Starting phenix.real_space_refine on Fri Mar 6 00:12:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kix_0694/03_2026/6kix_0694.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kix_0694/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6kix_0694/03_2026/6kix_0694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kix_0694/03_2026/6kix_0694.map" model { file = "/net/cci-nas-00/data/ceres_data/6kix_0694/03_2026/6kix_0694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kix_0694/03_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-dev-5986/lib/python3.9/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: 4.20, per 1000 atoms: 0.21 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: 1.39 Conformation dependent library (CDL) restraints added in 560.2 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: 2.58 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: 4.32 Time building geometry restraints manager: 1.96 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=" C2 SAH K4001 " pdb=" N3 SAH K4001 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" C8 SAH K4001 " pdb=" N7 SAH K4001 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C2 SAH K4001 " pdb=" N1 SAH K4001 " ideal model delta sigma weight residual 1.330 1.378 -0.048 2.00e-02 2.50e+03 5.68e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.58e+00 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.09e+00 ... (remaining 20881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 28335 1.98 - 3.96: 1011 3.96 - 5.94: 92 5.94 - 7.92: 23 7.92 - 9.90: 7 Bond angle restraints: 29468 Sorted by residual: 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=" C PRO N 107 " pdb=" N SER N 108 " pdb=" CA SER N 108 " ideal model delta sigma weight residual 120.58 126.88 -6.30 1.32e+00 5.74e-01 2.27e+01 angle pdb=" C ASP B 24 " pdb=" N ASN B 25 " pdb=" CA ASN B 25 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.27e+01 angle pdb=" N SER N 108 " pdb=" CA SER N 108 " pdb=" C SER N 108 " ideal model delta sigma weight residual 113.45 119.31 -5.86 1.39e+00 5.18e-01 1.78e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 122.58 -9.40 2.37e+00 1.78e-01 1.57e+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 - 0.047: 2314 0.047 - 0.095: 766 0.095 - 0.142: 195 0.142 - 0.190: 25 0.190 - 0.237: 7 Chirality restraints: 3307 Sorted by residual: chirality pdb=" C1' SAH K4001 " pdb=" C2' SAH K4001 " pdb=" N9 SAH K4001 " pdb=" O4' SAH K4001 " both_signs ideal model delta sigma weight residual False 2.35 2.58 -0.24 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 chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 21.860 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 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= 0.282 Angle : 0.845 9.897 29468 Z= 0.482 Chirality : 0.050 0.237 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 covalent geometry : bond 0.00569 (20886) covalent geometry : angle 0.84490 (29468) hydrogen bonds : bond 0.14583 ( 854) hydrogen bonds : angle 5.29545 ( 2142) metal coordination : bond 0.32612 ( 2) Misc. bond : bond 0.00101 ( 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 : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8260 (mtt) cc_final: 0.7801 (mtp) REVERT: C 76 THR cc_start: 0.9206 (m) cc_final: 0.8989 (p) REVERT: D 76 ARG cc_start: 0.7746 (ttm110) cc_final: 0.6985 (mtm180) REVERT: E 56 LYS cc_start: 0.8937 (ttmt) cc_final: 0.8467 (ttmm) REVERT: F 84 MET cc_start: 0.7158 (mmm) cc_final: 0.6748 (mmm) REVERT: G 36 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8241 (mptt) REVERT: G 94 ASN cc_start: 0.9171 (t0) cc_final: 0.8785 (t0) REVERT: N 294 ARG cc_start: 0.6626 (tpt90) cc_final: 0.6341 (mtp180) REVERT: N 320 ILE cc_start: 0.8180 (mp) cc_final: 0.7863 (mm) REVERT: K 3867 GLN cc_start: 0.6760 (mt0) cc_final: 0.6544 (tt0) REVERT: K 3941 THR cc_start: 0.8567 (p) cc_final: 0.7989 (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: 0.6144 (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: -0.0860 (mtt) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.1926 time to fit residues: 112.7845 Evaluate side-chains 212 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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: 10.0000 chunk 194 optimal weight: 0.0060 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 24 GLN C 73 ASN D 81 ASN E 68 GLN E 76 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN N 65 HIS N 88 ASN N 92 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 243 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.127203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.098400 restraints weight = 59226.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.097119 restraints weight = 81375.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.098073 restraints weight = 62717.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.098131 restraints weight = 44951.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.098405 restraints weight = 42173.925| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20889 Z= 0.160 Angle : 0.597 9.507 29468 Z= 0.342 Chirality : 0.040 0.194 3307 Planarity : 0.005 0.098 2726 Dihedral : 27.366 168.037 5095 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -2.36 (0.19), residues: 1728 helix: 0.90 (0.22), residues: 564 sheet: -2.71 (0.29), residues: 263 loop : -2.98 (0.17), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K3864 TYR 0.014 0.001 TYR B 88 PHE 0.012 0.001 PHE E 104 TRP 0.025 0.002 TRP N 51 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00334 (20886) covalent geometry : angle 0.59652 (29468) hydrogen bonds : bond 0.05593 ( 854) hydrogen bonds : angle 3.75184 ( 2142) metal coordination : bond 0.00446 ( 2) Misc. bond : bond 0.00193 ( 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 305 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7691 (ttt90) REVERT: A 73 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7085 (mt-10) REVERT: A 93 GLN cc_start: 0.8186 (tt0) cc_final: 0.7904 (tt0) REVERT: B 58 LEU cc_start: 0.8833 (tp) cc_final: 0.8633 (tp) REVERT: B 92 ARG cc_start: 0.8232 (mtp-110) cc_final: 0.7985 (mtp-110) REVERT: C 76 THR cc_start: 0.9010 (m) cc_final: 0.8798 (p) REVERT: D 76 ARG cc_start: 0.7352 (ttm110) cc_final: 0.6934 (mtm180) REVERT: E 56 LYS cc_start: 0.8912 (ttmt) cc_final: 0.8565 (ttmm) REVERT: E 129 ARG cc_start: 0.8366 (tmt-80) cc_final: 0.8115 (tmt-80) REVERT: F 50 ILE cc_start: 0.7826 (mm) cc_final: 0.7545 (mm) REVERT: F 59 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8115 (ttpt) REVERT: F 93 GLN cc_start: 0.7437 (mm-40) cc_final: 0.6936 (mm-40) REVERT: G 39 TYR cc_start: 0.8743 (m-80) cc_final: 0.8502 (m-80) REVERT: G 94 ASN cc_start: 0.9158 (t0) cc_final: 0.8907 (t0) REVERT: N 179 LYS cc_start: 0.5959 (tptp) cc_final: 0.5495 (tppt) REVERT: N 256 LYS cc_start: 0.7025 (mmpt) cc_final: 0.6811 (mmmt) REVERT: R 126 LYS cc_start: 0.7178 (mttm) cc_final: 0.5958 (tptp) REVERT: T 500 MET cc_start: -0.0522 (mmm) cc_final: -0.1086 (mtt) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1606 time to fit residues: 71.9977 Evaluate side-chains 204 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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: 3.9990 chunk 164 optimal weight: 0.7980 chunk 17 optimal weight: 0.0040 chunk 60 optimal weight: 7.9990 chunk 160 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 50 optimal weight: 0.0980 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K3958 ASN R 86 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 = 0.4022 r_free = 0.4022 target = 0.127202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.098481 restraints weight = 58955.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.097639 restraints weight = 73184.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.098368 restraints weight = 60547.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.098454 restraints weight = 43042.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.098564 restraints weight = 41602.018| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20889 Z= 0.148 Angle : 0.573 8.745 29468 Z= 0.328 Chirality : 0.039 0.211 3307 Planarity : 0.004 0.091 2726 Dihedral : 27.178 169.625 5095 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: -1.80 (0.20), residues: 1728 helix: 1.60 (0.23), residues: 560 sheet: -2.37 (0.30), residues: 268 loop : -2.80 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 228 TYR 0.020 0.001 TYR B 88 PHE 0.017 0.001 PHE K3820 TRP 0.026 0.001 TRP R 198 HIS 0.010 0.001 HIS K3822 Details of bonding type rmsd covalent geometry : bond 0.00320 (20886) covalent geometry : angle 0.57273 (29468) hydrogen bonds : bond 0.05321 ( 854) hydrogen bonds : angle 3.51053 ( 2142) metal coordination : bond 0.00052 ( 2) Misc. bond : bond 0.00096 ( 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 271 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.6996 (m-30) cc_final: 0.6554 (m-30) REVERT: B 58 LEU cc_start: 0.8843 (tp) cc_final: 0.8635 (tp) REVERT: B 73 THR cc_start: 0.8655 (m) cc_final: 0.8307 (p) REVERT: B 88 TYR cc_start: 0.8092 (m-80) cc_final: 0.7031 (m-80) REVERT: C 76 THR cc_start: 0.8959 (m) cc_final: 0.8730 (p) REVERT: E 56 LYS cc_start: 0.8963 (ttmt) cc_final: 0.8637 (ttmm) REVERT: F 50 ILE cc_start: 0.7892 (mm) cc_final: 0.7567 (mm) REVERT: F 59 LYS cc_start: 0.8237 (ttpt) cc_final: 0.7975 (ttpt) REVERT: G 39 TYR cc_start: 0.8729 (m-80) cc_final: 0.8479 (m-80) REVERT: G 94 ASN cc_start: 0.9205 (t0) cc_final: 0.8932 (t0) REVERT: N 179 LYS cc_start: 0.6019 (tptp) cc_final: 0.5697 (tppt) REVERT: N 256 LYS cc_start: 0.6908 (mmpt) cc_final: 0.6648 (mmmt) REVERT: N 294 ARG cc_start: 0.6787 (tpt90) cc_final: 0.6302 (mtp180) REVERT: K 3845 CYS cc_start: 0.7639 (p) cc_final: 0.6984 (m) REVERT: R 126 LYS cc_start: 0.6827 (mttm) cc_final: 0.6061 (tptp) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1529 time to fit residues: 61.2517 Evaluate side-chains 203 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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: 1.9990 chunk 128 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 188 optimal weight: 20.0000 chunk 156 optimal weight: 40.0000 chunk 179 optimal weight: 50.0000 chunk 131 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN D 46 HIS E 93 GLN 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 = 0.4035 r_free = 0.4035 target = 0.128132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.099591 restraints weight = 59795.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.099336 restraints weight = 64456.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.099959 restraints weight = 53543.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.099698 restraints weight = 40659.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.099884 restraints weight = 38795.434| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20889 Z= 0.135 Angle : 0.549 8.335 29468 Z= 0.313 Chirality : 0.038 0.140 3307 Planarity : 0.004 0.090 2726 Dihedral : 27.016 172.194 5095 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.07 % Allowed : 1.73 % Favored : 98.20 % 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: -1.44 (0.20), residues: 1728 helix: 2.00 (0.23), residues: 561 sheet: -2.32 (0.29), residues: 279 loop : -2.59 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 77 TYR 0.012 0.001 TYR B 88 PHE 0.012 0.001 PHE K3967 TRP 0.014 0.001 TRP R 198 HIS 0.005 0.001 HIS K3925 Details of bonding type rmsd covalent geometry : bond 0.00289 (20886) covalent geometry : angle 0.54862 (29468) hydrogen bonds : bond 0.04574 ( 854) hydrogen bonds : angle 3.16725 ( 2142) metal coordination : bond 0.00032 ( 2) Misc. bond : bond 0.00015 ( 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 261 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 THR cc_start: 0.8316 (m) cc_final: 0.8107 (p) REVERT: B 88 TYR cc_start: 0.8108 (m-80) cc_final: 0.6899 (m-80) REVERT: C 76 THR cc_start: 0.8974 (m) cc_final: 0.8637 (p) REVERT: E 56 LYS cc_start: 0.9023 (ttmt) cc_final: 0.8788 (ttmm) REVERT: F 93 GLN cc_start: 0.7489 (mm-40) cc_final: 0.6899 (mm-40) REVERT: G 78 ILE cc_start: 0.8566 (mm) cc_final: 0.8318 (mm) REVERT: G 94 ASN cc_start: 0.9086 (t0) cc_final: 0.8873 (t0) REVERT: H 42 LEU cc_start: 0.9199 (tp) cc_final: 0.8978 (tp) REVERT: N 179 LYS cc_start: 0.5952 (tptp) cc_final: 0.5664 (tppt) REVERT: N 256 LYS cc_start: 0.6974 (mmpt) cc_final: 0.6754 (mmmt) REVERT: N 294 ARG cc_start: 0.6882 (tpt90) cc_final: 0.5964 (mtp180) REVERT: N 340 ASP cc_start: 0.6404 (t0) cc_final: 0.6153 (t0) REVERT: K 3777 MET cc_start: 0.6252 (ptm) cc_final: 0.5688 (ppp) REVERT: K 3845 CYS cc_start: 0.7421 (p) cc_final: 0.7057 (m) REVERT: R 126 LYS cc_start: 0.6931 (mttm) cc_final: 0.5875 (tptp) outliers start: 1 outliers final: 0 residues processed: 260 average time/residue: 0.1426 time to fit residues: 56.6760 Evaluate side-chains 198 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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: 6.9990 chunk 56 optimal weight: 3.9990 chunk 166 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 34 optimal weight: 0.0070 chunk 74 optimal weight: 10.0000 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN H 81 ASN N 65 HIS ** T 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.124495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.096175 restraints weight = 58878.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.095471 restraints weight = 79398.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.096085 restraints weight = 78029.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.095878 restraints weight = 55308.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.096217 restraints weight = 50823.344| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20889 Z= 0.216 Angle : 0.642 7.972 29468 Z= 0.359 Chirality : 0.041 0.156 3307 Planarity : 0.005 0.091 2726 Dihedral : 27.207 169.823 5095 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -1.66 (0.20), residues: 1728 helix: 1.55 (0.22), residues: 562 sheet: -2.22 (0.31), residues: 262 loop : -2.63 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 92 TYR 0.022 0.002 TYR B 51 PHE 0.017 0.001 PHE E 104 TRP 0.026 0.002 TRP R 198 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00496 (20886) covalent geometry : angle 0.64161 (29468) hydrogen bonds : bond 0.06818 ( 854) hydrogen bonds : angle 3.69584 ( 2142) metal coordination : bond 0.00179 ( 2) Misc. bond : bond 0.00079 ( 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 236 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 THR cc_start: 0.8698 (m) cc_final: 0.8451 (p) REVERT: B 88 TYR cc_start: 0.8078 (m-80) cc_final: 0.6435 (m-80) REVERT: C 76 THR cc_start: 0.8935 (m) cc_final: 0.8697 (p) REVERT: D 65 ASP cc_start: 0.8487 (t0) cc_final: 0.8284 (t0) REVERT: D 88 SER cc_start: 0.8918 (p) cc_final: 0.8625 (t) REVERT: E 56 LYS cc_start: 0.9120 (ttmt) cc_final: 0.8763 (ttmm) REVERT: G 84 GLN cc_start: 0.9198 (tp-100) cc_final: 0.8979 (tp-100) REVERT: G 94 ASN cc_start: 0.9182 (t0) cc_final: 0.8915 (t0) REVERT: N 256 LYS cc_start: 0.7070 (mmpt) cc_final: 0.6724 (mmmt) REVERT: N 340 ASP cc_start: 0.6463 (t0) cc_final: 0.6223 (t0) REVERT: K 3825 LYS cc_start: 0.7926 (pttm) cc_final: 0.7686 (pttp) REVERT: K 3845 CYS cc_start: 0.7371 (p) cc_final: 0.7106 (m) REVERT: R 207 LYS cc_start: 0.6468 (mttm) cc_final: 0.5883 (tttt) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1461 time to fit residues: 52.6243 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 : 0.646 ------------------------------------------------------------------------------- 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: 2.9990 chunk 35 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN G 73 ASN ** N 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3848 ASN K3958 ASN T 348 GLN ** 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 = 0.4030 r_free = 0.4030 target = 0.127751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.098938 restraints weight = 58868.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.098928 restraints weight = 71910.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.099428 restraints weight = 61092.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.099091 restraints weight = 43835.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099306 restraints weight = 43567.503| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20889 Z= 0.137 Angle : 0.554 7.638 29468 Z= 0.315 Chirality : 0.038 0.208 3307 Planarity : 0.004 0.096 2726 Dihedral : 26.933 173.536 5095 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.07 % Allowed : 1.53 % Favored : 98.40 % 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: -1.25 (0.20), residues: 1728 helix: 2.03 (0.22), residues: 562 sheet: -1.92 (0.31), residues: 261 loop : -2.50 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 77 TYR 0.028 0.001 TYR B 51 PHE 0.010 0.001 PHE K3885 TRP 0.019 0.001 TRP R 114 HIS 0.006 0.001 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00294 (20886) covalent geometry : angle 0.55372 (29468) hydrogen bonds : bond 0.04751 ( 854) hydrogen bonds : angle 3.13581 ( 2142) metal coordination : bond 0.00053 ( 2) Misc. bond : bond 0.00023 ( 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 248 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 THR cc_start: 0.8505 (m) cc_final: 0.8242 (p) REVERT: B 88 TYR cc_start: 0.8202 (m-80) cc_final: 0.6691 (m-80) REVERT: C 76 THR cc_start: 0.8868 (m) cc_final: 0.8623 (p) REVERT: E 56 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8758 (ttmm) REVERT: F 93 GLN cc_start: 0.7107 (mm-40) cc_final: 0.6581 (mm-40) REVERT: N 26 MET cc_start: 0.3080 (mmt) cc_final: 0.2822 (tpp) REVERT: N 167 TYR cc_start: 0.5450 (m-10) cc_final: 0.5226 (m-10) REVERT: N 256 LYS cc_start: 0.7076 (mmpt) cc_final: 0.6809 (mmmt) REVERT: K 3777 MET cc_start: 0.6505 (ptm) cc_final: 0.5728 (ppp) REVERT: K 3845 CYS cc_start: 0.7343 (p) cc_final: 0.7114 (m) REVERT: K 3848 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8715 (p0) REVERT: R 207 LYS cc_start: 0.6517 (mttm) cc_final: 0.5917 (tttt) REVERT: T 315 MET cc_start: 0.3714 (mtp) cc_final: 0.3141 (mtp) outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.1361 time to fit residues: 52.3472 Evaluate side-chains 196 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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: 0.0270 chunk 89 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 152 optimal weight: 50.0000 chunk 164 optimal weight: 4.9990 overall best weight: 1.2040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 89 ASN H 81 ASN ** 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 = 0.4041 r_free = 0.4041 target = 0.128489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.101995 restraints weight = 59668.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.101730 restraints weight = 83268.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.102103 restraints weight = 78808.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.101941 restraints weight = 56101.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.102078 restraints weight = 56520.021| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20889 Z= 0.133 Angle : 0.545 9.646 29468 Z= 0.309 Chirality : 0.038 0.185 3307 Planarity : 0.004 0.096 2726 Dihedral : 26.812 173.732 5095 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: -1.05 (0.20), residues: 1728 helix: 2.27 (0.22), residues: 561 sheet: -1.87 (0.32), residues: 255 loop : -2.41 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 35 TYR 0.025 0.001 TYR B 51 PHE 0.021 0.001 PHE K3820 TRP 0.020 0.001 TRP R 114 HIS 0.006 0.001 HIS K3822 Details of bonding type rmsd covalent geometry : bond 0.00285 (20886) covalent geometry : angle 0.54500 (29468) hydrogen bonds : bond 0.04575 ( 854) hydrogen bonds : angle 2.99144 ( 2142) metal coordination : bond 0.00045 ( 2) Misc. bond : bond 0.00000 ( 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 248 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 THR cc_start: 0.8935 (m) cc_final: 0.8678 (p) REVERT: D 88 SER cc_start: 0.8642 (p) cc_final: 0.8422 (t) REVERT: F 74 GLU cc_start: 0.7925 (tt0) cc_final: 0.7710 (tt0) REVERT: F 93 GLN cc_start: 0.7093 (mm-40) cc_final: 0.6737 (mm-40) REVERT: G 78 ILE cc_start: 0.8697 (mm) cc_final: 0.8476 (mm) REVERT: N 26 MET cc_start: 0.3234 (mmt) cc_final: 0.2985 (tpp) REVERT: N 256 LYS cc_start: 0.7184 (mmpt) cc_final: 0.6922 (mmmt) REVERT: K 3825 LYS cc_start: 0.7708 (pttp) cc_final: 0.7419 (ptmt) REVERT: K 3828 LYS cc_start: 0.8387 (mmtp) cc_final: 0.8018 (mtpt) REVERT: K 3845 CYS cc_start: 0.7354 (p) cc_final: 0.7094 (m) REVERT: R 207 LYS cc_start: 0.6208 (mttm) cc_final: 0.5789 (tttt) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1368 time to fit residues: 52.7919 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 : 0.390 ------------------------------------------------------------------------------- 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: 10.0000 chunk 34 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 33 optimal weight: 0.0570 chunk 151 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 chunk 105 optimal weight: 0.0670 chunk 178 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 overall best weight: 4.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS F 75 HIS H 81 ASN N 274 HIS K3848 ASN ** 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 = 0.3983 r_free = 0.3983 target = 0.124483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098210 restraints weight = 59027.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097695 restraints weight = 100245.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.098038 restraints weight = 97424.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.098158 restraints weight = 65382.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.098420 restraints weight = 60607.416| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 20889 Z= 0.226 Angle : 0.663 14.655 29468 Z= 0.367 Chirality : 0.042 0.220 3307 Planarity : 0.005 0.094 2726 Dihedral : 27.045 171.301 5095 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.13 % Allowed : 1.46 % Favored : 98.40 % 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: -1.56 (0.20), residues: 1728 helix: 1.54 (0.22), residues: 568 sheet: -1.99 (0.32), residues: 256 loop : -2.58 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 272 TYR 0.028 0.002 TYR B 88 PHE 0.023 0.001 PHE K3820 TRP 0.022 0.002 TRP R 156 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00523 (20886) covalent geometry : angle 0.66340 (29468) hydrogen bonds : bond 0.07226 ( 854) hydrogen bonds : angle 3.67608 ( 2142) metal coordination : bond 0.00214 ( 2) Misc. bond : bond 0.00079 ( 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 218 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 THR cc_start: 0.8868 (m) cc_final: 0.8642 (p) REVERT: C 99 ARG cc_start: 0.7920 (mtt180) cc_final: 0.7648 (ptp-170) REVERT: D 65 ASP cc_start: 0.8691 (t0) cc_final: 0.8380 (t0) REVERT: D 88 SER cc_start: 0.8863 (p) cc_final: 0.8647 (t) REVERT: F 74 GLU cc_start: 0.8229 (tt0) cc_final: 0.7937 (tt0) REVERT: N 256 LYS cc_start: 0.7359 (mmpt) cc_final: 0.7126 (mmmt) REVERT: K 3828 LYS cc_start: 0.8513 (mmtp) cc_final: 0.8085 (mtpt) REVERT: R 207 LYS cc_start: 0.6559 (mttm) cc_final: 0.6128 (tttt) outliers start: 2 outliers final: 1 residues processed: 217 average time/residue: 0.1307 time to fit residues: 44.6289 Evaluate side-chains 174 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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: 10.0000 chunk 144 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 157 optimal weight: 30.0000 chunk 170 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 75 HIS G 73 ASN ** K3822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3848 ASN ** 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 = 0.4028 r_free = 0.4028 target = 0.127603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.100497 restraints weight = 58823.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.100065 restraints weight = 88928.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.100628 restraints weight = 78231.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100352 restraints weight = 55698.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.100631 restraints weight = 51956.473| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20889 Z= 0.141 Angle : 0.571 9.364 29468 Z= 0.322 Chirality : 0.039 0.208 3307 Planarity : 0.004 0.093 2726 Dihedral : 26.750 174.714 5095 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.07 % Allowed : 0.67 % Favored : 99.27 % 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: -1.17 (0.20), residues: 1728 helix: 2.03 (0.22), residues: 567 sheet: -1.73 (0.33), residues: 252 loop : -2.49 (0.18), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 35 TYR 0.025 0.001 TYR B 51 PHE 0.012 0.001 PHE K3885 TRP 0.022 0.001 TRP R 114 HIS 0.017 0.001 HIS K3822 Details of bonding type rmsd covalent geometry : bond 0.00304 (20886) covalent geometry : angle 0.57129 (29468) hydrogen bonds : bond 0.05084 ( 854) hydrogen bonds : angle 3.15248 ( 2142) metal coordination : bond 0.00072 ( 2) Misc. bond : bond 0.00023 ( 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 238 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8317 (tp30) cc_final: 0.8019 (tp30) REVERT: C 76 THR cc_start: 0.8832 (m) cc_final: 0.8545 (p) REVERT: C 99 ARG cc_start: 0.7805 (mtt180) cc_final: 0.7528 (ptp-170) REVERT: F 74 GLU cc_start: 0.8044 (tt0) cc_final: 0.7706 (tt0) REVERT: K 3777 MET cc_start: 0.6340 (ptm) cc_final: 0.5842 (ppp) REVERT: K 3825 LYS cc_start: 0.8312 (ptmt) cc_final: 0.7676 (pttm) REVERT: K 3828 LYS cc_start: 0.8448 (mmtp) cc_final: 0.8145 (mtpt) REVERT: K 3845 CYS cc_start: 0.7270 (p) cc_final: 0.7044 (m) REVERT: K 3884 MET cc_start: 0.5010 (mmm) cc_final: 0.4807 (mmm) REVERT: R 207 LYS cc_start: 0.6588 (mttm) cc_final: 0.6173 (tttt) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.1361 time to fit residues: 50.3869 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 : 0.474 ------------------------------------------------------------------------------- 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: 0.9980 chunk 134 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 166 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 160 optimal weight: 30.0000 chunk 185 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 ASN ** K3822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.127262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.099941 restraints weight = 58477.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099425 restraints weight = 83094.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.099638 restraints weight = 78014.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.099507 restraints weight = 52815.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.099681 restraints weight = 51395.523| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20889 Z= 0.150 Angle : 0.571 9.371 29468 Z= 0.321 Chirality : 0.039 0.182 3307 Planarity : 0.004 0.092 2726 Dihedral : 26.727 174.195 5095 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 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: -1.17 (0.20), residues: 1728 helix: 2.01 (0.22), residues: 567 sheet: -1.73 (0.33), residues: 253 loop : -2.47 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 35 TYR 0.022 0.001 TYR B 51 PHE 0.023 0.001 PHE K3820 TRP 0.022 0.001 TRP R 198 HIS 0.013 0.001 HIS K3822 Details of bonding type rmsd covalent geometry : bond 0.00331 (20886) covalent geometry : angle 0.57122 (29468) hydrogen bonds : bond 0.05314 ( 854) hydrogen bonds : angle 3.15625 ( 2142) metal coordination : bond 0.00097 ( 2) Misc. bond : bond 0.00024 ( 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 231 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8437 (tp30) cc_final: 0.8193 (tp30) REVERT: C 76 THR cc_start: 0.8847 (m) cc_final: 0.8570 (p) REVERT: C 99 ARG cc_start: 0.7781 (mtt180) cc_final: 0.7503 (ptp-170) REVERT: D 88 SER cc_start: 0.8721 (p) cc_final: 0.8510 (t) REVERT: F 74 GLU cc_start: 0.7997 (tt0) cc_final: 0.7659 (tt0) REVERT: F 84 MET cc_start: 0.6429 (tpp) cc_final: 0.5135 (mmm) REVERT: F 88 TYR cc_start: 0.7792 (m-10) cc_final: 0.7286 (m-80) REVERT: K 3777 MET cc_start: 0.6321 (ptm) cc_final: 0.5784 (ppp) REVERT: K 3825 LYS cc_start: 0.8316 (ptmt) cc_final: 0.7700 (pttm) REVERT: K 3828 LYS cc_start: 0.8496 (mmtp) cc_final: 0.8144 (mtpt) REVERT: K 3884 MET cc_start: 0.4591 (mmm) cc_final: 0.4325 (mmm) REVERT: R 198 TRP cc_start: 0.5814 (m100) cc_final: 0.5596 (m100) REVERT: R 207 LYS cc_start: 0.6476 (mttm) cc_final: 0.6040 (tttt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1353 time to fit residues: 48.7403 Evaluate side-chains 181 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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: 10.0000 chunk 72 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 73 ASN ** 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 = 0.3996 r_free = 0.3996 target = 0.125353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.099445 restraints weight = 59043.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.098989 restraints weight = 99885.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.099368 restraints weight = 100532.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.099302 restraints weight = 72452.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.099486 restraints weight = 67813.144| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20889 Z= 0.193 Angle : 0.623 10.466 29468 Z= 0.348 Chirality : 0.040 0.172 3307 Planarity : 0.005 0.092 2726 Dihedral : 26.887 173.028 5095 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 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: -1.42 (0.20), residues: 1728 helix: 1.66 (0.22), residues: 568 sheet: -1.98 (0.32), residues: 253 loop : -2.48 (0.18), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 154 TYR 0.023 0.002 TYR B 88 PHE 0.031 0.001 PHE E 104 TRP 0.025 0.002 TRP R 198 HIS 0.014 0.001 HIS K3822 Details of bonding type rmsd covalent geometry : bond 0.00438 (20886) covalent geometry : angle 0.62321 (29468) hydrogen bonds : bond 0.06657 ( 854) hydrogen bonds : angle 3.46510 ( 2142) metal coordination : bond 0.00206 ( 2) Misc. bond : bond 0.00061 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2707.83 seconds wall clock time: 47 minutes 37.66 seconds (2857.66 seconds total)