Starting phenix.real_space_refine on Mon Aug 25 10:58:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kiv_9999/08_2025/6kiv_9999.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kiv_9999/08_2025/6kiv_9999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kiv_9999/08_2025/6kiv_9999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kiv_9999/08_2025/6kiv_9999.map" model { file = "/net/cci-nas-00/data/ceres_data/6kiv_9999/08_2025/6kiv_9999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kiv_9999/08_2025/6kiv_9999.cif" } resolution = 4.0 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= 0.004 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 8596 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 61 5.16 5 C 12166 2.51 5 N 3759 2.21 5 O 4442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20719 Number of models: 1 Model: "" Number of chains: 16 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: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} 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: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} 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: "K" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1434 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2881 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 14, 'TRANS': 351} Chain breaks: 1 Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} 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: "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: "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 13389 SG CYS K3957 39.155 70.820 42.538 1.00167.86 S ATOM 13403 SG CYS K3959 42.422 71.072 44.036 1.00163.71 S Time building chain proxies: 3.42, per 1000 atoms: 0.17 Number of scatterers: 20719 At special positions: 0 Unit cell: (151.51, 141.7, 117.72, 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 61 16.00 P 290 15.00 O 4442 8.00 N 3759 7.00 C 12166 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 454.6 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K4002 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3957 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3959 " 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 35 sheets defined 31.8% alpha, 13.0% beta 145 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.554A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.997A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.858A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.671A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.917A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.843A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.797A 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 Processing helix chain 'D' and resid 87 through 99 removed outlier: 4.083A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 4.201A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.554A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.997A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.672A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 4.145A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.461A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.771A 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: 3.664A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 4.034A pdb=" N ALA H 121 " --> pdb=" O CYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 3815 through 3830 removed outlier: 3.755A pdb=" N ARG K3819 " --> pdb=" O PRO K3815 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LYS K3828 " --> pdb=" O LYS K3824 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLU K3829 " --> pdb=" O LYS K3825 " (cutoff:3.500A) Processing helix chain 'K' and resid 3866 through 3878 removed outlier: 4.719A pdb=" N LYS K3870 " --> pdb=" O ILE K3866 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 234 Processing helix chain 'O' and resid 22 through 34 removed outlier: 3.827A pdb=" N VAL O 26 " --> pdb=" O THR O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 41 removed outlier: 4.187A pdb=" N GLN O 41 " --> pdb=" O PRO O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 59 removed outlier: 3.536A pdb=" N ASP O 58 " --> pdb=" O THR O 55 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR O 59 " --> pdb=" O LEU O 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 55 through 59' Processing helix chain 'T' and resid 501 through 503 No H-bonds generated for 'chain 'T' and resid 501 through 503' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.620A 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 'B' and resid 96 through 98 removed outlier: 6.424A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.396A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.116A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.816A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'K' and resid 3831 through 3835 removed outlier: 4.089A pdb=" N GLY K3832 " --> pdb=" O PHE K3844 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 3884 through 3886 Processing sheet with id=AA8, first strand: chain 'K' and resid 3898 through 3899 removed outlier: 3.608A pdb=" N GLY K3899 " --> pdb=" O LYS N 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 3906 through 3907 removed outlier: 6.746A pdb=" N ASN K3906 " --> pdb=" O TYR K3942 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 3915 through 3920 removed outlier: 3.951A pdb=" N ARG K3916 " --> pdb=" O VAL K3927 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL K3927 " --> pdb=" O ARG K3916 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE K3918 " --> pdb=" O HIS K3925 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS K3925 " --> pdb=" O ILE K3918 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE K3920 " --> pdb=" O GLN K3923 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN K3923 " --> pdb=" O ILE K3920 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'N' and resid 30 through 32 removed outlier: 3.586A pdb=" N THR N 31 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 69 through 73 removed outlier: 3.852A pdb=" N SER N 71 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA N 84 " --> pdb=" O SER N 71 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER N 83 " --> pdb=" O SER N 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 113 through 115 removed outlier: 3.790A pdb=" N GLN N 114 " --> pdb=" O LEU N 124 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL N 123 " --> pdb=" O LEU N 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 156 through 159 removed outlier: 3.540A pdb=" N THR N 168 " --> pdb=" O LEU N 176 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 201 through 205 removed outlier: 7.131A pdb=" N ASN N 216 " --> pdb=" O LYS N 202 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE N 204 " --> pdb=" O LEU N 214 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU N 214 " --> pdb=" O ILE N 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 254 through 259 removed outlier: 6.977A pdb=" N GLY N 269 " --> pdb=" O LYS N 255 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N CYS N 257 " --> pdb=" O VAL N 267 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL N 267 " --> pdb=" O CYS N 257 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N PHE N 259 " --> pdb=" O TYR N 265 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR N 265 " --> pdb=" O PHE N 259 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU N 276 " --> pdb=" O ILE N 289 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE N 289 " --> pdb=" O LEU N 276 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE N 278 " --> pdb=" O VAL N 287 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 310 through 311 removed outlier: 3.968A pdb=" N ILE N 310 " --> pdb=" O TRP N 321 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP N 321 " --> pdb=" O ILE N 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'O' and resid 12 through 16 removed outlier: 8.104A pdb=" N LEU O 67 " --> pdb=" O GLN O 2 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE O 4 " --> pdb=" O LEU O 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 43 through 45 removed outlier: 4.114A pdb=" N LEU O 43 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 306 through 308 removed outlier: 3.722A pdb=" N VAL T 480 " --> pdb=" O VAL T 307 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 314 through 316 removed outlier: 3.545A pdb=" N VAL T 316 " --> pdb=" O ILE T 472 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 396 through 398 removed outlier: 4.781A pdb=" N ILE T 396 " --> pdb=" O TRP T 327 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP T 327 " --> pdb=" O ILE T 396 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU T 398 " --> pdb=" O GLY T 325 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY T 325 " --> pdb=" O LEU T 398 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA T 326 " --> pdb=" O ARG T 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'T' and resid 331 through 332 Processing sheet with id=AC6, first strand: chain 'T' and resid 346 through 347 Processing sheet with id=AC7, first strand: chain 'T' and resid 372 through 374 removed outlier: 3.581A pdb=" N LYS T 380 " --> pdb=" O LYS T 373 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 448 through 450 removed outlier: 4.483A pdb=" N GLY T 457 " --> pdb=" O PHE T 449 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 36 through 37 Processing sheet with id=AD1, first strand: chain 'R' and resid 41 through 42 Processing sheet with id=AD2, first strand: chain 'R' and resid 48 through 53 removed outlier: 4.260A pdb=" N LYS R 52 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA R 61 " --> pdb=" O LYS R 52 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS R 70 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU R 68 " --> pdb=" O SER R 64 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 90 through 93 removed outlier: 3.783A pdb=" N ASP R 92 " --> pdb=" O ALA R 105 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS R 112 " --> pdb=" O SER R 104 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 136 through 137 removed outlier: 3.700A pdb=" N ASN R 136 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 177 through 179 removed outlier: 6.091A pdb=" N CYS R 195 " --> pdb=" O THR R 208 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR R 208 " --> pdb=" O CYS R 195 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE R 197 " --> pdb=" O LEU R 206 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 219 through 222 removed outlier: 3.615A pdb=" N LYS R 239 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 264 through 266 Processing sheet with id=AD8, first strand: chain 'R' and resid 304 through 309 removed outlier: 3.519A pdb=" N ALA R 308 " --> pdb=" O ALA R 317 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1506 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 241 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 1.78 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: 4052 1.33 - 1.45: 6267 1.45 - 1.57: 10731 1.57 - 1.69: 578 1.69 - 1.81: 88 Bond restraints: 21716 Sorted by residual: bond pdb=" C2 SAH K4001 " pdb=" N3 SAH K4001 " ideal model delta sigma weight residual 1.322 1.375 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" C8 SAH K4001 " pdb=" N7 SAH K4001 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.84e+00 bond pdb=" C2 SAH K4001 " pdb=" N1 SAH K4001 " ideal model delta sigma weight residual 1.330 1.378 -0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" C6 SAH K4001 " pdb=" N1 SAH K4001 " ideal model delta sigma weight residual 1.338 1.386 -0.048 2.00e-02 2.50e+03 5.81e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.491 -0.069 3.00e-02 1.11e+03 5.28e+00 ... (remaining 21711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 29917 2.52 - 5.04: 609 5.04 - 7.55: 44 7.55 - 10.07: 13 10.07 - 12.59: 2 Bond angle restraints: 30585 Sorted by residual: angle pdb=" CG SAH K4001 " pdb=" SD SAH K4001 " pdb=" C5' SAH K4001 " ideal model delta sigma weight residual 101.77 89.61 12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 122.48 -9.30 2.37e+00 1.78e-01 1.54e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 120.20 125.89 -5.69 1.50e+00 4.44e-01 1.44e+01 angle pdb=" CA ARG G 99 " pdb=" CB ARG G 99 " pdb=" CG ARG G 99 " ideal model delta sigma weight residual 114.10 121.58 -7.48 2.00e+00 2.50e-01 1.40e+01 angle pdb=" N GLN N 323 " pdb=" CA GLN N 323 " pdb=" C GLN N 323 " ideal model delta sigma weight residual 110.80 118.14 -7.34 2.13e+00 2.20e-01 1.19e+01 ... (remaining 30580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 10875 35.82 - 71.65: 1373 71.65 - 107.47: 25 107.47 - 143.29: 4 143.29 - 179.11: 1 Dihedral angle restraints: 12278 sinusoidal: 6877 harmonic: 5401 Sorted by residual: dihedral pdb=" CA LYS B 31 " pdb=" C LYS B 31 " pdb=" N PRO B 32 " pdb=" CA PRO B 32 " ideal model delta harmonic sigma weight residual 180.00 133.83 46.17 0 5.00e+00 4.00e-02 8.53e+01 dihedral pdb=" CA ASN K3779 " pdb=" C ASN K3779 " pdb=" N PHE K3780 " pdb=" CA PHE K3780 " ideal model delta harmonic sigma weight residual 180.00 138.88 41.12 0 5.00e+00 4.00e-02 6.76e+01 dihedral pdb=" CA TYR N 13 " pdb=" C TYR N 13 " pdb=" N PRO N 14 " pdb=" CA PRO N 14 " ideal model delta harmonic sigma weight residual -180.00 -143.60 -36.40 0 5.00e+00 4.00e-02 5.30e+01 ... (remaining 12275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2253 0.046 - 0.092: 872 0.092 - 0.138: 258 0.138 - 0.184: 49 0.184 - 0.230: 6 Chirality restraints: 3438 Sorted by residual: chirality pdb=" C1' SAH K4001 " pdb=" C2' SAH K4001 " pdb=" N9 SAH K4001 " pdb=" O4' SAH K4001 " both_signs ideal model delta sigma weight residual False 2.35 2.58 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL D 45 " pdb=" CA VAL D 45 " pdb=" CG1 VAL D 45 " pdb=" CG2 VAL D 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CG LEU E 126 " pdb=" CB LEU E 126 " pdb=" CD1 LEU E 126 " pdb=" CD2 LEU E 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 3435 not shown) Planarity restraints: 2870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.071 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO B 32 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN K3779 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" CG ASN K3779 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN K3779 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN K3779 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL K3768 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C VAL K3768 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL K3768 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS K3769 " -0.015 2.00e-02 2.50e+03 ... (remaining 2867 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4488 2.79 - 3.32: 17385 3.32 - 3.85: 37394 3.85 - 4.37: 41446 4.37 - 4.90: 64179 Nonbonded interactions: 164892 Sorted by model distance: nonbonded pdb=" OG SER R 129 " pdb=" OD2 ASP R 150 " model vdw 2.263 3.040 nonbonded pdb=" OG SER R 96 " pdb=" OD1 ASP R 98 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.265 3.040 nonbonded pdb=" OG SER R 49 " pdb=" O SER R 63 " model vdw 2.268 3.040 ... (remaining 164887 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 21 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.910 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.007 0.241 21720 Z= 0.328 Angle : 0.904 12.590 30585 Z= 0.511 Chirality : 0.053 0.230 3438 Planarity : 0.007 0.108 2870 Dihedral : 22.703 179.114 8794 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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 aren not related in a simple way. whole: -3.80 (0.16), residues: 1830 helix: -1.38 (0.17), residues: 568 sheet: -2.89 (0.26), residues: 312 loop : -3.18 (0.17), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 39 TYR 0.031 0.003 TYR B 51 PHE 0.023 0.003 PHE N 189 TRP 0.025 0.003 TRP N 303 HIS 0.010 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00716 (21716) covalent geometry : angle 0.90391 (30585) hydrogen bonds : bond 0.15019 ( 898) hydrogen bonds : angle 6.04261 ( 2250) metal coordination : bond 0.21670 ( 2) Misc. bond : bond 0.00378 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 0.652 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 58 THR cc_start: 0.9254 (p) cc_final: 0.8948 (p) REVERT: A 123 ASP cc_start: 0.8318 (m-30) cc_final: 0.8093 (m-30) REVERT: B 35 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8090 (ttm-80) REVERT: B 58 LEU cc_start: 0.8871 (tp) cc_final: 0.8572 (tt) REVERT: B 92 ARG cc_start: 0.8717 (mtp-110) cc_final: 0.8403 (mtp-110) REVERT: D 27 ARG cc_start: 0.7875 (tmt170) cc_final: 0.7639 (tmt-80) REVERT: D 54 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8812 (mmmm) REVERT: D 65 ASP cc_start: 0.8143 (t0) cc_final: 0.7873 (t0) REVERT: D 81 ASN cc_start: 0.8438 (m-40) cc_final: 0.8151 (m110) REVERT: D 88 SER cc_start: 0.9070 (p) cc_final: 0.8865 (p) REVERT: F 88 TYR cc_start: 0.8891 (m-10) cc_final: 0.7807 (m-10) REVERT: G 18 SER cc_start: 0.8315 (m) cc_final: 0.7612 (p) REVERT: G 42 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7725 (mtm-85) REVERT: G 61 GLU cc_start: 0.8672 (tp30) cc_final: 0.8326 (tm-30) REVERT: H 73 GLU cc_start: 0.8267 (tp30) cc_final: 0.8059 (mt-10) REVERT: H 80 TYR cc_start: 0.7333 (m-10) cc_final: 0.6653 (m-10) REVERT: H 82 LYS cc_start: 0.8942 (mttt) cc_final: 0.8109 (mmtt) REVERT: K 3828 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8215 (pttt) REVERT: K 3846 LYS cc_start: 0.6392 (mtmt) cc_final: 0.6073 (tmtt) REVERT: N 60 LYS cc_start: 0.8170 (tptt) cc_final: 0.7546 (tppt) REVERT: N 115 TYR cc_start: 0.5656 (m-80) cc_final: 0.5142 (m-10) REVERT: N 226 ASP cc_start: 0.7903 (t0) cc_final: 0.7647 (t0) REVERT: N 320 ILE cc_start: 0.8932 (mp) cc_final: 0.8635 (pt) REVERT: T 503 MET cc_start: 0.6152 (mmm) cc_final: 0.5487 (mtm) REVERT: R 72 TRP cc_start: 0.6754 (m100) cc_final: 0.5445 (m100) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.1819 time to fit residues: 130.1306 Evaluate side-chains 290 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.0470 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.0270 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS C 94 ASN D 81 ASN F 25 ASN G 89 ASN G 110 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 328 ASN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 375 HIS T 381 HIS ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 265 ASN R 295 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.143225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.108652 restraints weight = 53404.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.108749 restraints weight = 32104.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.109433 restraints weight = 24596.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.109571 restraints weight = 20988.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.109695 restraints weight = 19426.155| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21720 Z= 0.145 Angle : 0.634 12.341 30585 Z= 0.359 Chirality : 0.041 0.193 3438 Planarity : 0.005 0.086 2870 Dihedral : 27.537 177.730 5203 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.45 % Allowed : 11.47 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.18), residues: 1830 helix: 0.70 (0.21), residues: 568 sheet: -2.30 (0.27), residues: 299 loop : -2.93 (0.17), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 45 TYR 0.027 0.002 TYR B 51 PHE 0.018 0.001 PHE N 189 TRP 0.027 0.002 TRP R 156 HIS 0.013 0.001 HIS R 44 Details of bonding type rmsd covalent geometry : bond 0.00308 (21716) covalent geometry : angle 0.63350 (30585) hydrogen bonds : bond 0.04511 ( 898) hydrogen bonds : angle 3.90012 ( 2250) metal coordination : bond 0.00271 ( 2) Misc. bond : bond 0.00164 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 369 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7537 (mmt180) REVERT: A 73 GLU cc_start: 0.6958 (tt0) cc_final: 0.6736 (tt0) REVERT: C 36 LYS cc_start: 0.8525 (tmtt) cc_final: 0.8317 (tmtt) REVERT: D 44 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8107 (tm-30) REVERT: D 81 ASN cc_start: 0.8493 (m110) cc_final: 0.8244 (m110) REVERT: D 88 SER cc_start: 0.8994 (p) cc_final: 0.8774 (p) REVERT: E 73 GLU cc_start: 0.8124 (tt0) cc_final: 0.7814 (tt0) REVERT: F 25 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7801 (t0) REVERT: F 82 THR cc_start: 0.9174 (p) cc_final: 0.8802 (m) REVERT: F 84 MET cc_start: 0.6974 (tpp) cc_final: 0.6726 (tpp) REVERT: F 88 TYR cc_start: 0.8688 (m-10) cc_final: 0.8425 (m-10) REVERT: H 82 LYS cc_start: 0.8496 (mttt) cc_final: 0.8012 (mmtt) REVERT: K 3818 MET cc_start: 0.8690 (mtp) cc_final: 0.8483 (tpt) REVERT: K 3846 LYS cc_start: 0.6555 (mtmt) cc_final: 0.5856 (tmtt) REVERT: K 3867 GLN cc_start: 0.7566 (mp10) cc_final: 0.7363 (pm20) REVERT: K 3873 LYS cc_start: 0.8156 (ptmt) cc_final: 0.7859 (ptpt) REVERT: K 3876 ASP cc_start: 0.8405 (m-30) cc_final: 0.7660 (p0) REVERT: K 3906 ASN cc_start: 0.7047 (m-40) cc_final: 0.6677 (m-40) REVERT: K 3938 GLU cc_start: 0.7959 (tt0) cc_final: 0.7373 (tm-30) REVERT: K 3940 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8305 (mm) REVERT: N 28 LEU cc_start: 0.8873 (tp) cc_final: 0.8635 (mp) REVERT: N 51 TRP cc_start: 0.5077 (t60) cc_final: 0.3873 (t60) REVERT: N 128 MET cc_start: 0.8255 (ttm) cc_final: 0.8029 (ttm) REVERT: N 226 ASP cc_start: 0.8299 (t0) cc_final: 0.7759 (t0) REVERT: N 320 ILE cc_start: 0.9096 (mp) cc_final: 0.8698 (pt) REVERT: T 500 MET cc_start: 0.0850 (ppp) cc_final: 0.0399 (tmm) REVERT: T 503 MET cc_start: 0.6382 (mmm) cc_final: 0.5765 (mpp) REVERT: R 72 TRP cc_start: 0.6791 (m100) cc_final: 0.5134 (m100) outliers start: 39 outliers final: 24 residues processed: 397 average time/residue: 0.1438 time to fit residues: 84.8377 Evaluate side-chains 298 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 271 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3940 LEU Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 73 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 189 optimal weight: 8.9990 chunk 175 optimal weight: 30.0000 chunk 180 optimal weight: 0.4980 chunk 105 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 84 GLN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 106 HIS E 113 HIS F 64 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 HIS ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 265 ASN R 295 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.137641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.099278 restraints weight = 54224.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.098910 restraints weight = 39862.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.100586 restraints weight = 28226.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.101055 restraints weight = 20044.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100956 restraints weight = 19277.059| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21720 Z= 0.233 Angle : 0.690 10.624 30585 Z= 0.384 Chirality : 0.043 0.200 3438 Planarity : 0.005 0.083 2870 Dihedral : 27.522 178.903 5203 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 4.26 % Allowed : 13.35 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.18), residues: 1830 helix: 1.07 (0.21), residues: 578 sheet: -2.38 (0.28), residues: 277 loop : -2.85 (0.17), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 162 TYR 0.028 0.002 TYR N 13 PHE 0.022 0.002 PHE K3885 TRP 0.023 0.002 TRP R 59 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00525 (21716) covalent geometry : angle 0.69026 (30585) hydrogen bonds : bond 0.06126 ( 898) hydrogen bonds : angle 4.11755 ( 2250) metal coordination : bond 0.00127 ( 2) Misc. bond : bond 0.00160 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 284 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7130 (tt0) cc_final: 0.6920 (tt0) REVERT: A 118 THR cc_start: 0.8698 (m) cc_final: 0.8366 (p) REVERT: A 125 GLN cc_start: 0.7638 (mt0) cc_final: 0.7397 (mm110) REVERT: C 94 ASN cc_start: 0.9375 (t0) cc_final: 0.9067 (t0) REVERT: D 44 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8320 (tm-30) REVERT: D 48 ASP cc_start: 0.6664 (t0) cc_final: 0.6335 (t0) REVERT: F 25 ASN cc_start: 0.8268 (t0) cc_final: 0.7829 (t0) REVERT: F 84 MET cc_start: 0.7272 (tpp) cc_final: 0.6984 (tpp) REVERT: F 88 TYR cc_start: 0.8732 (m-10) cc_final: 0.8444 (m-10) REVERT: G 18 SER cc_start: 0.8731 (m) cc_final: 0.8190 (p) REVERT: H 82 LYS cc_start: 0.8417 (mttt) cc_final: 0.8170 (mttm) REVERT: K 3867 GLN cc_start: 0.7817 (mp10) cc_final: 0.7550 (pm20) REVERT: K 3898 HIS cc_start: 0.8314 (m-70) cc_final: 0.7410 (m-70) REVERT: K 3938 GLU cc_start: 0.7466 (tt0) cc_final: 0.7076 (tm-30) REVERT: K 3940 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8568 (mm) REVERT: N 242 MET cc_start: 0.5817 (mtp) cc_final: 0.5616 (mtp) REVERT: N 320 ILE cc_start: 0.9269 (mp) cc_final: 0.8881 (pt) REVERT: T 503 MET cc_start: 0.6440 (mmm) cc_final: 0.5766 (mpp) REVERT: R 72 TRP cc_start: 0.6888 (m100) cc_final: 0.5973 (m100) REVERT: R 154 ARG cc_start: 0.5940 (mpp80) cc_final: 0.5673 (mpp80) REVERT: R 284 TYR cc_start: 0.1093 (m-10) cc_final: 0.0608 (m-80) outliers start: 68 outliers final: 46 residues processed: 330 average time/residue: 0.1320 time to fit residues: 67.0057 Evaluate side-chains 299 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 252 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3863 ILE Chi-restraints excluded: chain K residue 3866 ILE Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3927 VAL Chi-restraints excluded: chain K residue 3940 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain N residue 233 CYS Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 195 CYS Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 286 TRP Chi-restraints excluded: chain R residue 307 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 195 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 chunk 170 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 164 optimal weight: 50.0000 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN E 55 GLN F 64 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN N 273 GLN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 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 = 0.4181 r_free = 0.4181 target = 0.139383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.104223 restraints weight = 54390.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105560 restraints weight = 36312.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.105928 restraints weight = 27395.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.105814 restraints weight = 23711.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.105986 restraints weight = 21684.414| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21720 Z= 0.164 Angle : 0.616 11.317 30585 Z= 0.346 Chirality : 0.040 0.194 3438 Planarity : 0.004 0.073 2870 Dihedral : 27.419 177.222 5203 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.89 % Allowed : 14.98 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.19), residues: 1830 helix: 1.53 (0.21), residues: 574 sheet: -2.34 (0.27), residues: 306 loop : -2.69 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 69 TYR 0.026 0.002 TYR H 37 PHE 0.015 0.001 PHE N 189 TRP 0.019 0.002 TRP R 156 HIS 0.009 0.001 HIS K3898 Details of bonding type rmsd covalent geometry : bond 0.00363 (21716) covalent geometry : angle 0.61611 (30585) hydrogen bonds : bond 0.04708 ( 898) hydrogen bonds : angle 3.71439 ( 2250) metal coordination : bond 0.00121 ( 2) Misc. bond : bond 0.00170 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 282 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8686 (m) cc_final: 0.8414 (p) REVERT: B 31 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7553 (tptp) REVERT: C 94 ASN cc_start: 0.9295 (t0) cc_final: 0.8973 (t0) REVERT: D 54 LYS cc_start: 0.8809 (mmmm) cc_final: 0.8608 (mmmm) REVERT: F 25 ASN cc_start: 0.8479 (t0) cc_final: 0.8273 (t0) REVERT: F 84 MET cc_start: 0.7276 (tpp) cc_final: 0.6578 (tpp) REVERT: F 88 TYR cc_start: 0.8689 (m-10) cc_final: 0.7330 (m-10) REVERT: G 18 SER cc_start: 0.8617 (m) cc_final: 0.8117 (p) REVERT: G 92 GLU cc_start: 0.7771 (mm-30) cc_final: 0.6684 (mm-30) REVERT: H 30 ARG cc_start: 0.8569 (mpt180) cc_final: 0.7875 (mmp80) REVERT: H 40 LYS cc_start: 0.9067 (mptt) cc_final: 0.8822 (mptt) REVERT: H 82 LYS cc_start: 0.8386 (mttt) cc_final: 0.7940 (mmtt) REVERT: K 3818 MET cc_start: 0.8796 (mtp) cc_final: 0.8563 (tpt) REVERT: K 3845 CYS cc_start: 0.8893 (OUTLIER) cc_final: 0.7785 (m) REVERT: K 3867 GLN cc_start: 0.7875 (mp10) cc_final: 0.7642 (pm20) REVERT: K 3876 ASP cc_start: 0.8545 (m-30) cc_final: 0.7910 (p0) REVERT: K 3938 GLU cc_start: 0.7851 (tt0) cc_final: 0.7173 (tm-30) REVERT: K 3940 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8298 (mm) REVERT: N 226 ASP cc_start: 0.8553 (t0) cc_final: 0.7908 (t0) REVERT: N 242 MET cc_start: 0.5783 (mtp) cc_final: 0.5578 (mtp) REVERT: N 320 ILE cc_start: 0.9168 (mp) cc_final: 0.8845 (pt) REVERT: N 339 LEU cc_start: 0.8420 (pp) cc_final: 0.8146 (pp) REVERT: T 500 MET cc_start: -0.0507 (ptm) cc_final: -0.1460 (ptm) REVERT: T 503 MET cc_start: 0.6467 (mmm) cc_final: 0.5530 (mpp) REVERT: R 72 TRP cc_start: 0.6575 (m100) cc_final: 0.5579 (m100) REVERT: R 140 GLN cc_start: 0.4841 (mt0) cc_final: 0.4270 (mm110) REVERT: R 284 TYR cc_start: 0.1381 (m-10) cc_final: 0.1057 (m-80) outliers start: 62 outliers final: 45 residues processed: 325 average time/residue: 0.1312 time to fit residues: 66.7232 Evaluate side-chains 307 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3927 VAL Chi-restraints excluded: chain K residue 3940 LEU Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 100 optimal weight: 10.0000 chunk 171 optimal weight: 40.0000 chunk 207 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 chunk 19 optimal weight: 0.0470 overall best weight: 1.3080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN N 250 ASN N 273 GLN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 354 GLN ** R 255 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 = 0.4200 r_free = 0.4200 target = 0.140790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.106138 restraints weight = 54246.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106561 restraints weight = 34655.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.107094 restraints weight = 26893.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.107168 restraints weight = 22753.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.107264 restraints weight = 21483.203| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21720 Z= 0.142 Angle : 0.593 9.947 30585 Z= 0.334 Chirality : 0.040 0.203 3438 Planarity : 0.004 0.072 2870 Dihedral : 27.322 177.065 5203 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.64 % Allowed : 16.30 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.19), residues: 1830 helix: 1.76 (0.22), residues: 581 sheet: -2.14 (0.28), residues: 303 loop : -2.62 (0.18), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 83 TYR 0.024 0.002 TYR H 80 PHE 0.012 0.001 PHE N 189 TRP 0.021 0.001 TRP R 156 HIS 0.008 0.001 HIS K3898 Details of bonding type rmsd covalent geometry : bond 0.00310 (21716) covalent geometry : angle 0.59256 (30585) hydrogen bonds : bond 0.04265 ( 898) hydrogen bonds : angle 3.51952 ( 2250) metal coordination : bond 0.00052 ( 2) Misc. bond : bond 0.00139 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 286 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7961 (tp40) cc_final: 0.7638 (tt0) REVERT: A 118 THR cc_start: 0.8792 (m) cc_final: 0.8569 (p) REVERT: B 31 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7291 (tppt) REVERT: B 92 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8122 (ttp80) REVERT: C 56 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6889 (tp30) REVERT: C 94 ASN cc_start: 0.9290 (t0) cc_final: 0.8916 (t0) REVERT: D 48 ASP cc_start: 0.6458 (t0) cc_final: 0.6114 (t0) REVERT: F 25 ASN cc_start: 0.8620 (t0) cc_final: 0.8282 (t0) REVERT: G 18 SER cc_start: 0.8562 (m) cc_final: 0.8093 (p) REVERT: G 84 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: G 92 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7127 (mm-30) REVERT: H 30 ARG cc_start: 0.8531 (mpt180) cc_final: 0.7969 (mmp80) REVERT: H 76 ARG cc_start: 0.8323 (ttp-110) cc_final: 0.7985 (ttm170) REVERT: H 82 LYS cc_start: 0.8327 (mttt) cc_final: 0.7935 (mmtt) REVERT: K 3818 MET cc_start: 0.8730 (mtp) cc_final: 0.8513 (tpt) REVERT: K 3845 CYS cc_start: 0.8849 (OUTLIER) cc_final: 0.7813 (m) REVERT: K 3876 ASP cc_start: 0.8696 (m-30) cc_final: 0.7884 (p0) REVERT: K 3938 GLU cc_start: 0.7764 (tt0) cc_final: 0.7107 (tm-30) REVERT: N 134 MET cc_start: 0.7385 (ttp) cc_final: 0.6942 (tpp) REVERT: N 226 ASP cc_start: 0.8512 (t0) cc_final: 0.7875 (t0) REVERT: N 320 ILE cc_start: 0.9139 (mp) cc_final: 0.8799 (pt) REVERT: N 339 LEU cc_start: 0.8443 (pp) cc_final: 0.8148 (pp) REVERT: N 340 ASP cc_start: 0.8529 (t0) cc_final: 0.7996 (t0) REVERT: T 336 MET cc_start: 0.3413 (mmm) cc_final: 0.2600 (mmm) REVERT: T 500 MET cc_start: -0.0314 (ptm) cc_final: -0.1177 (ptm) REVERT: T 503 MET cc_start: 0.6453 (mmm) cc_final: 0.5531 (mpp) REVERT: R 68 LEU cc_start: 0.5260 (OUTLIER) cc_final: 0.4997 (mm) REVERT: R 72 TRP cc_start: 0.6510 (m100) cc_final: 0.5431 (m100) REVERT: R 140 GLN cc_start: 0.5183 (mt0) cc_final: 0.4761 (mm110) outliers start: 58 outliers final: 39 residues processed: 324 average time/residue: 0.1313 time to fit residues: 65.9155 Evaluate side-chains 305 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 260 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain T residue 384 SER Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Chi-restraints excluded: chain R residue 301 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 4 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 127 optimal weight: 0.0470 chunk 81 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 7 optimal weight: 0.0050 chunk 110 optimal weight: 5.9990 chunk 181 optimal weight: 20.0000 overall best weight: 2.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN N 250 ASN N 273 GLN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 255 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.138845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.101108 restraints weight = 54111.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.101755 restraints weight = 38267.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.101822 restraints weight = 24173.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.102204 restraints weight = 23253.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.102437 restraints weight = 21019.054| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21720 Z= 0.184 Angle : 0.630 9.148 30585 Z= 0.351 Chirality : 0.041 0.223 3438 Planarity : 0.004 0.075 2870 Dihedral : 27.383 177.630 5203 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 4.01 % Allowed : 16.74 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.19), residues: 1830 helix: 1.55 (0.21), residues: 580 sheet: -2.08 (0.28), residues: 298 loop : -2.55 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 83 TYR 0.028 0.002 TYR H 80 PHE 0.012 0.001 PHE K3885 TRP 0.022 0.002 TRP R 156 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00412 (21716) covalent geometry : angle 0.62977 (30585) hydrogen bonds : bond 0.05052 ( 898) hydrogen bonds : angle 3.71079 ( 2250) metal coordination : bond 0.00114 ( 2) Misc. bond : bond 0.00171 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 263 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8223 (ttp80) REVERT: C 56 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6905 (tp30) REVERT: C 94 ASN cc_start: 0.9307 (t0) cc_final: 0.8879 (t0) REVERT: D 48 ASP cc_start: 0.6702 (t0) cc_final: 0.6338 (t0) REVERT: D 54 LYS cc_start: 0.8960 (mmmm) cc_final: 0.8704 (mmmm) REVERT: E 63 ARG cc_start: 0.7877 (mmm-85) cc_final: 0.7529 (tpp-160) REVERT: F 25 ASN cc_start: 0.8717 (t0) cc_final: 0.8363 (t0) REVERT: G 18 SER cc_start: 0.8655 (m) cc_final: 0.8146 (p) REVERT: G 84 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: H 30 ARG cc_start: 0.8571 (mpt180) cc_final: 0.7897 (mmp80) REVERT: H 40 LYS cc_start: 0.9081 (mptt) cc_final: 0.8874 (mptt) REVERT: H 76 ARG cc_start: 0.8446 (ttp-110) cc_final: 0.8210 (ttm170) REVERT: H 82 LYS cc_start: 0.8400 (mttt) cc_final: 0.7966 (mmtt) REVERT: K 3777 MET cc_start: 0.3701 (mmp) cc_final: 0.3302 (mmp) REVERT: K 3818 MET cc_start: 0.8971 (mtp) cc_final: 0.8633 (tpt) REVERT: K 3845 CYS cc_start: 0.8568 (OUTLIER) cc_final: 0.7530 (m) REVERT: K 3867 GLN cc_start: 0.7713 (pm20) cc_final: 0.7508 (pm20) REVERT: K 3876 ASP cc_start: 0.8806 (m-30) cc_final: 0.8018 (p0) REVERT: K 3938 GLU cc_start: 0.7537 (tt0) cc_final: 0.6838 (tm-30) REVERT: N 134 MET cc_start: 0.7643 (ttp) cc_final: 0.7001 (tpp) REVERT: N 226 ASP cc_start: 0.8502 (t0) cc_final: 0.7578 (t0) REVERT: N 320 ILE cc_start: 0.9205 (mp) cc_final: 0.8870 (pt) REVERT: T 336 MET cc_start: 0.2842 (mmm) cc_final: 0.2215 (mmm) REVERT: T 476 LYS cc_start: 0.5946 (OUTLIER) cc_final: 0.5124 (tppp) REVERT: T 500 MET cc_start: -0.0314 (ptm) cc_final: -0.1430 (ptm) REVERT: T 503 MET cc_start: 0.6517 (mmm) cc_final: 0.5492 (mpp) REVERT: R 72 TRP cc_start: 0.6815 (m100) cc_final: 0.5518 (m100) REVERT: R 140 GLN cc_start: 0.5421 (mt0) cc_final: 0.4976 (mm110) REVERT: R 154 ARG cc_start: 0.5696 (mpp80) cc_final: 0.5433 (mpp80) REVERT: R 228 TYR cc_start: 0.7832 (m-80) cc_final: 0.7561 (m-80) outliers start: 64 outliers final: 45 residues processed: 306 average time/residue: 0.1330 time to fit residues: 62.7575 Evaluate side-chains 303 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 253 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain T residue 476 LYS Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Chi-restraints excluded: chain R residue 301 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 4 optimal weight: 6.9990 chunk 42 optimal weight: 0.0030 chunk 24 optimal weight: 0.0770 chunk 10 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 167 optimal weight: 0.0030 chunk 123 optimal weight: 0.0670 chunk 52 optimal weight: 0.7980 chunk 141 optimal weight: 0.0870 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.0474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3907 HIS N 12 ASN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 HIS ** 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 = 0.4251 r_free = 0.4251 target = 0.144425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.110752 restraints weight = 54538.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.111142 restraints weight = 32855.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.111771 restraints weight = 25268.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.111816 restraints weight = 21883.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.111996 restraints weight = 20287.206| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21720 Z= 0.132 Angle : 0.590 8.848 30585 Z= 0.327 Chirality : 0.039 0.210 3438 Planarity : 0.003 0.065 2870 Dihedral : 27.084 175.760 5203 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.76 % Allowed : 17.93 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.20), residues: 1830 helix: 1.93 (0.22), residues: 588 sheet: -1.84 (0.29), residues: 315 loop : -2.48 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 83 TYR 0.038 0.001 TYR F 88 PHE 0.015 0.001 PHE N 189 TRP 0.023 0.001 TRP R 156 HIS 0.006 0.001 HIS R 44 Details of bonding type rmsd covalent geometry : bond 0.00279 (21716) covalent geometry : angle 0.58973 (30585) hydrogen bonds : bond 0.03653 ( 898) hydrogen bonds : angle 3.18519 ( 2250) metal coordination : bond 0.00005 ( 2) Misc. bond : bond 0.00136 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 307 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8092 (ttp80) REVERT: C 56 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6883 (tp30) REVERT: C 94 ASN cc_start: 0.9263 (t0) cc_final: 0.8827 (t0) REVERT: D 48 ASP cc_start: 0.6506 (t0) cc_final: 0.6225 (t0) REVERT: D 54 LYS cc_start: 0.8688 (mmmm) cc_final: 0.8418 (mmmm) REVERT: F 25 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8123 (t0) REVERT: F 88 TYR cc_start: 0.8533 (m-10) cc_final: 0.8233 (m-80) REVERT: G 18 SER cc_start: 0.8497 (m) cc_final: 0.8064 (p) REVERT: G 92 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7137 (mm-30) REVERT: H 70 ILE cc_start: 0.9146 (tp) cc_final: 0.8938 (tp) REVERT: H 82 LYS cc_start: 0.8075 (mttt) cc_final: 0.7795 (mmtt) REVERT: K 3777 MET cc_start: 0.3977 (OUTLIER) cc_final: 0.3559 (mmp) REVERT: K 3845 CYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7545 (m) REVERT: K 3867 GLN cc_start: 0.7759 (pm20) cc_final: 0.7515 (pm20) REVERT: K 3876 ASP cc_start: 0.8831 (m-30) cc_final: 0.8034 (p0) REVERT: K 3886 ARG cc_start: 0.8566 (tpp80) cc_final: 0.8354 (tpt-90) REVERT: K 3906 ASN cc_start: 0.6596 (m-40) cc_final: 0.6361 (m110) REVERT: K 3931 MET cc_start: 0.7077 (tpp) cc_final: 0.6730 (tpt) REVERT: K 3938 GLU cc_start: 0.7323 (tt0) cc_final: 0.7011 (tm-30) REVERT: N 51 TRP cc_start: 0.4639 (t60) cc_final: 0.3592 (t60) REVERT: N 134 MET cc_start: 0.7389 (ttp) cc_final: 0.6972 (tpp) REVERT: N 226 ASP cc_start: 0.8513 (t0) cc_final: 0.7574 (t0) REVERT: N 320 ILE cc_start: 0.9154 (mp) cc_final: 0.8845 (pt) REVERT: N 339 LEU cc_start: 0.8490 (pp) cc_final: 0.8204 (pp) REVERT: N 340 ASP cc_start: 0.8397 (t0) cc_final: 0.7776 (t0) REVERT: T 336 MET cc_start: 0.3155 (mmm) cc_final: 0.2651 (mmm) REVERT: T 476 LYS cc_start: 0.5798 (OUTLIER) cc_final: 0.4863 (tppp) REVERT: T 500 MET cc_start: -0.0360 (ptm) cc_final: -0.1209 (ptm) REVERT: T 503 MET cc_start: 0.6485 (mmm) cc_final: 0.5523 (mpp) REVERT: R 44 HIS cc_start: 0.3843 (OUTLIER) cc_final: 0.3484 (t-90) REVERT: R 72 TRP cc_start: 0.6461 (m100) cc_final: 0.5168 (m100) REVERT: R 204 GLN cc_start: 0.7655 (mp10) cc_final: 0.7255 (tt0) REVERT: R 228 TYR cc_start: 0.7704 (m-80) cc_final: 0.7437 (m-80) outliers start: 44 outliers final: 26 residues processed: 333 average time/residue: 0.1377 time to fit residues: 70.2820 Evaluate side-chains 305 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3777 MET Chi-restraints excluded: chain K residue 3816 MET Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3926 ILE Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 128 MET Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain T residue 384 SER Chi-restraints excluded: chain T residue 476 LYS Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 188 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 200 optimal weight: 30.0000 chunk 82 optimal weight: 10.0000 chunk 41 optimal weight: 0.3980 chunk 91 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3907 HIS N 12 ASN ** N 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 170 HIS ** 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 = 0.4168 r_free = 0.4168 target = 0.138527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.100615 restraints weight = 53496.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.101014 restraints weight = 37443.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.101192 restraints weight = 25306.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.101723 restraints weight = 23900.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.101874 restraints weight = 20537.176| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21720 Z= 0.209 Angle : 0.653 10.797 30585 Z= 0.360 Chirality : 0.042 0.192 3438 Planarity : 0.004 0.077 2870 Dihedral : 27.358 178.681 5203 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.51 % Allowed : 18.50 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.19), residues: 1830 helix: 1.45 (0.21), residues: 586 sheet: -1.94 (0.28), residues: 310 loop : -2.51 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 307 TYR 0.029 0.002 TYR F 88 PHE 0.014 0.002 PHE K3885 TRP 0.018 0.002 TRP R 156 HIS 0.010 0.001 HIS K3898 Details of bonding type rmsd covalent geometry : bond 0.00473 (21716) covalent geometry : angle 0.65271 (30585) hydrogen bonds : bond 0.05427 ( 898) hydrogen bonds : angle 3.67213 ( 2250) metal coordination : bond 0.00100 ( 2) Misc. bond : bond 0.00169 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 262 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.7870 (tpt) cc_final: 0.7453 (tpt) REVERT: B 92 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8202 (ttp80) REVERT: C 73 ASN cc_start: 0.8937 (t160) cc_final: 0.8641 (t0) REVERT: D 48 ASP cc_start: 0.6662 (t0) cc_final: 0.6316 (t0) REVERT: F 25 ASN cc_start: 0.8495 (t0) cc_final: 0.8243 (t0) REVERT: F 88 TYR cc_start: 0.8611 (m-10) cc_final: 0.8323 (m-80) REVERT: G 18 SER cc_start: 0.8654 (m) cc_final: 0.8153 (p) REVERT: G 104 GLN cc_start: 0.8765 (mp10) cc_final: 0.8137 (mp10) REVERT: H 30 ARG cc_start: 0.8631 (mpt180) cc_final: 0.7928 (mmp80) REVERT: H 82 LYS cc_start: 0.8325 (mttt) cc_final: 0.8083 (mttm) REVERT: K 3777 MET cc_start: 0.3555 (OUTLIER) cc_final: 0.3176 (mmp) REVERT: K 3845 CYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7577 (m) REVERT: K 3867 GLN cc_start: 0.7728 (pm20) cc_final: 0.7459 (pm20) REVERT: K 3876 ASP cc_start: 0.8854 (m-30) cc_final: 0.8130 (p0) REVERT: K 3906 ASN cc_start: 0.6671 (m-40) cc_final: 0.6116 (m-40) REVERT: K 3938 GLU cc_start: 0.7392 (tt0) cc_final: 0.6893 (tm-30) REVERT: N 134 MET cc_start: 0.7745 (ttp) cc_final: 0.7092 (tpp) REVERT: N 256 LYS cc_start: 0.8723 (tppt) cc_final: 0.8387 (tppt) REVERT: N 320 ILE cc_start: 0.9188 (mp) cc_final: 0.8833 (pt) REVERT: N 339 LEU cc_start: 0.8389 (pp) cc_final: 0.8130 (pp) REVERT: O 1 MET cc_start: 0.3739 (mmt) cc_final: 0.3396 (ptm) REVERT: T 336 MET cc_start: 0.2813 (mmm) cc_final: 0.2271 (mmm) REVERT: T 476 LYS cc_start: 0.6084 (OUTLIER) cc_final: 0.5182 (tppp) REVERT: T 500 MET cc_start: -0.0509 (ptm) cc_final: -0.1633 (ptm) REVERT: T 503 MET cc_start: 0.6293 (mmm) cc_final: 0.5525 (mpp) REVERT: R 44 HIS cc_start: 0.4971 (OUTLIER) cc_final: 0.4341 (t-90) REVERT: R 53 PHE cc_start: 0.5078 (OUTLIER) cc_final: 0.3784 (m-80) REVERT: R 72 TRP cc_start: 0.6806 (m100) cc_final: 0.5511 (m100) outliers start: 56 outliers final: 44 residues processed: 304 average time/residue: 0.1360 time to fit residues: 63.8580 Evaluate side-chains 305 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3777 MET Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3863 ILE Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3898 HIS Chi-restraints excluded: chain K residue 3940 LEU Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 476 LYS Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 41 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN ** N 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 140 GLN ** R 170 HIS ** 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 = 0.4155 r_free = 0.4155 target = 0.137826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.099609 restraints weight = 53571.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.099382 restraints weight = 38660.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.100593 restraints weight = 26861.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.101373 restraints weight = 20507.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.101461 restraints weight = 19422.166| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21720 Z= 0.214 Angle : 0.675 12.143 30585 Z= 0.370 Chirality : 0.042 0.193 3438 Planarity : 0.004 0.076 2870 Dihedral : 27.341 178.160 5203 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.70 % Allowed : 18.93 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.19), residues: 1830 helix: 1.28 (0.21), residues: 582 sheet: -1.94 (0.28), residues: 307 loop : -2.53 (0.18), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 307 TYR 0.028 0.002 TYR B 88 PHE 0.014 0.002 PHE E 84 TRP 0.017 0.002 TRP N 35 HIS 0.009 0.001 HIS K3898 Details of bonding type rmsd covalent geometry : bond 0.00487 (21716) covalent geometry : angle 0.67523 (30585) hydrogen bonds : bond 0.05416 ( 898) hydrogen bonds : angle 3.79015 ( 2250) metal coordination : bond 0.00121 ( 2) Misc. bond : bond 0.00184 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 263 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.7881 (tpt) cc_final: 0.7651 (tpt) REVERT: B 92 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8207 (ttp80) REVERT: D 48 ASP cc_start: 0.6611 (t0) cc_final: 0.6277 (t0) REVERT: D 54 LYS cc_start: 0.9008 (mmmm) cc_final: 0.8701 (mmmm) REVERT: F 88 TYR cc_start: 0.8720 (m-10) cc_final: 0.8398 (m-80) REVERT: G 18 SER cc_start: 0.8709 (m) cc_final: 0.8183 (p) REVERT: G 84 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: H 30 ARG cc_start: 0.8631 (mpt180) cc_final: 0.7966 (mmp80) REVERT: H 82 LYS cc_start: 0.8408 (mttt) cc_final: 0.8142 (mttm) REVERT: K 3777 MET cc_start: 0.3475 (OUTLIER) cc_final: 0.3088 (mmp) REVERT: K 3845 CYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7716 (m) REVERT: K 3867 GLN cc_start: 0.7769 (pm20) cc_final: 0.7531 (pm20) REVERT: K 3876 ASP cc_start: 0.8848 (m-30) cc_final: 0.8147 (p0) REVERT: K 3906 ASN cc_start: 0.6615 (m-40) cc_final: 0.6395 (m110) REVERT: K 3925 HIS cc_start: 0.6140 (m-70) cc_final: 0.5806 (m90) REVERT: K 3931 MET cc_start: 0.7132 (tpp) cc_final: 0.6597 (tpt) REVERT: K 3938 GLU cc_start: 0.7355 (tt0) cc_final: 0.6960 (tm-30) REVERT: N 134 MET cc_start: 0.7743 (ttp) cc_final: 0.7093 (tpp) REVERT: N 256 LYS cc_start: 0.8676 (tppt) cc_final: 0.8377 (tppt) REVERT: N 320 ILE cc_start: 0.9231 (mp) cc_final: 0.8893 (pt) REVERT: T 336 MET cc_start: 0.3550 (mmm) cc_final: 0.2867 (mmm) REVERT: T 476 LYS cc_start: 0.6100 (OUTLIER) cc_final: 0.5236 (tppp) REVERT: T 500 MET cc_start: -0.0500 (ptm) cc_final: -0.1646 (ptm) REVERT: T 503 MET cc_start: 0.6343 (mmm) cc_final: 0.5682 (mpp) REVERT: R 44 HIS cc_start: 0.5043 (OUTLIER) cc_final: 0.4437 (t-90) REVERT: R 72 TRP cc_start: 0.6579 (m100) cc_final: 0.5456 (m100) REVERT: R 154 ARG cc_start: 0.6876 (mtt180) cc_final: 0.6570 (mtt180) REVERT: R 196 ARG cc_start: 0.6380 (mtt180) cc_final: 0.6072 (mtt90) outliers start: 59 outliers final: 48 residues processed: 305 average time/residue: 0.1648 time to fit residues: 77.7778 Evaluate side-chains 307 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 253 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3777 MET Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3839 HIS Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3863 ILE Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3898 HIS Chi-restraints excluded: chain K residue 3940 LEU Chi-restraints excluded: chain K residue 3946 PHE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 258 CYS Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain T residue 316 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 476 LYS Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Chi-restraints excluded: chain R residue 309 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 170 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 = 0.4197 r_free = 0.4197 target = 0.140805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.106207 restraints weight = 53494.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.106671 restraints weight = 31529.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.107225 restraints weight = 23158.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.107343 restraints weight = 19849.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.107431 restraints weight = 18641.677| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21720 Z= 0.142 Angle : 0.625 11.116 30585 Z= 0.344 Chirality : 0.040 0.180 3438 Planarity : 0.004 0.072 2870 Dihedral : 27.155 176.737 5203 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.70 % Allowed : 20.00 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.20), residues: 1830 helix: 1.66 (0.22), residues: 584 sheet: -1.90 (0.28), residues: 321 loop : -2.47 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 307 TYR 0.026 0.002 TYR F 88 PHE 0.014 0.001 PHE N 189 TRP 0.019 0.001 TRP N 35 HIS 0.008 0.001 HIS K3898 Details of bonding type rmsd covalent geometry : bond 0.00316 (21716) covalent geometry : angle 0.62534 (30585) hydrogen bonds : bond 0.04314 ( 898) hydrogen bonds : angle 3.45721 ( 2250) metal coordination : bond 0.00076 ( 2) Misc. bond : bond 0.00156 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 271 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8129 (ttp80) REVERT: C 94 ASN cc_start: 0.9310 (t0) cc_final: 0.8852 (t0) REVERT: D 48 ASP cc_start: 0.6692 (t0) cc_final: 0.6371 (t0) REVERT: D 54 LYS cc_start: 0.8903 (mmmm) cc_final: 0.8565 (mmmm) REVERT: F 25 ASN cc_start: 0.8296 (t0) cc_final: 0.8014 (t0) REVERT: F 88 TYR cc_start: 0.8626 (m-10) cc_final: 0.8407 (m-80) REVERT: G 18 SER cc_start: 0.8560 (m) cc_final: 0.8083 (p) REVERT: G 24 GLN cc_start: 0.8544 (mm-40) cc_final: 0.7715 (tp-100) REVERT: G 104 GLN cc_start: 0.8653 (mp10) cc_final: 0.8057 (mp10) REVERT: H 30 ARG cc_start: 0.8673 (mpt180) cc_final: 0.8003 (mmp80) REVERT: H 82 LYS cc_start: 0.8436 (mttt) cc_final: 0.8195 (mttm) REVERT: K 3777 MET cc_start: 0.3336 (OUTLIER) cc_final: 0.3103 (mmp) REVERT: K 3845 CYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7758 (m) REVERT: K 3867 GLN cc_start: 0.7761 (pm20) cc_final: 0.7526 (pm20) REVERT: K 3876 ASP cc_start: 0.8785 (m-30) cc_final: 0.8041 (p0) REVERT: K 3906 ASN cc_start: 0.6645 (m-40) cc_final: 0.6063 (m-40) REVERT: K 3925 HIS cc_start: 0.6040 (m-70) cc_final: 0.5673 (m90) REVERT: K 3931 MET cc_start: 0.6985 (tpp) cc_final: 0.6552 (tpt) REVERT: N 134 MET cc_start: 0.7490 (ttp) cc_final: 0.7006 (tpp) REVERT: N 256 LYS cc_start: 0.8654 (tppt) cc_final: 0.8351 (tppt) REVERT: N 288 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7990 (ttmt) REVERT: N 320 ILE cc_start: 0.9132 (mp) cc_final: 0.8828 (pt) REVERT: N 339 LEU cc_start: 0.8420 (pp) cc_final: 0.8133 (pp) REVERT: N 340 ASP cc_start: 0.8976 (t0) cc_final: 0.8412 (t0) REVERT: T 336 MET cc_start: 0.4045 (mmm) cc_final: 0.3378 (mmm) REVERT: T 476 LYS cc_start: 0.5840 (OUTLIER) cc_final: 0.4884 (tppp) REVERT: T 500 MET cc_start: -0.0257 (ptm) cc_final: -0.1238 (ptm) REVERT: T 503 MET cc_start: 0.6220 (mmm) cc_final: 0.5725 (mpp) REVERT: R 44 HIS cc_start: 0.4035 (OUTLIER) cc_final: 0.3658 (t-90) REVERT: R 53 PHE cc_start: 0.4791 (OUTLIER) cc_final: 0.3318 (m-80) REVERT: R 72 TRP cc_start: 0.6274 (m100) cc_final: 0.5238 (m100) outliers start: 43 outliers final: 33 residues processed: 304 average time/residue: 0.1548 time to fit residues: 73.5309 Evaluate side-chains 300 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3777 MET Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3898 HIS Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain T residue 476 LYS Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Chi-restraints excluded: chain R residue 309 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 15 optimal weight: 0.4980 chunk 155 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 201 optimal weight: 50.0000 chunk 159 optimal weight: 0.0570 chunk 73 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 overall best weight: 3.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.137906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.101661 restraints weight = 53842.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.101597 restraints weight = 33364.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.102311 restraints weight = 22852.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.102576 restraints weight = 21627.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.102550 restraints weight = 19442.299| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21720 Z= 0.212 Angle : 0.679 12.391 30585 Z= 0.371 Chirality : 0.043 0.345 3438 Planarity : 0.004 0.076 2870 Dihedral : 27.299 177.983 5203 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 3.26 % Allowed : 20.00 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.19), residues: 1830 helix: 1.38 (0.21), residues: 582 sheet: -1.82 (0.28), residues: 311 loop : -2.48 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 196 TYR 0.024 0.002 TYR F 88 PHE 0.015 0.002 PHE K3885 TRP 0.018 0.002 TRP N 35 HIS 0.008 0.001 HIS K3898 Details of bonding type rmsd covalent geometry : bond 0.00482 (21716) covalent geometry : angle 0.67938 (30585) hydrogen bonds : bond 0.05497 ( 898) hydrogen bonds : angle 3.80716 ( 2250) metal coordination : bond 0.00108 ( 2) Misc. bond : bond 0.00176 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3101.97 seconds wall clock time: 54 minutes 22.26 seconds (3262.26 seconds total)