Starting phenix.real_space_refine on Sun Sep 13 23:12:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kix_0694/09_2026/6kix_0694.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kix_0694/09_2026/6kix_0694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6kix_0694/09_2026/6kix_0694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kix_0694/09_2026/6kix_0694.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kix_0694/09_2026/6kix_0694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kix_0694/09_2026/6kix_0694.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6kix_0694/09_2026/6kix_0694.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kix_0694/09_2026/6kix_0694.cif" } resolution = 4.1 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= 0.003 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 8554 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 290 5.49 5 S 60 5.16 5 C 11646 2.51 5 N 3619 2.21 5 O 4284 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19900 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 738 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "N" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2768 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain breaks: 1 Chain: "K" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1436 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2326 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain: "T" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1399 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 12, 'TRANS': 163} Chain breaks: 1 Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {' ZN': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 2} Not linked: pdbres="SAH K4001 " pdbres=" ZN K4002 " Not linked: pdbres=" ZN K4002 " pdbres="LYS K4003 " List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16036 SG CYS K3957 95.433 67.783 25.595 1.00104.51 S ATOM 16050 SG CYS K3959 93.563 70.018 23.360 1.00110.33 S Time building chain proxies: 4.00, per 1000 atoms: 0.20 Number of scatterers: 19900 At special positions: 0 Unit cell: (162.8, 150.7, 121, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 60 16.00 P 290 15.00 O 4284 8.00 N 3619 7.00 C 11646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 665.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K4002 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3959 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3957 " 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3292 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 28 sheets defined 32.5% alpha, 11.8% beta 145 base pairs and 238 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.832A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 4.093A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.707A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.771A 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 77 removed outlier: 4.732A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.838A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.939A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 4.094A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.196A 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 52 through 81 removed outlier: 3.668A pdb=" N MET D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.905A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 4.028A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.832A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.094A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.707A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.550A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 29' Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.768A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.560A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 4.182A 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: 4.023A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 4.430A 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 removed outlier: 3.535A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.813A pdb=" N MET H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'N' and resid 228 through 234 Processing helix chain 'K' and resid 3815 through 3828 removed outlier: 3.725A pdb=" N ARG K3819 " --> pdb=" O PRO K3815 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS K3822 " --> pdb=" O MET K3818 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS K3824 " --> pdb=" O PHE K3820 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS K3825 " --> pdb=" O ARG K3821 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS K3828 " --> pdb=" O LYS K3824 " (cutoff:3.500A) Processing helix chain 'K' and resid 3866 through 3879 removed outlier: 3.637A pdb=" N LYS K3870 " --> pdb=" O ILE K3866 " (cutoff:3.500A) Processing helix chain 'K' and resid 3900 through 3904 removed outlier: 4.181A pdb=" N ARG K3903 " --> pdb=" O ASN K3900 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE K3904 " --> pdb=" O ALA K3901 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 3900 through 3904' Processing helix chain 'T' and resid 368 through 372 removed outlier: 3.778A pdb=" N GLY T 371 " --> pdb=" O SER T 368 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR T 372 " --> pdb=" O LYS T 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 368 through 372' Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.599A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.133A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.163A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'N' and resid 31 through 32 removed outlier: 3.755A pdb=" N THR N 31 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA N 40 " --> pdb=" O THR N 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 112 through 115 removed outlier: 3.909A pdb=" N LYS N 112 " --> pdb=" O CYS N 126 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET N 134 " --> pdb=" O VAL N 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 156 through 159 removed outlier: 3.668A pdb=" N PHE N 189 " --> pdb=" O ILE N 175 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 212 through 216 removed outlier: 3.669A pdb=" N GLN N 243 " --> pdb=" O VAL N 224 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 254 through 259 removed outlier: 3.850A pdb=" N LYS N 256 " --> pdb=" O GLY N 269 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS N 258 " --> pdb=" O VAL N 267 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL N 267 " --> pdb=" O CYS N 258 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE N 266 " --> pdb=" O TRP N 279 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR N 277 " --> pdb=" O ALA N 268 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU N 276 " --> pdb=" O LEU N 290 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS N 288 " --> pdb=" O ILE N 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 300 through 303 removed outlier: 3.721A pdb=" N ASP N 300 " --> pdb=" O ILE N 313 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE N 310 " --> pdb=" O TRP N 321 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP N 321 " --> pdb=" O ILE N 310 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER N 312 " --> pdb=" O SER N 319 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL N 317 " --> pdb=" O SER N 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 337 through 338 removed outlier: 6.699A pdb=" N LYS N 337 " --> pdb=" O GLY K3899 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 3834 through 3835 Processing sheet with id=AB4, first strand: chain 'K' and resid 3856 through 3857 removed outlier: 4.053A pdb=" N ILE K3856 " --> pdb=" O ILE K3928 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL K3927 " --> pdb=" O ARG K3916 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG K3916 " --> pdb=" O VAL K3927 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 3862 through 3864 Processing sheet with id=AB6, first strand: chain 'K' and resid 3919 through 3920 removed outlier: 3.971A pdb=" N ILE K3920 " --> pdb=" O GLN K3923 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 36 through 40 removed outlier: 7.499A pdb=" N LEU R 329 " --> pdb=" O LYS R 38 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER R 318 " --> pdb=" O LYS R 328 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP R 330 " --> pdb=" O ILE R 316 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE R 316 " --> pdb=" O TRP R 330 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER R 306 " --> pdb=" O ALA R 319 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 48 through 53 removed outlier: 3.985A pdb=" N SER R 50 " --> pdb=" O SER R 63 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER R 63 " --> pdb=" O SER R 50 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS R 52 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA R 61 " --> pdb=" O LYS R 52 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'R' and resid 69 through 70 Processing sheet with id=AC1, first strand: chain 'R' and resid 90 through 93 removed outlier: 3.900A pdb=" N ASP R 92 " --> pdb=" O ALA R 105 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 132 through 137 removed outlier: 3.890A pdb=" N CYS R 134 " --> pdb=" O GLY R 147 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY R 147 " --> pdb=" O CYS R 134 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN R 136 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 174 through 179 removed outlier: 7.401A pdb=" N SER R 189 " --> pdb=" O SER R 175 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL R 177 " --> pdb=" O VAL R 187 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL R 187 " --> pdb=" O VAL R 177 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE R 179 " --> pdb=" O LEU R 185 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU R 185 " --> pdb=" O PHE R 179 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG R 196 " --> pdb=" O SER R 188 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE R 197 " --> pdb=" O LEU R 206 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 228 through 231 removed outlier: 3.583A pdb=" N ILE R 229 " --> pdb=" O TRP R 241 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 273 through 276 removed outlier: 3.608A pdb=" N TRP R 286 " --> pdb=" O ILE R 274 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL R 283 " --> pdb=" O LEU R 297 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU R 297 " --> pdb=" O VAL R 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'T' and resid 299 through 300 Processing sheet with id=AC7, first strand: chain 'T' and resid 316 through 317 removed outlier: 3.672A pdb=" N SER T 347 " --> pdb=" O PHE T 469 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA T 471 " --> pdb=" O GLY T 345 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY T 345 " --> pdb=" O ALA T 471 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER T 473 " --> pdb=" O ARG T 343 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG T 343 " --> pdb=" O SER T 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 331 through 332 Processing sheet with id=AC9, first strand: chain 'T' and resid 373 through 374 Processing sheet with id=AD1, first strand: chain 'T' and resid 447 through 451 removed outlier: 7.551A pdb=" N ILE T 447 " --> pdb=" O ALA T 459 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY T 457 " --> pdb=" O PHE T 449 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS T 451 " --> pdb=" O ASN T 455 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASN T 455 " --> pdb=" O LYS T 451 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 238 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 2.27 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: 4120 1.33 - 1.45: 5971 1.45 - 1.57: 10130 1.57 - 1.69: 578 1.69 - 1.81: 87 Bond restraints: 20886 Sorted by residual: bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.435 1.486 -0.051 1.30e-02 5.92e+03 1.55e+01 bond pdb=" C5' DA I 131 " pdb=" C4' DA I 131 " ideal model delta sigma weight residual 1.512 1.539 -0.027 7.00e-03 2.04e+04 1.43e+01 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.435 1.483 -0.048 1.30e-02 5.92e+03 1.35e+01 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.25e+01 bond pdb=" C3' DC I 54 " pdb=" C2' DC I 54 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 ... (remaining 20881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 27845 1.98 - 3.96: 1490 3.96 - 5.94: 103 5.94 - 7.92: 23 7.92 - 9.90: 7 Bond angle restraints: 29468 Sorted by residual: angle pdb=" O4' DA I 139 " pdb=" C4' DA I 139 " pdb=" C3' DA I 139 " ideal model delta sigma weight residual 106.00 102.59 3.41 6.00e-01 2.78e+00 3.23e+01 angle pdb=" O4' DA J 14 " pdb=" C4' DA J 14 " pdb=" C3' DA J 14 " ideal model delta sigma weight residual 106.00 102.63 3.37 6.00e-01 2.78e+00 3.15e+01 angle pdb=" O4' DG J 32 " pdb=" C4' DG J 32 " pdb=" C3' DG J 32 " ideal model delta sigma weight residual 106.00 102.89 3.11 6.00e-01 2.78e+00 2.69e+01 angle pdb=" N ILE K3866 " pdb=" CA ILE K3866 " pdb=" C ILE K3866 " ideal model delta sigma weight residual 113.47 108.30 5.17 1.01e+00 9.80e-01 2.62e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.87 -2.97 6.00e-01 2.78e+00 2.46e+01 ... (remaining 29463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 10304 34.20 - 68.40: 1421 68.40 - 102.60: 28 102.60 - 136.80: 1 136.80 - 171.00: 3 Dihedral angle restraints: 11757 sinusoidal: 6651 harmonic: 5106 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 180.00 134.57 45.43 0 5.00e+00 4.00e-02 8.25e+01 dihedral pdb=" CA ARG K3864 " pdb=" C ARG K3864 " pdb=" N SER K3865 " pdb=" CA SER K3865 " ideal model delta harmonic sigma weight residual -180.00 -143.11 -36.89 0 5.00e+00 4.00e-02 5.44e+01 dihedral pdb=" CA ARG N 251 " pdb=" C ARG N 251 " pdb=" N THR N 252 " pdb=" CA THR N 252 " ideal model delta harmonic sigma weight residual 180.00 146.80 33.20 0 5.00e+00 4.00e-02 4.41e+01 ... (remaining 11754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2170 0.048 - 0.095: 869 0.095 - 0.143: 234 0.143 - 0.190: 25 0.190 - 0.238: 9 Chirality restraints: 3307 Sorted by residual: chirality pdb=" C3' DT J 15 " pdb=" C4' DT J 15 " pdb=" O3' DT J 15 " pdb=" C2' DT J 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C1' SAH K4001 " pdb=" C2' SAH K4001 " pdb=" N9 SAH K4001 " pdb=" O4' SAH K4001 " both_signs ideal model delta sigma weight residual False 2.35 2.58 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA SER N 108 " pdb=" N SER N 108 " pdb=" C SER N 108 " pdb=" CB SER N 108 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 3304 not shown) Planarity restraints: 2726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.073 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO B 32 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 223 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO R 224 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO R 224 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 224 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 30 " 0.034 2.00e-02 2.50e+03 1.54e-02 6.51e+00 pdb=" N9 DA I 30 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA I 30 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 30 " -0.017 2.00e-02 2.50e+03 pdb=" C5 DA I 30 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 30 " 0.010 2.00e-02 2.50e+03 pdb=" N6 DA I 30 " 0.016 2.00e-02 2.50e+03 pdb=" N1 DA I 30 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA I 30 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 30 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DA I 30 " -0.006 2.00e-02 2.50e+03 ... (remaining 2723 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2366 2.75 - 3.29: 16728 3.29 - 3.83: 34756 3.83 - 4.36: 39208 4.36 - 4.90: 61528 Nonbonded interactions: 154586 Sorted by model distance: nonbonded pdb=" N CYS K3959 " pdb="ZN ZN K4002 " model vdw 2.219 2.310 nonbonded pdb=" OD1 ASP R 108 " pdb=" OG1 THR R 110 " model vdw 2.257 3.040 nonbonded pdb=" O TYR R 131 " pdb=" OG SER R 148 " model vdw 2.263 3.040 nonbonded pdb=" OG SER R 278 " pdb=" OD1 ASP R 280 " model vdw 2.298 3.040 nonbonded pdb=" OG SER R 223 " pdb=" OD1 ASN R 225 " model vdw 2.301 3.040 ... (remaining 154581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 120) selection = (chain 'H' and resid 28 through 120) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.910 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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 0.403 20889 Z= 0.527 Angle : 0.936 9.897 29468 Z= 0.703 Chirality : 0.054 0.238 3307 Planarity : 0.007 0.111 2726 Dihedral : 22.722 171.004 8465 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.17), residues: 1728 helix: -1.12 (0.18), residues: 556 sheet: -3.16 (0.28), residues: 246 loop : -3.27 (0.16), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K3765 TYR 0.035 0.002 TYR B 51 PHE 0.017 0.002 PHE N 213 TRP 0.025 0.003 TRP N 51 HIS 0.011 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.52 (20886) covalent geometry : angle 0.93586 / 0.70 (29468) hydrogen bonds : bond 0.14583 / 9.72 ( 854) hydrogen bonds : angle 5.29545 / 3.69 ( 2142) metal coordination : bond 0.32612 / 22.12 ( 2) Misc. bond : bond 0.00101 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8260 (mtt) cc_final: 0.7800 (mtp) REVERT: B 58 LEU cc_start: 0.9156 (tp) cc_final: 0.8952 (tp) REVERT: D 76 ARG cc_start: 0.7746 (ttm110) cc_final: 0.6987 (mtm180) REVERT: E 56 LYS cc_start: 0.8937 (ttmt) cc_final: 0.8466 (ttmm) REVERT: F 84 MET cc_start: 0.7158 (mmm) cc_final: 0.6753 (mmm) REVERT: G 36 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8236 (mptt) REVERT: G 94 ASN cc_start: 0.9171 (t0) cc_final: 0.8784 (t0) REVERT: N 294 ARG cc_start: 0.6626 (tpt90) cc_final: 0.6342 (mtp180) REVERT: N 320 ILE cc_start: 0.8180 (mp) cc_final: 0.7856 (mm) REVERT: K 3875 TYR cc_start: 0.5074 (m-80) cc_final: 0.4805 (m-10) REVERT: K 3941 THR cc_start: 0.8567 (p) cc_final: 0.7991 (t) REVERT: R 82 THR cc_start: 0.7739 (m) cc_final: 0.7440 (p) REVERT: R 126 LYS cc_start: 0.6974 (mttm) cc_final: 0.6142 (tptp) REVERT: R 137 PHE cc_start: 0.4901 (m-80) cc_final: 0.3943 (p90) REVERT: T 500 MET cc_start: -0.0257 (mmm) cc_final: -0.0864 (mtt) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.1964 time to fit residues: 116.7167 Evaluate side-chains 210 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 40.0000 chunk 194 optimal weight: 0.0060 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 31 HIS C 73 ASN D 81 ASN E 76 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN H 81 ASN N 65 HIS N 88 ASN N 92 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 ASN N 216 ASN N 243 GLN R 86 HIS T 348 GLN ** T 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 354 GLN ** T 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 381 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.126802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.098895 restraints weight = 58988.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.098628 restraints weight = 74210.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099160 restraints weight = 62439.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.099018 restraints weight = 42992.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099193 restraints weight = 42694.755| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20889 Z= 0.167 Angle : 0.689 8.834 29468 Z= 0.396 Chirality : 0.049 0.328 3307 Planarity : 0.005 0.093 2726 Dihedral : 27.984 165.044 5095 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.07 % Allowed : 2.66 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.19), residues: 1728 helix: 0.69 (0.22), residues: 563 sheet: -2.60 (0.30), residues: 253 loop : -3.16 (0.16), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 251 TYR 0.015 0.001 TYR B 88 PHE 0.021 0.001 PHE K3904 TRP 0.024 0.002 TRP N 51 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.17 (20886) covalent geometry : angle 0.68924 / 0.40 (29468) hydrogen bonds : bond 0.07133 / 4.75 ( 854) hydrogen bonds : angle 4.25001 / 2.95 ( 2142) metal coordination : bond 0.02090 / 1.43 ( 2) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8179 (tt0) cc_final: 0.7346 (tt0) REVERT: B 34 ILE cc_start: 0.9394 (mt) cc_final: 0.9141 (mt) REVERT: B 88 TYR cc_start: 0.8432 (m-80) cc_final: 0.7884 (m-80) REVERT: D 76 ARG cc_start: 0.7434 (ttm110) cc_final: 0.6939 (mtm180) REVERT: E 56 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8518 (ttmm) REVERT: E 73 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6916 (mm-30) REVERT: G 94 ASN cc_start: 0.9194 (t0) cc_final: 0.8855 (t0) REVERT: N 179 LYS cc_start: 0.6019 (tptp) cc_final: 0.5435 (tppt) REVERT: K 3867 GLN cc_start: 0.7109 (mt0) cc_final: 0.6805 (mp10) REVERT: K 3875 TYR cc_start: 0.4997 (m-80) cc_final: 0.4760 (m-10) REVERT: R 126 LYS cc_start: 0.7204 (mttm) cc_final: 0.6237 (tptp) REVERT: T 500 MET cc_start: -0.0520 (mmm) cc_final: -0.1077 (mtt) outliers start: 1 outliers final: 0 residues processed: 294 average time/residue: 0.1669 time to fit residues: 72.9592 Evaluate side-chains 205 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 16 optimal weight: 2.9990 chunk 164 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 160 optimal weight: 0.4980 chunk 91 optimal weight: 30.0000 chunk 192 optimal weight: 0.8980 chunk 71 optimal weight: 40.0000 chunk 43 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN E 68 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 352 ASN ** 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 = 0.4025 r_free = 0.4025 target = 0.127443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.099212 restraints weight = 58516.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.098869 restraints weight = 67125.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.099632 restraints weight = 58298.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.099367 restraints weight = 42744.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.099617 restraints weight = 42386.711| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 20889 Z= 0.144 Angle : 0.641 12.074 29468 Z= 0.367 Chirality : 0.047 0.335 3307 Planarity : 0.005 0.091 2726 Dihedral : 27.808 165.695 5095 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.19), residues: 1728 helix: 1.39 (0.23), residues: 564 sheet: -2.27 (0.31), residues: 239 loop : -2.99 (0.17), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG T 294 TYR 0.021 0.001 TYR K3834 PHE 0.030 0.001 PHE K3904 TRP 0.028 0.002 TRP R 198 HIS 0.011 0.001 HIS K3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (20886) covalent geometry : angle 0.64089 / 0.37 (29468) hydrogen bonds : bond 0.06078 / 4.04 ( 854) hydrogen bonds : angle 3.91761 / 2.73 ( 2142) metal coordination : bond 0.00052 / 0.03 ( 2) Misc. bond : bond 0.00047 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8065 (tt0) cc_final: 0.7779 (tt0) REVERT: B 88 TYR cc_start: 0.8367 (m-80) cc_final: 0.7041 (m-80) REVERT: D 76 ARG cc_start: 0.7277 (ttm110) cc_final: 0.7063 (mtm180) REVERT: E 56 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8527 (ttmm) REVERT: F 50 ILE cc_start: 0.8074 (mm) cc_final: 0.7775 (mm) REVERT: F 93 GLN cc_start: 0.7355 (mm-40) cc_final: 0.7151 (mt0) REVERT: G 94 ASN cc_start: 0.9090 (t0) cc_final: 0.8837 (t0) REVERT: N 179 LYS cc_start: 0.5983 (tptp) cc_final: 0.5319 (tppt) REVERT: N 230 ILE cc_start: 0.7887 (mt) cc_final: 0.7528 (mt) REVERT: K 3931 MET cc_start: 0.7659 (ttm) cc_final: 0.7302 (mtm) REVERT: R 126 LYS cc_start: 0.7032 (mttm) cc_final: 0.6057 (tptp) REVERT: T 315 MET cc_start: 0.2871 (mtp) cc_final: 0.2349 (mtp) REVERT: T 500 MET cc_start: -0.0509 (mmm) cc_final: -0.0994 (mtt) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1623 time to fit residues: 68.3514 Evaluate side-chains 213 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 36 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 89 optimal weight: 30.0000 chunk 188 optimal weight: 7.9990 chunk 156 optimal weight: 40.0000 chunk 179 optimal weight: 50.0000 chunk 131 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 38 ASN D 79 HIS H 81 ASN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K3848 ASN ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 354 GLN ** 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 = 0.3961 r_free = 0.3961 target = 0.123272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.094191 restraints weight = 59416.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.093220 restraints weight = 78740.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.093740 restraints weight = 68887.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.093735 restraints weight = 53866.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.093863 restraints weight = 47966.335| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20889 Z= 0.247 Angle : 0.768 9.386 29468 Z= 0.424 Chirality : 0.051 0.322 3307 Planarity : 0.006 0.093 2726 Dihedral : 27.870 164.634 5095 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 0.07 % Allowed : 2.93 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.19), residues: 1728 helix: 0.82 (0.21), residues: 568 sheet: -2.20 (0.32), residues: 231 loop : -2.96 (0.17), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 77 TYR 0.037 0.002 TYR K3875 PHE 0.017 0.002 PHE N 104 TRP 0.034 0.002 TRP R 198 HIS 0.013 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.25 (20886) covalent geometry : angle 0.76770 / 0.42 (29468) hydrogen bonds : bond 0.08242 / 5.50 ( 854) hydrogen bonds : angle 4.34637 / 3.04 ( 2142) metal coordination : bond 0.00326 / 0.23 ( 2) Misc. bond : bond 0.00142 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7412 (m-30) cc_final: 0.6912 (m-30) REVERT: D 76 ARG cc_start: 0.7613 (ttm110) cc_final: 0.7076 (mtm180) REVERT: D 88 SER cc_start: 0.9086 (p) cc_final: 0.8815 (t) REVERT: E 56 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8674 (ttmm) REVERT: F 59 LYS cc_start: 0.8642 (ttpt) cc_final: 0.8176 (ttpt) REVERT: F 93 GLN cc_start: 0.7427 (mm-40) cc_final: 0.7224 (mt0) REVERT: G 94 ASN cc_start: 0.9235 (t0) cc_final: 0.8973 (t0) REVERT: N 294 ARG cc_start: 0.7283 (tpt90) cc_final: 0.6788 (mtp180) REVERT: K 3777 MET cc_start: 0.5976 (ptm) cc_final: 0.5454 (ttp) REVERT: K 3845 CYS cc_start: 0.7501 (p) cc_final: 0.7002 (m) REVERT: K 3863 ILE cc_start: 0.4878 (pt) cc_final: 0.4664 (pt) REVERT: K 3867 GLN cc_start: 0.7254 (mp10) cc_final: 0.6636 (tt0) REVERT: R 126 LYS cc_start: 0.7260 (mttm) cc_final: 0.6169 (tptp) REVERT: T 500 MET cc_start: -0.0904 (mmm) cc_final: -0.1193 (mtt) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.1562 time to fit residues: 58.6659 Evaluate side-chains 193 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 166 optimal weight: 30.0000 chunk 123 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 119 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 170 HIS ** T 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.126142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.097973 restraints weight = 58542.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097410 restraints weight = 72033.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.097933 restraints weight = 67835.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.097922 restraints weight = 47468.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.098106 restraints weight = 47153.562| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20889 Z= 0.141 Angle : 0.624 10.749 29468 Z= 0.358 Chirality : 0.046 0.313 3307 Planarity : 0.005 0.098 2726 Dihedral : 27.633 167.917 5095 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.07 % Allowed : 1.40 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.20), residues: 1728 helix: 1.60 (0.22), residues: 560 sheet: -2.27 (0.30), residues: 278 loop : -2.87 (0.17), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 30 TYR 0.027 0.002 TYR B 88 PHE 0.016 0.001 PHE N 104 TRP 0.024 0.002 TRP N 51 HIS 0.007 0.001 HIS K3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (20886) covalent geometry : angle 0.62429 / 0.36 (29468) hydrogen bonds : bond 0.06254 / 4.18 ( 854) hydrogen bonds : angle 3.75489 / 2.62 ( 2142) metal coordination : bond 0.00039 / 0.03 ( 2) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9325 (tt) cc_final: 0.9023 (tt) REVERT: B 88 TYR cc_start: 0.7770 (m-80) cc_final: 0.7446 (m-80) REVERT: E 56 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8635 (ttmm) REVERT: F 50 ILE cc_start: 0.8201 (mm) cc_final: 0.7974 (mm) REVERT: F 93 GLN cc_start: 0.7261 (mm-40) cc_final: 0.6966 (mt0) REVERT: G 94 ASN cc_start: 0.9178 (t0) cc_final: 0.8919 (t0) REVERT: G 101 THR cc_start: 0.9108 (m) cc_final: 0.8565 (p) REVERT: N 179 LYS cc_start: 0.6088 (tptp) cc_final: 0.5322 (tppt) REVERT: K 3845 CYS cc_start: 0.7316 (p) cc_final: 0.6962 (m) REVERT: R 126 LYS cc_start: 0.7155 (mttm) cc_final: 0.6017 (tptp) REVERT: R 198 TRP cc_start: 0.6769 (m-90) cc_final: 0.6397 (m100) outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.1440 time to fit residues: 57.2835 Evaluate side-chains 195 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 76 optimal weight: 40.0000 chunk 106 optimal weight: 30.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN C 38 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 170 HIS ** T 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.125621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097097 restraints weight = 59409.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.096370 restraints weight = 87220.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.096969 restraints weight = 72361.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.097032 restraints weight = 51875.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097216 restraints weight = 48417.471| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20889 Z= 0.147 Angle : 0.620 11.030 29468 Z= 0.354 Chirality : 0.046 0.328 3307 Planarity : 0.005 0.092 2726 Dihedral : 27.560 169.882 5095 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.07 % Allowed : 1.13 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.20), residues: 1728 helix: 1.74 (0.22), residues: 560 sheet: -2.31 (0.30), residues: 277 loop : -2.80 (0.18), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 92 TYR 0.027 0.002 TYR K3875 PHE 0.019 0.001 PHE K3820 TRP 0.032 0.002 TRP N 51 HIS 0.006 0.001 HIS K3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (20886) covalent geometry : angle 0.62016 / 0.35 (29468) hydrogen bonds : bond 0.06126 / 4.09 ( 854) hydrogen bonds : angle 3.67035 / 2.56 ( 2142) metal coordination : bond 0.00100 / 0.07 ( 2) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.7878 (m-80) cc_final: 0.7612 (m-80) REVERT: E 56 LYS cc_start: 0.9060 (ttmt) cc_final: 0.8685 (ttmm) REVERT: F 50 ILE cc_start: 0.8280 (mm) cc_final: 0.7956 (mm) REVERT: F 93 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6971 (mt0) REVERT: G 94 ASN cc_start: 0.9132 (t0) cc_final: 0.8881 (t0) REVERT: G 101 THR cc_start: 0.8957 (m) cc_final: 0.8538 (p) REVERT: H 85 THR cc_start: 0.8811 (m) cc_final: 0.8538 (m) REVERT: N 179 LYS cc_start: 0.6118 (tptp) cc_final: 0.5639 (tppt) REVERT: K 3777 MET cc_start: 0.6134 (ptm) cc_final: 0.5863 (ttp) REVERT: K 3845 CYS cc_start: 0.7055 (p) cc_final: 0.6822 (m) REVERT: R 126 LYS cc_start: 0.7161 (mttm) cc_final: 0.6013 (tptp) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.1482 time to fit residues: 55.2783 Evaluate side-chains 190 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 19 optimal weight: 3.9990 chunk 89 optimal weight: 40.0000 chunk 70 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 164 optimal weight: 30.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 HIS ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 170 HIS ** T 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.126541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.097844 restraints weight = 59258.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.097650 restraints weight = 79289.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.098218 restraints weight = 64800.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.098060 restraints weight = 47463.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.098217 restraints weight = 45037.848| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20889 Z= 0.135 Angle : 0.606 10.893 29468 Z= 0.347 Chirality : 0.045 0.324 3307 Planarity : 0.005 0.096 2726 Dihedral : 27.464 171.700 5095 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.07 % Allowed : 0.73 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.20), residues: 1728 helix: 1.92 (0.22), residues: 560 sheet: -2.03 (0.31), residues: 272 loop : -2.75 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 190 TYR 0.021 0.001 TYR K3875 PHE 0.014 0.001 PHE K3885 TRP 0.031 0.002 TRP N 51 HIS 0.005 0.001 HIS K3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 (20886) covalent geometry : angle 0.60595 / 0.35 (29468) hydrogen bonds : bond 0.05586 / 3.74 ( 854) hydrogen bonds : angle 3.48837 / 2.45 ( 2142) metal coordination : bond 0.00035 / 0.02 ( 2) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8613 (ttmm) REVERT: E 97 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6894 (mt-10) REVERT: F 50 ILE cc_start: 0.8139 (mm) cc_final: 0.7868 (mm) REVERT: F 93 GLN cc_start: 0.7064 (mm-40) cc_final: 0.6787 (mt0) REVERT: G 94 ASN cc_start: 0.9105 (t0) cc_final: 0.8852 (t0) REVERT: N 179 LYS cc_start: 0.5990 (tptp) cc_final: 0.5564 (tppt) REVERT: N 230 ILE cc_start: 0.7595 (mm) cc_final: 0.7392 (mm) REVERT: K 3777 MET cc_start: 0.6244 (ptm) cc_final: 0.5977 (ttp) REVERT: K 3845 CYS cc_start: 0.7251 (p) cc_final: 0.6955 (m) REVERT: T 336 MET cc_start: 0.1292 (ttt) cc_final: 0.0524 (ttt) outliers start: 1 outliers final: 0 residues processed: 244 average time/residue: 0.1379 time to fit residues: 52.7793 Evaluate side-chains 197 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 82 optimal weight: 40.0000 chunk 34 optimal weight: 0.7980 chunk 119 optimal weight: 30.0000 chunk 33 optimal weight: 0.6980 chunk 151 optimal weight: 30.0000 chunk 146 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN E 93 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 HIS R 170 HIS ** T 352 ASN ** 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 = 0.3968 r_free = 0.3968 target = 0.123825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.095096 restraints weight = 58937.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093926 restraints weight = 92535.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.094579 restraints weight = 76096.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.094618 restraints weight = 52723.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.094747 restraints weight = 52557.139| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20889 Z= 0.203 Angle : 0.695 11.677 29468 Z= 0.385 Chirality : 0.048 0.316 3307 Planarity : 0.005 0.092 2726 Dihedral : 27.580 171.295 5095 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.07 % Allowed : 1.26 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.20), residues: 1728 helix: 1.48 (0.22), residues: 561 sheet: -2.33 (0.31), residues: 248 loop : -2.69 (0.18), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.019 0.002 TYR K3875 PHE 0.031 0.002 PHE E 104 TRP 0.031 0.002 TRP N 51 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (20886) covalent geometry : angle 0.69467 / 0.38 (29468) hydrogen bonds : bond 0.07196 / 4.81 ( 854) hydrogen bonds : angle 3.83227 / 2.68 ( 2142) metal coordination : bond 0.00216 / 0.15 ( 2) Misc. bond : bond 0.00100 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7055 (m-30) cc_final: 0.6603 (m-30) REVERT: B 88 TYR cc_start: 0.7674 (m-80) cc_final: 0.5735 (m-80) REVERT: D 88 SER cc_start: 0.8984 (p) cc_final: 0.8747 (t) REVERT: E 56 LYS cc_start: 0.9110 (ttmt) cc_final: 0.8809 (ttmm) REVERT: G 94 ASN cc_start: 0.9251 (t0) cc_final: 0.8960 (t0) REVERT: K 3777 MET cc_start: 0.6390 (ptm) cc_final: 0.5878 (ttp) REVERT: K 3828 LYS cc_start: 0.8343 (mppt) cc_final: 0.7906 (mppt) REVERT: K 3845 CYS cc_start: 0.7301 (p) cc_final: 0.7004 (m) REVERT: T 315 MET cc_start: 0.3939 (mmm) cc_final: 0.3656 (mmm) REVERT: T 336 MET cc_start: 0.1086 (ttt) cc_final: 0.0425 (ttm) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.1372 time to fit residues: 49.5667 Evaluate side-chains 185 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 72 optimal weight: 40.0000 chunk 144 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 0.0020 chunk 107 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 157 optimal weight: 20.0000 chunk 170 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 81 ASN N 65 HIS N 120 GLN R 170 HIS ** T 352 ASN ** 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 = 0.4018 r_free = 0.4018 target = 0.127138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.097599 restraints weight = 58377.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.096981 restraints weight = 69581.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.097651 restraints weight = 58591.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.097166 restraints weight = 47857.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.097457 restraints weight = 42428.255| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20889 Z= 0.132 Angle : 0.617 11.504 29468 Z= 0.351 Chirality : 0.045 0.315 3307 Planarity : 0.005 0.091 2726 Dihedral : 27.410 173.706 5095 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.13 % Allowed : 0.80 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.20), residues: 1728 helix: 2.00 (0.22), residues: 562 sheet: -1.95 (0.32), residues: 256 loop : -2.63 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 294 TYR 0.024 0.001 TYR F 88 PHE 0.017 0.001 PHE N 206 TRP 0.014 0.001 TRP N 51 HIS 0.006 0.001 HIS K3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 (20886) covalent geometry : angle 0.61740 / 0.35 (29468) hydrogen bonds : bond 0.05505 / 3.71 ( 854) hydrogen bonds : angle 3.35781 / 2.36 ( 2142) metal coordination : bond 0.00074 / 0.05 ( 2) Misc. bond : bond 0.00051 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 235 time to evaluate : 0.678 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: E 56 LYS cc_start: 0.9028 (ttmt) cc_final: 0.8711 (ttmm) REVERT: F 50 ILE cc_start: 0.8164 (mm) cc_final: 0.7902 (mm) REVERT: G 94 ASN cc_start: 0.9053 (t0) cc_final: 0.8826 (t0) REVERT: G 101 THR cc_start: 0.9035 (m) cc_final: 0.8567 (p) REVERT: K 3777 MET cc_start: 0.6419 (ptm) cc_final: 0.6114 (ttp) REVERT: K 3825 LYS cc_start: 0.7710 (pttm) cc_final: 0.7204 (ptmt) REVERT: K 3845 CYS cc_start: 0.7497 (p) cc_final: 0.7210 (m) REVERT: T 315 MET cc_start: 0.3698 (mmm) cc_final: 0.3435 (mmm) outliers start: 2 outliers final: 0 residues processed: 236 average time/residue: 0.1431 time to fit residues: 53.1284 Evaluate side-chains 188 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 44 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 84 optimal weight: 50.0000 chunk 166 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 185 optimal weight: 0.0470 chunk 124 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN H 81 ASN ** N 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 170 HIS ** T 352 ASN ** 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 = 0.4002 r_free = 0.4002 target = 0.125973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097427 restraints weight = 58937.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.097321 restraints weight = 71859.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.097695 restraints weight = 63965.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.097292 restraints weight = 49202.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.097500 restraints weight = 45427.938| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20889 Z= 0.141 Angle : 0.617 12.359 29468 Z= 0.347 Chirality : 0.045 0.324 3307 Planarity : 0.005 0.090 2726 Dihedral : 27.426 174.279 5095 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.07 % Allowed : 0.20 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.20), residues: 1728 helix: 2.01 (0.22), residues: 562 sheet: -1.91 (0.33), residues: 242 loop : -2.61 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 92 TYR 0.039 0.002 TYR K3834 PHE 0.024 0.001 PHE K3820 TRP 0.014 0.001 TRP T 327 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (20886) covalent geometry : angle 0.61696 / 0.35 (29468) hydrogen bonds : bond 0.05761 / 3.87 ( 854) hydrogen bonds : angle 3.35463 / 2.35 ( 2142) metal coordination : bond 0.00088 / 0.06 ( 2) Misc. bond : bond 0.00026 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 LYS cc_start: 0.9041 (ttmt) cc_final: 0.8757 (ttmm) REVERT: K 3777 MET cc_start: 0.6406 (ptm) cc_final: 0.6107 (ttp) REVERT: K 3825 LYS cc_start: 0.7470 (pttm) cc_final: 0.7038 (ptmt) REVERT: K 3845 CYS cc_start: 0.7232 (p) cc_final: 0.6929 (m) REVERT: T 315 MET cc_start: 0.3603 (mmm) cc_final: 0.3324 (mmm) outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 0.1395 time to fit residues: 50.2273 Evaluate side-chains 187 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 30.0000 chunk 72 optimal weight: 40.0000 chunk 1 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 90 optimal weight: 40.0000 chunk 11 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN ** N 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 170 HIS ** T 352 ASN ** 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 = 0.3992 r_free = 0.3992 target = 0.125293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.096077 restraints weight = 59308.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095023 restraints weight = 82706.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.095469 restraints weight = 65969.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.095424 restraints weight = 51678.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.095591 restraints weight = 45775.989| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20889 Z= 0.164 Angle : 0.647 12.320 29468 Z= 0.361 Chirality : 0.046 0.313 3307 Planarity : 0.005 0.088 2726 Dihedral : 27.457 174.066 5095 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.07 % Allowed : 0.47 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.20), residues: 1728 helix: 1.85 (0.22), residues: 562 sheet: -2.06 (0.32), residues: 255 loop : -2.61 (0.18), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 92 TYR 0.015 0.002 TYR G 39 PHE 0.016 0.001 PHE K3904 TRP 0.014 0.002 TRP R 114 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (20886) covalent geometry : angle 0.64711 / 0.36 (29468) hydrogen bonds : bond 0.06210 / 4.17 ( 854) hydrogen bonds : angle 3.47765 / 2.43 ( 2142) metal coordination : bond 0.00123 / 0.09 ( 2) Misc. bond : bond 0.00053 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2964.93 seconds wall clock time: 52 minutes 8.48 seconds (3128.48 seconds total)