.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.036296 restraints weight = 26499.486| |-----------------------------------------------------------------------------| r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20879 Z= 0.135 Angle : 0.602 7.821 29457 Z= 0.346 Chirality : 0.045 0.331 3307 Planarity : 0.004 0.036 2724 Dihedral : 28.171 175.078 5095 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % 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 : 0.06 % 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: 2.24 (0.22), residues: 563 sheet: -2.66 (0.30), residues: 251 loop : -2.38 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 181 TYR 0.019 0.001 TYR H 80 PHE 0.008 0.001 PHE N 159 TRP 0.028 0.002 TRP R 241 HIS 0.006 0.001 HIS R 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (20876) covalent geometry : angle 0.60181 / 0.35 (29457) hydrogen bonds : bond 0.05394 / 3.65 ( 870) hydrogen bonds : angle 4.06565 / 2.87 ( 2195) metal coordination : bond 0.00115 / 0.08 ( 2) Misc. bond : bond 0.00029 / 0.02 ( 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 208 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.689 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 46 VAL cc_start: 0.9185 (t) cc_final: 0.8911 (t) REVERT: A 50 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8638 (mt-10) REVERT: B 25 ASN cc_start: 0.8490 (m110) cc_final: 0.8202 (m110) REVERT: B 63 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8464 (mt-10) REVERT: B 68 ASP cc_start: 0.8739 (m-30) cc_final: 0.8526 (m-30) REVERT: B 84 MET cc_start: 0.8411 (mmm) cc_final: 0.8037 (mmm) REVERT: C 64 GLU cc_start: 0.8780 (tp30) cc_final: 0.8533 (tp30) REVERT: C 90 ASP cc_start: 0.8807 (t70) cc_final: 0.8392 (t70) REVERT: C 92 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7726 (pm20) REVERT: C 110 ASN cc_start: 0.8976 (t0) cc_final: 0.8613 (m-40) REVERT: D 27 ARG cc_start: 0.6496 (tmt170) cc_final: 0.4740 (ptm160) REVERT: D 90 GLU cc_start: 0.8818 (mp0) cc_final: 0.8330 (mp0) REVERT: E 54 TYR cc_start: 0.8691 (m-80) cc_final: 0.8460 (m-10) REVERT: E 106 ASP cc_start: 0.8839 (m-30) cc_final: 0.8589 (m-30) REVERT: F 79 LYS cc_start: 0.9527 (mttm) cc_final: 0.9123 (mtpp) REVERT: F 84 MET cc_start: 0.8443 (tpp) cc_final: 0.7892 (tpp) REVERT: G 90 ASP cc_start: 0.9067 (t70) cc_final: 0.8697 (t70) REVERT: N 115 TYR cc_start: 0.7566 (m-80) cc_final: 0.6712 (m-80) REVERT: N 128 MET cc_start: 0.9216 (tpt) cc_final: 0.8806 (tpt) REVERT: N 167 TYR cc_start: 0.9172 (m-10) cc_final: 0.8792 (m-80) REVERT: K 3816 MET cc_start: 0.5254 (ttt) cc_final: 0.4479 (mtt) REVERT: T 500 MET cc_start: 0.4724 (mtt) cc_final: 0.4389 (mtt) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1541 time to fit residues: 47.9994 Evaluate side-chains 164 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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: 30.0000 chunk 195 optimal weight: 30.0000 chunk 191 optimal weight: 9.9990 chunk 145 optimal weight: 50.0000 chunk 176 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 134 optimal weight: 30.0000 chunk 15 optimal weight: 0.8980 chunk 189 optimal weight: 30.0000 chunk 131 optimal weight: 8.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS F 25 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3861 ASN ** 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 = 0.3450 r_free = 0.3450 target = 0.060850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.032103 restraints weight = 143649.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.033247 restraints weight = 70674.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.033951 restraints weight = 44865.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.034376 restraints weight = 33672.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 76)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.034623 restraints weight = 28263.715| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 20879 Z= 0.264 Angle : 0.694 8.379 29457 Z= 0.386 Chirality : 0.047 0.305 3307 Planarity : 0.005 0.051 2724 Dihedral : 28.225 172.830 5095 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: -1.33 (0.20), residues: 1729 helix: 1.94 (0.22), residues: 563 sheet: -2.49 (0.30), residues: 265 loop : -2.34 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 181 TYR 0.020 0.002 TYR R 228 PHE 0.018 0.001 PHE C 25 TRP 0.030 0.002 TRP T 327 HIS 0.008 0.002 HIS R 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.26 (20876) covalent geometry : angle 0.69417 / 0.39 (29457) hydrogen bonds : bond 0.07611 / 5.19 ( 870) hydrogen bonds : angle 4.46186 / 3.17 ( 2195) metal coordination : bond 0.00063 / 0.04 ( 2) Misc. bond : bond 0.00053 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4585.02 seconds wall clock time: 79 minutes 22.29 seconds (4762.29 seconds total)