Starting phenix.real_space_refine on Sun Sep 13 23:06:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mbm_23738/09_2026/7mbm_23738.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mbm_23738/09_2026/7mbm_23738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mbm_23738/09_2026/7mbm_23738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mbm_23738/09_2026/7mbm_23738.map" model { file = "/net/cci-nas-00/data/ceres_data/7mbm_23738/09_2026/7mbm_23738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mbm_23738/09_2026/7mbm_23738.cif" } resolution = 4.76 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= 0.001 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 8542 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: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 57 5.16 5 C 11568 2.51 5 N 3596 2.21 5 O 4246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19757 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2665 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "B" 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: "C" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1435 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: "D" 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: "G" 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: "H" 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: "I" 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: "J" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "K" 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: "L" 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: "M" 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: "N" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "O" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "P" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Time building chain proxies: 3.60, per 1000 atoms: 0.18 Number of scatterers: 19757 At special positions: 0 Unit cell: (142.04, 121.9, 156.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 290 15.00 O 4246 8.00 N 3596 7.00 C 11568 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=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 493.9 milliseconds 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 27 sheets defined 32.7% alpha, 11.8% beta 138 base pairs and 238 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'C' and resid 3815 through 3828 removed outlier: 3.725A pdb=" N ARG C3819 " --> pdb=" O PRO C3815 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS C3822 " --> pdb=" O MET C3818 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS C3824 " --> pdb=" O PHE C3820 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS C3825 " --> pdb=" O ARG C3821 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C3828 " --> pdb=" O LYS C3824 " (cutoff:3.500A) Processing helix chain 'C' and resid 3866 through 3879 removed outlier: 3.636A pdb=" N LYS C3870 " --> pdb=" O ILE C3866 " (cutoff:3.500A) Processing helix chain 'C' and resid 3900 through 3904 removed outlier: 4.180A pdb=" N ARG C3903 " --> pdb=" O ASN C3900 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE C3904 " --> pdb=" O ALA C3901 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3900 through 3904' Processing helix chain 'D' and resid 368 through 372 removed outlier: 3.776A pdb=" N GLY D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR D 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 372' Processing helix chain 'G' and resid 44 through 57 removed outlier: 3.830A pdb=" N SER G 57 " --> pdb=" O ARG G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 76 Processing helix chain 'G' and resid 85 through 114 removed outlier: 4.092A pdb=" N VAL G 89 " --> pdb=" O GLN G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 132 removed outlier: 3.707A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 42 Processing helix chain 'H' and resid 49 through 77 removed outlier: 4.732A pdb=" N ASP H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 94 removed outlier: 3.836A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 36 Processing helix chain 'I' and resid 46 through 73 removed outlier: 3.938A pdb=" N LEU I 65 " --> pdb=" O GLU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 removed outlier: 4.093A pdb=" N LEU I 83 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 97 Processing helix chain 'J' and resid 34 through 46 Processing helix chain 'J' and resid 52 through 81 removed outlier: 3.670A pdb=" N MET J 56 " --> pdb=" O SER J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 99 removed outlier: 3.904A pdb=" N ILE J 91 " --> pdb=" O THR J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 120 removed outlier: 4.028A pdb=" N SER J 109 " --> pdb=" O LYS J 105 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER J 120 " --> pdb=" O THR J 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 57 removed outlier: 3.833A pdb=" N SER K 57 " --> pdb=" O ARG K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 76 Processing helix chain 'K' and resid 85 through 114 removed outlier: 4.096A pdb=" N VAL K 89 " --> pdb=" O GLN K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.707A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY K 132 " --> pdb=" O ARG K 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 29 removed outlier: 3.549A pdb=" N GLY L 28 " --> pdb=" O ASN L 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE L 29 " --> pdb=" O ILE L 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 25 through 29' Processing helix chain 'L' and resid 30 through 42 removed outlier: 3.767A pdb=" N ILE L 34 " --> pdb=" O THR L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 76 removed outlier: 4.559A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 94 removed outlier: 4.181A pdb=" N VAL L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 22 Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 46 through 73 removed outlier: 4.024A pdb=" N ASN M 68 " --> pdb=" O GLU M 64 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA M 69 " --> pdb=" O LEU M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 89 Processing helix chain 'M' and resid 92 through 97 Processing helix chain 'N' and resid 34 through 46 removed outlier: 3.535A pdb=" N VAL N 38 " --> pdb=" O TYR N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 81 removed outlier: 3.811A pdb=" N MET N 56 " --> pdb=" O SER N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 99 Processing helix chain 'N' and resid 100 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 3.755A pdb=" N THR A 31 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 40 " --> pdb=" O THR A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 115 removed outlier: 3.906A pdb=" N LYS A 112 " --> pdb=" O CYS A 126 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET A 134 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 159 removed outlier: 3.666A pdb=" N PHE A 189 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA A 187 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 216 removed outlier: 3.668A pdb=" N GLN A 243 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 254 through 259 removed outlier: 3.849A pdb=" N LYS A 256 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS A 258 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 267 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 266 " --> pdb=" O TRP A 279 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 277 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 276 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 288 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 303 removed outlier: 3.721A pdb=" N ASP A 300 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE A 310 " --> pdb=" O TRP A 321 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP A 321 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 312 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 317 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 40 removed outlier: 7.500A pdb=" N LEU B 329 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER B 318 " --> pdb=" O LYS B 328 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP B 330 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE B 316 " --> pdb=" O TRP B 330 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 306 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 48 through 53 removed outlier: 3.984A pdb=" N SER B 50 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 63 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS B 52 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA B 61 " --> pdb=" O LYS B 52 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 93 removed outlier: 3.899A pdb=" N ASP B 92 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 132 through 137 removed outlier: 3.889A pdb=" N CYS B 134 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 147 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN B 136 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 174 through 179 removed outlier: 7.402A pdb=" N SER B 189 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL B 177 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 187 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE B 179 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 185 " --> pdb=" O PHE B 179 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG B 196 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE B 197 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 228 through 231 removed outlier: 3.583A pdb=" N ILE B 229 " --> pdb=" O TRP B 241 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 273 through 276 removed outlier: 3.608A pdb=" N TRP B 286 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 283 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU B 297 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 3834 through 3835 Processing sheet with id=AB7, first strand: chain 'C' and resid 3856 through 3857 removed outlier: 4.054A pdb=" N ILE C3856 " --> pdb=" O ILE C3928 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C3927 " --> pdb=" O ARG C3916 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C3916 " --> pdb=" O VAL C3927 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 3862 through 3864 Processing sheet with id=AB9, first strand: chain 'C' and resid 3919 through 3920 removed outlier: 3.972A pdb=" N ILE C3920 " --> pdb=" O GLN C3923 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 299 through 300 Processing sheet with id=AC2, first strand: chain 'D' and resid 316 through 317 removed outlier: 3.671A pdb=" N SER D 347 " --> pdb=" O PHE D 469 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA D 471 " --> pdb=" O GLY D 345 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY D 345 " --> pdb=" O ALA D 471 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER D 473 " --> pdb=" O ARG D 343 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG D 343 " --> pdb=" O SER D 473 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 331 through 332 Processing sheet with id=AC4, first strand: chain 'D' and resid 373 through 374 Processing sheet with id=AC5, first strand: chain 'D' and resid 447 through 451 removed outlier: 7.551A pdb=" N ILE D 447 " --> pdb=" O ALA D 459 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY D 457 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS D 451 " --> pdb=" O ASN D 455 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASN D 455 " --> pdb=" O LYS D 451 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 96 through 98 removed outlier: 6.636A pdb=" N THR H 96 " --> pdb=" O THR M 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'I' and resid 42 through 43 removed outlier: 7.204A pdb=" N ARG I 42 " --> pdb=" O ILE J 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.558A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'M' and resid 77 through 78 removed outlier: 3.529A pdb=" N ILE M 78 " --> pdb=" O GLY N 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 481 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 358 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 238 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 2.14 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: 4080 1.33 - 1.45: 5991 1.45 - 1.57: 10009 1.57 - 1.69: 580 1.69 - 1.81: 83 Bond restraints: 20743 Sorted by residual: bond pdb=" CA ILE C3861 " pdb=" CB ILE C3861 " ideal model delta sigma weight residual 1.533 1.583 -0.051 1.20e-02 6.94e+03 1.78e+01 bond pdb=" C3' DT O 15 " pdb=" O3' DT O 15 " ideal model delta sigma weight residual 1.435 1.489 -0.054 1.30e-02 5.92e+03 1.73e+01 bond pdb=" C5' DA P 131 " pdb=" C4' DA P 131 " ideal model delta sigma weight residual 1.512 1.537 -0.025 7.00e-03 2.04e+04 1.31e+01 bond pdb=" C3' DC O 126 " pdb=" O3' DC O 126 " ideal model delta sigma weight residual 1.435 1.482 -0.047 1.30e-02 5.92e+03 1.31e+01 bond pdb=" C3' DG O 94 " pdb=" O3' DG O 94 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.27e+01 ... (remaining 20738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 27733 2.02 - 4.05: 1430 4.05 - 6.07: 85 6.07 - 8.10: 22 8.10 - 10.12: 4 Bond angle restraints: 29274 Sorted by residual: angle pdb=" N THR A 195 " pdb=" CA THR A 195 " pdb=" CB THR A 195 " ideal model delta sigma weight residual 110.49 120.61 -10.12 1.69e+00 3.50e-01 3.59e+01 angle pdb=" O4' DA O 14 " pdb=" C4' DA O 14 " pdb=" C3' DA O 14 " ideal model delta sigma weight residual 106.00 102.63 3.37 6.00e-01 2.78e+00 3.15e+01 angle pdb=" O4' DA P 139 " pdb=" C4' DA P 139 " pdb=" C3' DA P 139 " ideal model delta sigma weight residual 106.00 102.64 3.36 6.00e-01 2.78e+00 3.13e+01 angle pdb=" O4' DG O 32 " pdb=" C4' DG O 32 " pdb=" C3' DG O 32 " ideal model delta sigma weight residual 106.00 102.86 3.14 6.00e-01 2.78e+00 2.73e+01 angle pdb=" N ILE C3866 " pdb=" CA ILE C3866 " pdb=" C ILE C3866 " ideal model delta sigma weight residual 113.47 108.37 5.10 1.01e+00 9.80e-01 2.55e+01 ... (remaining 29269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.21: 10232 34.21 - 68.42: 1422 68.42 - 102.63: 26 102.63 - 136.84: 1 136.84 - 171.05: 3 Dihedral angle restraints: 11684 sinusoidal: 6623 harmonic: 5061 Sorted by residual: dihedral pdb=" CA LYS H 31 " pdb=" C LYS H 31 " pdb=" N PRO H 32 " pdb=" CA PRO H 32 " ideal model delta harmonic sigma weight residual 180.00 134.55 45.45 0 5.00e+00 4.00e-02 8.26e+01 dihedral pdb=" N THR A 195 " pdb=" C THR A 195 " pdb=" CA THR A 195 " pdb=" CB THR A 195 " ideal model delta harmonic sigma weight residual 123.40 144.12 -20.72 0 2.50e+00 1.60e-01 6.87e+01 dihedral pdb=" C THR A 195 " pdb=" N THR A 195 " pdb=" CA THR A 195 " pdb=" CB THR A 195 " ideal model delta harmonic sigma weight residual -122.00 -140.79 18.79 0 2.50e+00 1.60e-01 5.65e+01 ... (remaining 11681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 3258 0.151 - 0.302: 26 0.302 - 0.452: 0 0.452 - 0.603: 0 0.603 - 0.754: 1 Chirality restraints: 3285 Sorted by residual: chirality pdb=" CA THR A 195 " pdb=" N THR A 195 " pdb=" C THR A 195 " pdb=" CB THR A 195 " both_signs ideal model delta sigma weight residual False 2.53 1.77 0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" C3' DT O 15 " pdb=" C4' DT O 15 " pdb=" O3' DT O 15 " pdb=" C2' DT O 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA SER A 108 " pdb=" N SER A 108 " pdb=" C SER A 108 " pdb=" CB SER A 108 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 3282 not shown) Planarity restraints: 2701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 31 " 0.072 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO H 32 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO H 32 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO H 32 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 223 " 0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO B 224 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 224 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 224 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 126 " 0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO A 127 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 127 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 127 " 0.035 5.00e-02 4.00e+02 ... (remaining 2698 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 17 2.19 - 2.87: 6208 2.87 - 3.55: 26361 3.55 - 4.22: 47280 4.22 - 4.90: 73348 Nonbonded interactions: 153214 Sorted by model distance: nonbonded pdb=" O PHE A 332 " pdb=" OG1 THR B 208 " model vdw 1.513 3.040 nonbonded pdb=" CG PRO A 334 " pdb=" O THR B 208 " model vdw 1.669 3.440 nonbonded pdb=" O PHE A 332 " pdb=" CB THR B 208 " model vdw 1.695 3.470 nonbonded pdb=" C PHE A 332 " pdb=" OG1 THR B 208 " model vdw 1.723 3.270 nonbonded pdb=" O PHE A 332 " pdb=" CG2 THR B 208 " model vdw 1.771 3.460 ... (remaining 153209 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 'G' selection = chain 'K' } ncs_group { reference = (chain 'H' and resid 24 through 101) selection = chain 'L' } ncs_group { reference = (chain 'I' and resid 13 through 117) selection = chain 'M' } ncs_group { reference = (chain 'J' and resid 28 through 120) selection = (chain 'N' 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.590 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 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 0.068 20743 Z= 0.524 Angle : 0.935 10.121 29274 Z= 0.708 Chirality : 0.055 0.754 3285 Planarity : 0.007 0.110 2701 Dihedral : 22.769 171.047 8424 Min Nonbonded Distance : 1.513 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.07 % Allowed : 1.82 % Favored : 98.12 % Cbeta Deviations : 0.06 % 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: 1717 helix: -1.12 (0.18), residues: 556 sheet: -3.15 (0.28), residues: 246 loop : -3.27 (0.16), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C3765 TYR 0.034 0.003 TYR H 51 PHE 0.017 0.002 PHE A 213 TRP 0.024 0.003 TRP A 51 HIS 0.011 0.002 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.52 (20743) covalent geometry : angle 0.93516 / 0.71 (29274) hydrogen bonds : bond 0.18191 / 12.09 ( 839) hydrogen bonds : angle 5.46859 / 3.69 ( 2107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 566 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ASP cc_start: 0.7250 (t0) cc_final: 0.6940 (p0) REVERT: A 245 LEU cc_start: 0.9036 (mt) cc_final: 0.8594 (mt) REVERT: A 248 LEU cc_start: 0.8950 (mt) cc_final: 0.8644 (mt) REVERT: A 250 ASN cc_start: 0.9051 (m-40) cc_final: 0.8543 (p0) REVERT: A 262 ASP cc_start: 0.8125 (p0) cc_final: 0.7763 (p0) REVERT: A 277 TYR cc_start: 0.8073 (m-10) cc_final: 0.7278 (m-80) REVERT: B 53 PHE cc_start: 0.1419 (m-80) cc_final: 0.1181 (p90) REVERT: B 252 TYR cc_start: 0.4022 (m-80) cc_final: 0.2869 (t80) REVERT: C 3823 LEU cc_start: 0.8217 (tp) cc_final: 0.7212 (tp) REVERT: C 3844 PHE cc_start: 0.7844 (m-80) cc_final: 0.7448 (m-80) REVERT: C 3855 VAL cc_start: 0.8449 (t) cc_final: 0.7690 (p) REVERT: C 3867 LEU cc_start: 0.8357 (tp) cc_final: 0.8142 (tp) REVERT: C 3871 ARG cc_start: 0.8453 (mtt-85) cc_final: 0.8210 (mmp-170) REVERT: D 315 MET cc_start: 0.5782 (ttp) cc_final: 0.5155 (ppp) REVERT: D 338 PRO cc_start: 0.6609 (Cg_exo) cc_final: 0.6398 (Cg_endo) REVERT: D 397 ASN cc_start: 0.6647 (t0) cc_final: 0.6359 (t0) REVERT: D 448 ILE cc_start: 0.6713 (mt) cc_final: 0.5888 (mp) REVERT: D 500 MET cc_start: 0.1472 (mmm) cc_final: 0.1174 (mtm) REVERT: G 48 LEU cc_start: 0.9220 (mt) cc_final: 0.8984 (mm) REVERT: G 62 ILE cc_start: 0.9001 (mt) cc_final: 0.8738 (mm) REVERT: G 64 LYS cc_start: 0.9159 (ptpp) cc_final: 0.8558 (mmmm) REVERT: G 65 LEU cc_start: 0.9294 (mp) cc_final: 0.8929 (mm) REVERT: G 68 GLN cc_start: 0.9396 (tt0) cc_final: 0.9120 (pt0) REVERT: G 76 GLN cc_start: 0.8480 (tt0) cc_final: 0.7669 (tp-100) REVERT: G 89 VAL cc_start: 0.9776 (t) cc_final: 0.9471 (t) REVERT: G 99 TYR cc_start: 0.9094 (t80) cc_final: 0.8646 (t80) REVERT: G 105 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8423 (mm-30) REVERT: G 107 THR cc_start: 0.9726 (m) cc_final: 0.9511 (p) REVERT: G 120 MET cc_start: 0.6823 (mtt) cc_final: 0.6391 (mtp) REVERT: H 49 LEU cc_start: 0.9499 (mt) cc_final: 0.9164 (mt) REVERT: H 64 ASN cc_start: 0.9245 (m-40) cc_final: 0.8949 (t0) REVERT: H 67 ARG cc_start: 0.8647 (ttp-170) cc_final: 0.8409 (tpp-160) REVERT: H 75 HIS cc_start: 0.8717 (t70) cc_final: 0.7910 (t-170) REVERT: H 79 LYS cc_start: 0.8568 (mttt) cc_final: 0.8342 (ptpp) REVERT: H 93 GLN cc_start: 0.9348 (mm-40) cc_final: 0.8899 (tp40) REVERT: H 97 LEU cc_start: 0.9490 (tp) cc_final: 0.9171 (mm) REVERT: H 98 TYR cc_start: 0.8106 (m-10) cc_final: 0.7253 (m-80) REVERT: I 56 GLU cc_start: 0.8794 (tt0) cc_final: 0.8340 (tm-30) REVERT: I 72 ASP cc_start: 0.8213 (m-30) cc_final: 0.8006 (p0) REVERT: I 73 ASN cc_start: 0.8854 (m-40) cc_final: 0.8641 (p0) REVERT: I 81 ARG cc_start: 0.9289 (tpt-90) cc_final: 0.8902 (tpt170) REVERT: I 85 LEU cc_start: 0.9471 (mt) cc_final: 0.9189 (mm) REVERT: I 89 ASN cc_start: 0.9545 (m-40) cc_final: 0.9175 (m110) REVERT: I 90 ASP cc_start: 0.9163 (t0) cc_final: 0.8910 (p0) REVERT: J 54 LYS cc_start: 0.9591 (mmmt) cc_final: 0.9363 (mmmt) REVERT: J 59 MET cc_start: 0.9471 (mmm) cc_final: 0.9117 (mmm) REVERT: J 65 ASP cc_start: 0.9270 (t0) cc_final: 0.9065 (t0) REVERT: J 76 ARG cc_start: 0.9379 (ttm110) cc_final: 0.8906 (ttm110) REVERT: J 77 LEU cc_start: 0.9352 (mt) cc_final: 0.8747 (mt) REVERT: J 85 THR cc_start: 0.9039 (m) cc_final: 0.8754 (p) REVERT: J 96 ARG cc_start: 0.9286 (ttm170) cc_final: 0.9039 (ttm170) REVERT: K 48 LEU cc_start: 0.8928 (mt) cc_final: 0.8290 (mm) REVERT: K 100 LEU cc_start: 0.9790 (mt) cc_final: 0.9453 (pp) REVERT: L 27 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8454 (mp10) REVERT: L 53 GLU cc_start: 0.9436 (tp30) cc_final: 0.9053 (tt0) REVERT: L 63 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8172 (mm-30) REVERT: L 66 ILE cc_start: 0.9211 (mt) cc_final: 0.8831 (pt) REVERT: L 91 LYS cc_start: 0.8855 (ttmt) cc_final: 0.8647 (tptm) REVERT: M 61 GLU cc_start: 0.9448 (tp30) cc_final: 0.8959 (tm-30) REVERT: M 88 ARG cc_start: 0.9403 (mmt-90) cc_final: 0.9172 (mmt180) REVERT: N 40 LYS cc_start: 0.9453 (mttt) cc_final: 0.9172 (mttt) REVERT: N 59 MET cc_start: 0.9478 (mmm) cc_final: 0.9079 (mmm) REVERT: N 65 ASP cc_start: 0.8939 (t0) cc_final: 0.8678 (t0) REVERT: N 68 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8764 (mm-30) REVERT: N 69 ARG cc_start: 0.9489 (ttm110) cc_final: 0.9036 (ttm110) REVERT: N 82 LYS cc_start: 0.9673 (mttt) cc_final: 0.9340 (tptt) REVERT: N 87 THR cc_start: 0.7521 (p) cc_final: 0.6423 (p) REVERT: N 90 GLU cc_start: 0.9231 (mp0) cc_final: 0.8508 (mp0) REVERT: N 92 GLN cc_start: 0.9102 (tt0) cc_final: 0.8840 (mt0) REVERT: N 98 LEU cc_start: 0.9539 (tp) cc_final: 0.9214 (tp) REVERT: N 113 LYS cc_start: 0.8985 (ttpp) cc_final: 0.8783 (ttmm) REVERT: N 116 THR cc_start: 0.9573 (m) cc_final: 0.9341 (p) outliers start: 1 outliers final: 1 residues processed: 567 average time/residue: 0.1759 time to fit residues: 140.6010 Evaluate side-chains 285 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.0980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 HIS A 88 ASN A 120 GLN A 323 GLN B 310 HIS D 320 HIS D 354 GLN D 381 HIS G 68 GLN L 64 ASN ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.094201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.067718 restraints weight = 108250.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.069678 restraints weight = 59790.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.070927 restraints weight = 39170.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.071746 restraints weight = 29190.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.072285 restraints weight = 23839.851| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 20743 Z= 0.167 Angle : 0.726 8.979 29274 Z= 0.411 Chirality : 0.049 0.375 3285 Planarity : 0.006 0.087 2701 Dihedral : 28.033 171.241 5080 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.34 % Allowed : 2.62 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.18), residues: 1717 helix: 0.26 (0.21), residues: 560 sheet: -2.48 (0.32), residues: 223 loop : -3.04 (0.17), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 83 TYR 0.031 0.002 TYR C3942 PHE 0.018 0.001 PHE K 67 TRP 0.012 0.002 TRP B 241 HIS 0.009 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.17 (20743) covalent geometry : angle 0.72642 / 0.41 (29274) hydrogen bonds : bond 0.07078 / 4.77 ( 839) hydrogen bonds : angle 4.33183 / 2.95 ( 2107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 383 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ASP cc_start: 0.7181 (t0) cc_final: 0.6924 (p0) REVERT: A 184 ASP cc_start: 0.8709 (t0) cc_final: 0.8352 (t0) REVERT: A 186 VAL cc_start: 0.9044 (m) cc_final: 0.7991 (m) REVERT: A 250 ASN cc_start: 0.9417 (m-40) cc_final: 0.8672 (p0) REVERT: A 277 TYR cc_start: 0.8116 (m-10) cc_final: 0.7368 (m-80) REVERT: A 315 SER cc_start: 0.7913 (m) cc_final: 0.7671 (p) REVERT: B 53 PHE cc_start: 0.2210 (m-80) cc_final: 0.1413 (p90) REVERT: B 252 TYR cc_start: 0.4015 (m-80) cc_final: 0.2837 (t80) REVERT: C 3844 PHE cc_start: 0.7872 (m-80) cc_final: 0.7650 (m-80) REVERT: C 3867 LEU cc_start: 0.8522 (tp) cc_final: 0.8182 (tp) REVERT: C 3871 ARG cc_start: 0.8434 (mtt-85) cc_final: 0.8120 (mmp-170) REVERT: C 3897 MET cc_start: 0.4495 (ttm) cc_final: 0.4097 (ptp) REVERT: D 315 MET cc_start: 0.6031 (ttp) cc_final: 0.5370 (ppp) REVERT: D 397 ASN cc_start: 0.6907 (t0) cc_final: 0.6603 (t0) REVERT: D 469 PHE cc_start: 0.7638 (m-80) cc_final: 0.7424 (m-10) REVERT: D 500 MET cc_start: 0.1336 (mmm) cc_final: 0.1100 (mtm) REVERT: G 50 GLU cc_start: 0.9419 (tp30) cc_final: 0.8708 (tm-30) REVERT: G 60 LEU cc_start: 0.7989 (pt) cc_final: 0.7631 (pt) REVERT: G 65 LEU cc_start: 0.9382 (mp) cc_final: 0.8474 (mt) REVERT: G 76 GLN cc_start: 0.8400 (tt0) cc_final: 0.7644 (tp-100) REVERT: G 93 GLN cc_start: 0.9248 (mt0) cc_final: 0.9016 (mt0) REVERT: G 99 TYR cc_start: 0.8926 (t80) cc_final: 0.8669 (t80) REVERT: G 105 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8500 (mm-30) REVERT: G 119 ILE cc_start: 0.8253 (mt) cc_final: 0.7919 (mt) REVERT: G 120 MET cc_start: 0.7153 (mtt) cc_final: 0.6634 (mtm) REVERT: H 44 LYS cc_start: 0.8679 (tppp) cc_final: 0.8146 (tppt) REVERT: H 75 HIS cc_start: 0.8874 (t70) cc_final: 0.8483 (t70) REVERT: H 79 LYS cc_start: 0.8707 (mttt) cc_final: 0.8104 (mtmm) REVERT: H 92 ARG cc_start: 0.9410 (mtp-110) cc_final: 0.9158 (ttt180) REVERT: H 93 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8896 (tp40) REVERT: H 97 LEU cc_start: 0.9606 (tp) cc_final: 0.9336 (mm) REVERT: H 98 TYR cc_start: 0.8762 (m-10) cc_final: 0.7886 (m-80) REVERT: I 23 LEU cc_start: 0.9106 (mm) cc_final: 0.8790 (mm) REVERT: I 38 ASN cc_start: 0.7216 (t0) cc_final: 0.6948 (t0) REVERT: I 56 GLU cc_start: 0.8953 (tt0) cc_final: 0.8388 (tm-30) REVERT: I 71 ARG cc_start: 0.9110 (ttp80) cc_final: 0.8891 (ttp80) REVERT: I 72 ASP cc_start: 0.8450 (m-30) cc_final: 0.8098 (p0) REVERT: I 89 ASN cc_start: 0.9538 (m-40) cc_final: 0.9076 (m110) REVERT: I 104 GLN cc_start: 0.8390 (mp10) cc_final: 0.7969 (mp10) REVERT: J 76 ARG cc_start: 0.9384 (ttm110) cc_final: 0.9178 (ttm110) REVERT: J 77 LEU cc_start: 0.9538 (mt) cc_final: 0.9251 (mt) REVERT: J 96 ARG cc_start: 0.9335 (ttm170) cc_final: 0.9071 (ttm170) REVERT: K 50 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8900 (mm-30) REVERT: K 77 ASP cc_start: 0.8473 (m-30) cc_final: 0.8002 (p0) REVERT: K 105 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8277 (tm-30) REVERT: L 44 LYS cc_start: 0.9181 (mttm) cc_final: 0.8933 (mmtt) REVERT: L 64 ASN cc_start: 0.9280 (OUTLIER) cc_final: 0.9069 (t0) REVERT: L 88 TYR cc_start: 0.9469 (m-10) cc_final: 0.8882 (m-80) REVERT: M 61 GLU cc_start: 0.9293 (tp30) cc_final: 0.8997 (tm-30) REVERT: M 72 ASP cc_start: 0.9379 (m-30) cc_final: 0.9133 (t0) REVERT: M 83 LEU cc_start: 0.9450 (mt) cc_final: 0.9202 (mm) REVERT: N 40 LYS cc_start: 0.9585 (mttt) cc_final: 0.9193 (mttt) REVERT: N 59 MET cc_start: 0.9188 (mmm) cc_final: 0.8834 (mmm) REVERT: N 69 ARG cc_start: 0.9245 (ttm110) cc_final: 0.9017 (ttm110) REVERT: N 73 GLU cc_start: 0.8743 (tp30) cc_final: 0.8480 (tp30) REVERT: N 90 GLU cc_start: 0.9176 (mp0) cc_final: 0.8852 (mp0) REVERT: N 98 LEU cc_start: 0.9288 (tp) cc_final: 0.9047 (tt) outliers start: 5 outliers final: 0 residues processed: 386 average time/residue: 0.1524 time to fit residues: 85.9606 Evaluate side-chains 270 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 143 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 ASN B 310 HIS G 125 GLN J 46 HIS K 113 HIS M 89 ASN N 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.088672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.062783 restraints weight = 113136.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.064606 restraints weight = 62094.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.065765 restraints weight = 40799.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.066540 restraints weight = 30415.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.067051 restraints weight = 24878.984| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 20743 Z= 0.201 Angle : 0.708 11.936 29274 Z= 0.401 Chirality : 0.047 0.422 3285 Planarity : 0.006 0.089 2701 Dihedral : 27.859 179.736 5080 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.24 % 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: 1717 helix: 0.65 (0.21), residues: 562 sheet: -2.43 (0.29), residues: 272 loop : -2.88 (0.17), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 53 TYR 0.035 0.002 TYR K 54 PHE 0.015 0.002 PHE H 100 TRP 0.020 0.002 TRP A 51 HIS 0.010 0.001 HIS K 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.20 (20743) covalent geometry : angle 0.70822 / 0.40 (29274) hydrogen bonds : bond 0.07232 / 4.80 ( 839) hydrogen bonds : angle 4.19799 / 2.86 ( 2107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 348 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ASP cc_start: 0.7397 (t0) cc_final: 0.7116 (p0) REVERT: A 184 ASP cc_start: 0.8700 (t0) cc_final: 0.8368 (t0) REVERT: A 186 VAL cc_start: 0.9034 (m) cc_final: 0.7954 (m) REVERT: A 215 ILE cc_start: 0.9272 (pt) cc_final: 0.9030 (pt) REVERT: A 250 ASN cc_start: 0.9547 (m-40) cc_final: 0.8498 (t0) REVERT: A 273 GLN cc_start: 0.8080 (mt0) cc_final: 0.7572 (pm20) REVERT: A 276 LEU cc_start: 0.8511 (mt) cc_final: 0.7962 (tp) REVERT: A 277 TYR cc_start: 0.8227 (m-10) cc_final: 0.7590 (m-80) REVERT: A 279 TRP cc_start: 0.8420 (m-90) cc_final: 0.7620 (m-90) REVERT: B 53 PHE cc_start: 0.2190 (m-80) cc_final: 0.1318 (p90) REVERT: B 100 ASN cc_start: 0.6201 (OUTLIER) cc_final: 0.5810 (t0) REVERT: B 252 TYR cc_start: 0.4339 (m-80) cc_final: 0.2904 (t80) REVERT: C 3897 MET cc_start: 0.4696 (ttm) cc_final: 0.4406 (ptp) REVERT: D 315 MET cc_start: 0.5985 (ttp) cc_final: 0.5342 (ppp) REVERT: D 327 TRP cc_start: 0.6614 (m-90) cc_final: 0.6025 (m-90) REVERT: D 397 ASN cc_start: 0.6840 (t0) cc_final: 0.6558 (t0) REVERT: G 50 GLU cc_start: 0.9337 (tp30) cc_final: 0.8696 (tm-30) REVERT: G 59 GLU cc_start: 0.8551 (tp30) cc_final: 0.8251 (tp30) REVERT: G 60 LEU cc_start: 0.8466 (pt) cc_final: 0.7763 (pt) REVERT: G 65 LEU cc_start: 0.9235 (mp) cc_final: 0.8751 (mm) REVERT: G 67 PHE cc_start: 0.9384 (t80) cc_final: 0.9078 (t80) REVERT: G 76 GLN cc_start: 0.8469 (tt0) cc_final: 0.7669 (tp-100) REVERT: G 93 GLN cc_start: 0.9243 (mt0) cc_final: 0.9025 (mt0) REVERT: G 94 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8989 (mm-30) REVERT: G 99 TYR cc_start: 0.9054 (t80) cc_final: 0.8634 (t80) REVERT: G 120 MET cc_start: 0.7229 (mtt) cc_final: 0.6451 (mtm) REVERT: H 44 LYS cc_start: 0.8741 (tppp) cc_final: 0.8270 (tppt) REVERT: H 67 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.7882 (tpp-160) REVERT: H 75 HIS cc_start: 0.8885 (t70) cc_final: 0.8652 (t70) REVERT: H 79 LYS cc_start: 0.8813 (mttt) cc_final: 0.8294 (mtmm) REVERT: H 88 TYR cc_start: 0.8885 (m-80) cc_final: 0.8357 (m-80) REVERT: H 92 ARG cc_start: 0.9426 (mtp-110) cc_final: 0.9207 (ttt180) REVERT: H 97 LEU cc_start: 0.9634 (tp) cc_final: 0.9300 (mm) REVERT: H 98 TYR cc_start: 0.8988 (m-10) cc_final: 0.8169 (m-80) REVERT: I 23 LEU cc_start: 0.9153 (mm) cc_final: 0.8910 (mm) REVERT: I 38 ASN cc_start: 0.7137 (t0) cc_final: 0.6885 (t0) REVERT: I 56 GLU cc_start: 0.8829 (tt0) cc_final: 0.8406 (tm-30) REVERT: I 64 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8866 (tm-30) REVERT: I 73 ASN cc_start: 0.9365 (t0) cc_final: 0.9156 (t0) REVERT: I 75 LYS cc_start: 0.7190 (tptt) cc_final: 0.6676 (mtpt) REVERT: I 76 THR cc_start: 0.8591 (m) cc_final: 0.8355 (p) REVERT: I 92 GLU cc_start: 0.8425 (tt0) cc_final: 0.7390 (tt0) REVERT: I 104 GLN cc_start: 0.8565 (mp10) cc_final: 0.8153 (mp10) REVERT: J 76 ARG cc_start: 0.9428 (ttm110) cc_final: 0.9068 (ttm110) REVERT: J 96 ARG cc_start: 0.9409 (ttm170) cc_final: 0.9031 (ttm170) REVERT: J 103 LEU cc_start: 0.9159 (mt) cc_final: 0.8582 (mt) REVERT: K 48 LEU cc_start: 0.8544 (mt) cc_final: 0.8305 (mt) REVERT: K 68 GLN cc_start: 0.9626 (pt0) cc_final: 0.9399 (pt0) REVERT: K 76 GLN cc_start: 0.9114 (tt0) cc_final: 0.8269 (tp-100) REVERT: K 77 ASP cc_start: 0.8822 (m-30) cc_final: 0.8387 (p0) REVERT: K 105 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8570 (tm-30) REVERT: K 106 ASP cc_start: 0.7710 (m-30) cc_final: 0.7146 (m-30) REVERT: K 120 MET cc_start: 0.8426 (mmm) cc_final: 0.8089 (mmp) REVERT: L 44 LYS cc_start: 0.9337 (mttm) cc_final: 0.8862 (mmtt) REVERT: L 53 GLU cc_start: 0.9560 (tp30) cc_final: 0.9133 (tt0) REVERT: L 88 TYR cc_start: 0.9470 (m-10) cc_final: 0.8786 (m-80) REVERT: M 38 ASN cc_start: 0.8681 (p0) cc_final: 0.8179 (p0) REVERT: M 61 GLU cc_start: 0.9277 (tp30) cc_final: 0.9063 (tm-30) REVERT: M 64 GLU cc_start: 0.8999 (tp30) cc_final: 0.8512 (mm-30) REVERT: M 72 ASP cc_start: 0.9371 (m-30) cc_final: 0.9041 (t0) REVERT: M 83 LEU cc_start: 0.9524 (mt) cc_final: 0.9284 (mm) REVERT: N 40 LYS cc_start: 0.9638 (mttt) cc_final: 0.9379 (mmtt) REVERT: N 59 MET cc_start: 0.9308 (mmm) cc_final: 0.8924 (mmp) REVERT: N 65 ASP cc_start: 0.9040 (t0) cc_final: 0.8738 (t0) REVERT: N 82 LYS cc_start: 0.9115 (tppt) cc_final: 0.8844 (tppt) REVERT: N 90 GLU cc_start: 0.9156 (mp0) cc_final: 0.8830 (mp0) REVERT: N 98 LEU cc_start: 0.9274 (tp) cc_final: 0.9003 (tt) outliers start: 1 outliers final: 0 residues processed: 348 average time/residue: 0.1540 time to fit residues: 79.3108 Evaluate side-chains 263 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 86 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 165 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 40 optimal weight: 30.0000 chunk 173 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 86 HIS ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.088266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.062085 restraints weight = 115211.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.063791 restraints weight = 65400.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.064899 restraints weight = 43851.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.065655 restraints weight = 33236.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.066066 restraints weight = 27501.674| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20743 Z= 0.142 Angle : 0.637 9.804 29274 Z= 0.363 Chirality : 0.045 0.418 3285 Planarity : 0.005 0.090 2701 Dihedral : 27.784 179.292 5080 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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: -1.96 (0.19), residues: 1717 helix: 1.11 (0.22), residues: 555 sheet: -2.11 (0.32), residues: 240 loop : -2.75 (0.17), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG J 30 TYR 0.018 0.001 TYR H 51 PHE 0.018 0.001 PHE G 67 TRP 0.013 0.001 TRP A 51 HIS 0.008 0.001 HIS C3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (20743) covalent geometry : angle 0.63723 / 0.36 (29274) hydrogen bonds : bond 0.05259 / 3.59 ( 839) hydrogen bonds : angle 3.87206 / 2.63 ( 2107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ASP cc_start: 0.7505 (t0) cc_final: 0.7231 (p0) REVERT: A 184 ASP cc_start: 0.8690 (t0) cc_final: 0.8357 (t0) REVERT: A 186 VAL cc_start: 0.9064 (m) cc_final: 0.7961 (m) REVERT: A 215 ILE cc_start: 0.9288 (pt) cc_final: 0.9040 (pt) REVERT: A 250 ASN cc_start: 0.9534 (m-40) cc_final: 0.8890 (p0) REVERT: A 273 GLN cc_start: 0.8016 (mt0) cc_final: 0.7657 (pm20) REVERT: A 276 LEU cc_start: 0.8543 (mt) cc_final: 0.8031 (tp) REVERT: A 277 TYR cc_start: 0.8225 (m-10) cc_final: 0.7547 (m-80) REVERT: A 279 TRP cc_start: 0.8554 (m-90) cc_final: 0.7807 (m-90) REVERT: A 315 SER cc_start: 0.8070 (m) cc_final: 0.7690 (p) REVERT: A 341 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7354 (mm-30) REVERT: B 53 PHE cc_start: 0.2009 (m-80) cc_final: 0.1266 (p90) REVERT: C 3867 LEU cc_start: 0.8639 (tp) cc_final: 0.8251 (tp) REVERT: C 3871 ARG cc_start: 0.8576 (mtt-85) cc_final: 0.8235 (mmp-170) REVERT: C 3897 MET cc_start: 0.4725 (ttm) cc_final: 0.4284 (ptp) REVERT: C 3932 ARG cc_start: 0.8520 (mpp-170) cc_final: 0.7854 (ppt170) REVERT: D 315 MET cc_start: 0.5929 (ttp) cc_final: 0.5413 (ppp) REVERT: D 327 TRP cc_start: 0.6424 (m-90) cc_final: 0.6171 (t60) REVERT: D 329 PHE cc_start: 0.5941 (p90) cc_final: 0.5579 (p90) REVERT: D 397 ASN cc_start: 0.6858 (t0) cc_final: 0.6559 (t0) REVERT: G 50 GLU cc_start: 0.9334 (tp30) cc_final: 0.8722 (tm-30) REVERT: G 65 LEU cc_start: 0.9203 (mp) cc_final: 0.8809 (mt) REVERT: G 76 GLN cc_start: 0.8459 (tt0) cc_final: 0.7679 (tp-100) REVERT: G 92 LEU cc_start: 0.9550 (mt) cc_final: 0.9321 (mt) REVERT: G 94 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8825 (mm-30) REVERT: G 112 ILE cc_start: 0.9246 (mm) cc_final: 0.8942 (mm) REVERT: G 120 MET cc_start: 0.7123 (mtt) cc_final: 0.6484 (mtm) REVERT: H 44 LYS cc_start: 0.8795 (tppp) cc_final: 0.8529 (tppt) REVERT: H 67 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.7776 (tpp-160) REVERT: H 75 HIS cc_start: 0.8843 (t70) cc_final: 0.8555 (t70) REVERT: H 79 LYS cc_start: 0.8842 (mttt) cc_final: 0.8385 (mtmm) REVERT: H 88 TYR cc_start: 0.8942 (m-10) cc_final: 0.8365 (m-80) REVERT: H 92 ARG cc_start: 0.9384 (mtp-110) cc_final: 0.9121 (ttt180) REVERT: H 95 ARG cc_start: 0.8815 (mmm-85) cc_final: 0.8580 (mtt-85) REVERT: H 98 TYR cc_start: 0.9089 (m-10) cc_final: 0.8493 (m-80) REVERT: I 23 LEU cc_start: 0.9108 (mm) cc_final: 0.8908 (mm) REVERT: I 38 ASN cc_start: 0.7350 (t0) cc_final: 0.7061 (t0) REVERT: I 56 GLU cc_start: 0.8795 (tt0) cc_final: 0.8472 (tm-30) REVERT: I 64 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8786 (tm-30) REVERT: I 74 LYS cc_start: 0.9149 (tttp) cc_final: 0.8567 (tptp) REVERT: I 75 LYS cc_start: 0.7461 (tptt) cc_final: 0.6635 (mtpt) REVERT: I 104 GLN cc_start: 0.8649 (mp10) cc_final: 0.8282 (mp10) REVERT: J 92 GLN cc_start: 0.9494 (tt0) cc_final: 0.9234 (tt0) REVERT: J 95 VAL cc_start: 0.9567 (t) cc_final: 0.9333 (p) REVERT: J 96 ARG cc_start: 0.9350 (ttm170) cc_final: 0.8980 (ttm170) REVERT: K 76 GLN cc_start: 0.9096 (tt0) cc_final: 0.8193 (tp-100) REVERT: K 77 ASP cc_start: 0.8805 (m-30) cc_final: 0.8378 (p0) REVERT: K 79 LYS cc_start: 0.9100 (tptp) cc_final: 0.8822 (tppt) REVERT: K 94 GLU cc_start: 0.9373 (mm-30) cc_final: 0.9041 (mm-30) REVERT: K 97 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8870 (mt-10) REVERT: K 105 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8502 (tm-30) REVERT: K 106 ASP cc_start: 0.7727 (m-30) cc_final: 0.7233 (m-30) REVERT: L 43 VAL cc_start: 0.8936 (t) cc_final: 0.8645 (m) REVERT: L 44 LYS cc_start: 0.9270 (mttm) cc_final: 0.8710 (mttt) REVERT: L 53 GLU cc_start: 0.9511 (tp30) cc_final: 0.9088 (tt0) REVERT: L 63 GLU cc_start: 0.8877 (pp20) cc_final: 0.8142 (mt-10) REVERT: L 88 TYR cc_start: 0.9400 (m-10) cc_final: 0.8822 (m-80) REVERT: M 38 ASN cc_start: 0.8621 (p0) cc_final: 0.8095 (p0) REVERT: M 64 GLU cc_start: 0.8954 (tp30) cc_final: 0.8305 (mm-30) REVERT: M 72 ASP cc_start: 0.9315 (m-30) cc_final: 0.9070 (t0) REVERT: N 30 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7428 (tpp-160) REVERT: N 40 LYS cc_start: 0.9655 (mttt) cc_final: 0.9332 (mmtt) REVERT: N 59 MET cc_start: 0.9194 (mmm) cc_final: 0.8829 (mmp) REVERT: N 90 GLU cc_start: 0.9109 (mp0) cc_final: 0.8667 (mp0) REVERT: N 92 GLN cc_start: 0.8831 (mt0) cc_final: 0.8561 (mt0) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1401 time to fit residues: 72.5698 Evaluate side-chains 263 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 143 optimal weight: 1.9990 chunk 40 optimal weight: 40.0000 chunk 70 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.084600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.058653 restraints weight = 114987.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.060432 restraints weight = 63185.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.061572 restraints weight = 41741.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.062330 restraints weight = 31255.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.062828 restraints weight = 25542.000| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 20743 Z= 0.178 Angle : 0.664 13.856 29274 Z= 0.373 Chirality : 0.045 0.369 3285 Planarity : 0.005 0.104 2701 Dihedral : 27.607 176.876 5080 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.59 % Favored : 94.35 % Rotamer: Outliers : 0.13 % Allowed : 2.42 % Favored : 97.44 % 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: -1.86 (0.19), residues: 1717 helix: 1.08 (0.22), residues: 557 sheet: -1.84 (0.32), residues: 241 loop : -2.68 (0.17), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG L 45 TYR 0.022 0.002 TYR H 51 PHE 0.020 0.002 PHE J 62 TRP 0.013 0.001 TRP D 327 HIS 0.015 0.001 HIS C3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 (20743) covalent geometry : angle 0.66367 / 0.37 (29274) hydrogen bonds : bond 0.06577 / 4.41 ( 839) hydrogen bonds : angle 3.92255 / 2.67 ( 2107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 321 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ASP cc_start: 0.7396 (t0) cc_final: 0.7185 (p0) REVERT: A 184 ASP cc_start: 0.8698 (t0) cc_final: 0.8361 (t70) REVERT: A 186 VAL cc_start: 0.9072 (m) cc_final: 0.7729 (m) REVERT: A 215 ILE cc_start: 0.9307 (pt) cc_final: 0.9058 (pt) REVERT: A 250 ASN cc_start: 0.9617 (m-40) cc_final: 0.8956 (p0) REVERT: A 257 CYS cc_start: 0.8404 (m) cc_final: 0.8154 (t) REVERT: A 273 GLN cc_start: 0.8128 (mt0) cc_final: 0.7700 (pm20) REVERT: A 276 LEU cc_start: 0.8521 (mt) cc_final: 0.8032 (tp) REVERT: A 277 TYR cc_start: 0.8152 (m-10) cc_final: 0.7553 (m-80) REVERT: A 279 TRP cc_start: 0.8538 (m-90) cc_final: 0.7983 (m-90) REVERT: A 341 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7276 (mm-30) REVERT: B 53 PHE cc_start: 0.2287 (m-80) cc_final: 0.1360 (p90) REVERT: C 3818 MET cc_start: 0.8869 (mtm) cc_final: 0.8663 (mtm) REVERT: C 3897 MET cc_start: 0.4882 (ttm) cc_final: 0.4553 (ptm) REVERT: D 315 MET cc_start: 0.6153 (ttp) cc_final: 0.5615 (ppp) REVERT: D 397 ASN cc_start: 0.6843 (t0) cc_final: 0.6529 (t0) REVERT: G 50 GLU cc_start: 0.9346 (tp30) cc_final: 0.8718 (tm-30) REVERT: G 65 LEU cc_start: 0.9221 (mp) cc_final: 0.8848 (mm) REVERT: G 76 GLN cc_start: 0.8569 (tt0) cc_final: 0.7843 (tp-100) REVERT: G 92 LEU cc_start: 0.9583 (mt) cc_final: 0.9354 (mt) REVERT: G 112 ILE cc_start: 0.9281 (mm) cc_final: 0.8996 (mm) REVERT: G 119 ILE cc_start: 0.8241 (mt) cc_final: 0.8004 (mt) REVERT: G 120 MET cc_start: 0.7144 (mtt) cc_final: 0.6336 (mtm) REVERT: G 122 LYS cc_start: 0.8535 (ptpp) cc_final: 0.8247 (ptpp) REVERT: H 43 VAL cc_start: 0.9425 (t) cc_final: 0.9060 (p) REVERT: H 75 HIS cc_start: 0.8840 (t70) cc_final: 0.8475 (t70) REVERT: H 79 LYS cc_start: 0.8994 (mttt) cc_final: 0.8483 (mtmm) REVERT: H 88 TYR cc_start: 0.9042 (m-10) cc_final: 0.8478 (m-80) REVERT: H 92 ARG cc_start: 0.9477 (mtp-110) cc_final: 0.9199 (ttt180) REVERT: H 98 TYR cc_start: 0.9207 (m-10) cc_final: 0.8448 (m-80) REVERT: I 23 LEU cc_start: 0.9184 (mm) cc_final: 0.8966 (mm) REVERT: I 56 GLU cc_start: 0.8820 (tt0) cc_final: 0.8495 (tm-30) REVERT: I 64 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8878 (tm-30) REVERT: I 72 ASP cc_start: 0.8352 (p0) cc_final: 0.8129 (p0) REVERT: I 74 LYS cc_start: 0.9157 (tttp) cc_final: 0.8617 (tptp) REVERT: I 75 LYS cc_start: 0.7953 (tptt) cc_final: 0.6981 (mtpt) REVERT: J 61 SER cc_start: 0.9458 (m) cc_final: 0.9120 (p) REVERT: J 62 PHE cc_start: 0.9488 (t80) cc_final: 0.9250 (t80) REVERT: J 76 ARG cc_start: 0.9504 (ttm110) cc_final: 0.9103 (ttm110) REVERT: J 92 GLN cc_start: 0.9518 (tt0) cc_final: 0.9293 (tt0) REVERT: J 96 ARG cc_start: 0.9415 (ttm170) cc_final: 0.9004 (ttm170) REVERT: K 60 LEU cc_start: 0.8452 (mm) cc_final: 0.7861 (mm) REVERT: K 61 LEU cc_start: 0.9634 (mm) cc_final: 0.8232 (tt) REVERT: K 62 ILE cc_start: 0.9038 (mp) cc_final: 0.8773 (mp) REVERT: K 76 GLN cc_start: 0.9215 (tt0) cc_final: 0.8553 (tp-100) REVERT: K 79 LYS cc_start: 0.9080 (tptp) cc_final: 0.8867 (tppt) REVERT: K 94 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9195 (mm-30) REVERT: K 97 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8992 (mt-10) REVERT: K 105 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8308 (tm-30) REVERT: K 120 MET cc_start: 0.8626 (mmm) cc_final: 0.8200 (mmm) REVERT: K 130 ILE cc_start: 0.9668 (mm) cc_final: 0.9418 (tp) REVERT: L 43 VAL cc_start: 0.8798 (t) cc_final: 0.8532 (m) REVERT: L 44 LYS cc_start: 0.9218 (mttm) cc_final: 0.8703 (mttt) REVERT: L 53 GLU cc_start: 0.9574 (tp30) cc_final: 0.9108 (tt0) REVERT: L 68 ASP cc_start: 0.9270 (m-30) cc_final: 0.8883 (p0) REVERT: L 88 TYR cc_start: 0.9474 (m-10) cc_final: 0.8940 (m-80) REVERT: M 61 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8848 (tm-30) REVERT: M 64 GLU cc_start: 0.9078 (tp30) cc_final: 0.8407 (mm-30) REVERT: M 72 ASP cc_start: 0.9315 (m-30) cc_final: 0.9090 (t0) REVERT: N 40 LYS cc_start: 0.9651 (mttt) cc_final: 0.9311 (mmtt) REVERT: N 48 ASP cc_start: 0.8460 (p0) cc_final: 0.8113 (t0) REVERT: N 59 MET cc_start: 0.9270 (mmm) cc_final: 0.8879 (mmm) REVERT: N 90 GLU cc_start: 0.9105 (mp0) cc_final: 0.8649 (mp0) REVERT: N 92 GLN cc_start: 0.8920 (mt0) cc_final: 0.8657 (mt0) REVERT: N 117 LYS cc_start: 0.8767 (tptt) cc_final: 0.8299 (tptt) outliers start: 2 outliers final: 0 residues processed: 323 average time/residue: 0.1443 time to fit residues: 71.7845 Evaluate side-chains 254 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 100 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 178 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 149 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 274 HIS A 285 ASN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 HIS ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN N 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.082981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.057073 restraints weight = 115246.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.058838 restraints weight = 63249.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.059993 restraints weight = 41740.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.060736 restraints weight = 31172.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.061172 restraints weight = 25631.894| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 20743 Z= 0.169 Angle : 0.650 15.429 29274 Z= 0.366 Chirality : 0.045 0.330 3285 Planarity : 0.005 0.128 2701 Dihedral : 27.601 176.915 5080 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.13 % Allowed : 1.82 % Favored : 98.05 % 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: -1.67 (0.19), residues: 1717 helix: 1.17 (0.21), residues: 557 sheet: -1.68 (0.33), residues: 250 loop : -2.54 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 30 TYR 0.020 0.002 TYR G 99 PHE 0.021 0.002 PHE H 100 TRP 0.011 0.001 TRP B 95 HIS 0.012 0.001 HIS C3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.17 (20743) covalent geometry : angle 0.65010 / 0.37 (29274) hydrogen bonds : bond 0.05561 / 3.77 ( 839) hydrogen bonds : angle 3.83699 / 2.61 ( 2107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 318 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ASP cc_start: 0.7530 (t0) cc_final: 0.7284 (p0) REVERT: A 184 ASP cc_start: 0.8703 (t0) cc_final: 0.8426 (t0) REVERT: A 186 VAL cc_start: 0.9085 (m) cc_final: 0.7913 (m) REVERT: A 215 ILE cc_start: 0.9332 (pt) cc_final: 0.9064 (pt) REVERT: A 250 ASN cc_start: 0.9627 (m-40) cc_final: 0.8766 (p0) REVERT: A 273 GLN cc_start: 0.8191 (mt0) cc_final: 0.7719 (pm20) REVERT: A 277 TYR cc_start: 0.8267 (m-10) cc_final: 0.7924 (m-80) REVERT: A 279 TRP cc_start: 0.8624 (m-90) cc_final: 0.7706 (m-90) REVERT: A 341 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7611 (mm-30) REVERT: B 53 PHE cc_start: 0.1974 (m-80) cc_final: 0.1104 (p90) REVERT: C 3818 MET cc_start: 0.8922 (mtm) cc_final: 0.8666 (mtm) REVERT: C 3897 MET cc_start: 0.4996 (ttm) cc_final: 0.4555 (ptm) REVERT: C 3932 ARG cc_start: 0.7835 (mpp80) cc_final: 0.7384 (ppt170) REVERT: D 315 MET cc_start: 0.6288 (ttp) cc_final: 0.5625 (ppp) REVERT: D 327 TRP cc_start: 0.6780 (t60) cc_final: 0.6219 (m-90) REVERT: D 397 ASN cc_start: 0.6746 (t0) cc_final: 0.6490 (t0) REVERT: G 50 GLU cc_start: 0.9355 (tp30) cc_final: 0.8725 (tm-30) REVERT: G 65 LEU cc_start: 0.9199 (mp) cc_final: 0.8839 (mt) REVERT: G 76 GLN cc_start: 0.8601 (tt0) cc_final: 0.7905 (tp-100) REVERT: G 112 ILE cc_start: 0.9214 (mm) cc_final: 0.8974 (mm) REVERT: H 43 VAL cc_start: 0.9507 (t) cc_final: 0.9212 (p) REVERT: H 53 GLU cc_start: 0.9322 (mt-10) cc_final: 0.8993 (pt0) REVERT: H 75 HIS cc_start: 0.8873 (t70) cc_final: 0.8499 (t70) REVERT: H 79 LYS cc_start: 0.9077 (mttt) cc_final: 0.8568 (mtmm) REVERT: H 88 TYR cc_start: 0.9115 (m-10) cc_final: 0.8609 (m-80) REVERT: H 91 LYS cc_start: 0.9523 (tttt) cc_final: 0.9315 (ttmt) REVERT: H 92 ARG cc_start: 0.9498 (mtp-110) cc_final: 0.9161 (ttt180) REVERT: H 100 PHE cc_start: 0.8842 (m-10) cc_final: 0.8436 (m-10) REVERT: I 23 LEU cc_start: 0.9147 (mm) cc_final: 0.8886 (mm) REVERT: I 56 GLU cc_start: 0.8616 (tt0) cc_final: 0.8347 (tm-30) REVERT: I 64 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8911 (tm-30) REVERT: I 68 ASN cc_start: 0.9402 (t0) cc_final: 0.9158 (t0) REVERT: I 72 ASP cc_start: 0.8356 (p0) cc_final: 0.8141 (p0) REVERT: I 74 LYS cc_start: 0.9155 (tttp) cc_final: 0.8564 (tptp) REVERT: I 75 LYS cc_start: 0.8077 (tptt) cc_final: 0.7079 (mtpp) REVERT: J 31 LYS cc_start: 0.8979 (ptpp) cc_final: 0.8560 (tptt) REVERT: J 96 ARG cc_start: 0.9399 (ttm170) cc_final: 0.9034 (ttm170) REVERT: K 50 GLU cc_start: 0.8746 (tt0) cc_final: 0.8450 (tt0) REVERT: K 60 LEU cc_start: 0.8468 (mm) cc_final: 0.8224 (mm) REVERT: K 76 GLN cc_start: 0.9193 (tt0) cc_final: 0.8615 (tp-100) REVERT: K 79 LYS cc_start: 0.9075 (tptp) cc_final: 0.8822 (tppt) REVERT: K 97 GLU cc_start: 0.9240 (mt-10) cc_final: 0.9032 (mt-10) REVERT: K 105 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8419 (tm-30) REVERT: K 106 ASP cc_start: 0.7840 (m-30) cc_final: 0.7632 (m-30) REVERT: K 120 MET cc_start: 0.8615 (mmm) cc_final: 0.8330 (mmm) REVERT: K 130 ILE cc_start: 0.9673 (mm) cc_final: 0.9407 (tp) REVERT: L 43 VAL cc_start: 0.8948 (t) cc_final: 0.8630 (p) REVERT: L 44 LYS cc_start: 0.9166 (mttm) cc_final: 0.8856 (mttt) REVERT: L 52 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8252 (tm-30) REVERT: L 63 GLU cc_start: 0.8878 (pp20) cc_final: 0.8252 (mt-10) REVERT: L 68 ASP cc_start: 0.9349 (m-30) cc_final: 0.8891 (p0) REVERT: L 88 TYR cc_start: 0.9428 (m-10) cc_final: 0.9061 (m-80) REVERT: M 61 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8830 (tm-30) REVERT: M 64 GLU cc_start: 0.9092 (tp30) cc_final: 0.8392 (mm-30) REVERT: N 40 LYS cc_start: 0.9652 (mttt) cc_final: 0.9382 (mmtm) REVERT: N 48 ASP cc_start: 0.8488 (p0) cc_final: 0.8139 (t0) REVERT: N 59 MET cc_start: 0.9285 (mmm) cc_final: 0.8931 (mmm) REVERT: N 90 GLU cc_start: 0.9088 (mp0) cc_final: 0.8578 (mp0) REVERT: N 92 GLN cc_start: 0.8930 (mt0) cc_final: 0.8555 (mt0) REVERT: N 117 LYS cc_start: 0.8832 (tptt) cc_final: 0.8413 (ptmt) outliers start: 2 outliers final: 0 residues processed: 320 average time/residue: 0.1418 time to fit residues: 69.7937 Evaluate side-chains 253 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 25 optimal weight: 10.0000 chunk 126 optimal weight: 0.0970 chunk 143 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN A 285 ASN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN M 94 ASN N 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.081977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.056152 restraints weight = 115920.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.057822 restraints weight = 65092.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.058896 restraints weight = 43377.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.059596 restraints weight = 32764.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.060060 restraints weight = 27153.736| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20743 Z= 0.151 Angle : 0.629 9.507 29274 Z= 0.355 Chirality : 0.044 0.311 3285 Planarity : 0.005 0.092 2701 Dihedral : 27.568 175.607 5080 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.13 % Allowed : 1.41 % Favored : 98.45 % 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: -1.46 (0.20), residues: 1717 helix: 1.31 (0.22), residues: 557 sheet: -1.55 (0.33), residues: 248 loop : -2.39 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 42 TYR 0.023 0.001 TYR H 51 PHE 0.024 0.002 PHE G 104 TRP 0.014 0.001 TRP A 279 HIS 0.004 0.001 HIS C3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (20743) covalent geometry : angle 0.62879 / 0.36 (29274) hydrogen bonds : bond 0.05599 / 3.79 ( 839) hydrogen bonds : angle 3.74389 / 2.57 ( 2107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 313 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.8647 (t0) cc_final: 0.8396 (t0) REVERT: A 186 VAL cc_start: 0.9070 (m) cc_final: 0.7968 (m) REVERT: A 215 ILE cc_start: 0.9286 (pt) cc_final: 0.9015 (pt) REVERT: A 250 ASN cc_start: 0.9618 (m-40) cc_final: 0.8530 (t0) REVERT: A 273 GLN cc_start: 0.8331 (mt0) cc_final: 0.7686 (pm20) REVERT: A 276 LEU cc_start: 0.8511 (mm) cc_final: 0.7813 (tp) REVERT: A 277 TYR cc_start: 0.8259 (m-10) cc_final: 0.7769 (m-80) REVERT: A 279 TRP cc_start: 0.8752 (m-90) cc_final: 0.7915 (m-90) REVERT: A 341 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7803 (mm-30) REVERT: B 53 PHE cc_start: 0.1822 (m-80) cc_final: 0.0890 (p90) REVERT: C 3777 MET cc_start: -0.3099 (ptt) cc_final: -0.3448 (ptt) REVERT: C 3812 MET cc_start: 0.8103 (ptt) cc_final: 0.7857 (ppp) REVERT: C 3818 MET cc_start: 0.8884 (mtm) cc_final: 0.8679 (mtm) REVERT: C 3867 LEU cc_start: 0.8687 (tp) cc_final: 0.8221 (tp) REVERT: C 3871 ARG cc_start: 0.8590 (mtt-85) cc_final: 0.8247 (mmp-170) REVERT: C 3897 MET cc_start: 0.5065 (ttm) cc_final: 0.4478 (ptm) REVERT: C 3932 ARG cc_start: 0.8099 (mpp80) cc_final: 0.7646 (ppt170) REVERT: D 315 MET cc_start: 0.6267 (ttp) cc_final: 0.5714 (ppp) REVERT: D 397 ASN cc_start: 0.6651 (t0) cc_final: 0.6346 (t0) REVERT: D 448 ILE cc_start: 0.6630 (mt) cc_final: 0.6256 (mp) REVERT: D 461 LYS cc_start: 0.6804 (pttm) cc_final: 0.6559 (mptt) REVERT: G 50 GLU cc_start: 0.9327 (tp30) cc_final: 0.8695 (tm-30) REVERT: G 56 LYS cc_start: 0.8830 (tppp) cc_final: 0.8608 (tppp) REVERT: G 65 LEU cc_start: 0.9214 (mp) cc_final: 0.8821 (mt) REVERT: G 76 GLN cc_start: 0.8664 (tt0) cc_final: 0.7947 (tp-100) REVERT: G 92 LEU cc_start: 0.9591 (mt) cc_final: 0.9389 (mt) REVERT: G 93 GLN cc_start: 0.9224 (mt0) cc_final: 0.8563 (mt0) REVERT: G 97 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8696 (mm-30) REVERT: G 112 ILE cc_start: 0.9224 (mm) cc_final: 0.8981 (mm) REVERT: G 120 MET cc_start: 0.7148 (mtt) cc_final: 0.6464 (mtm) REVERT: G 122 LYS cc_start: 0.8585 (ptpp) cc_final: 0.8284 (ptpp) REVERT: H 43 VAL cc_start: 0.9443 (t) cc_final: 0.9226 (p) REVERT: H 75 HIS cc_start: 0.8862 (t70) cc_final: 0.8520 (t70) REVERT: H 79 LYS cc_start: 0.9141 (mttt) cc_final: 0.8639 (mtmm) REVERT: H 88 TYR cc_start: 0.9008 (m-10) cc_final: 0.8432 (m-80) REVERT: H 92 ARG cc_start: 0.9448 (mtp-110) cc_final: 0.9150 (ttt180) REVERT: H 100 PHE cc_start: 0.8917 (m-10) cc_final: 0.8418 (m-10) REVERT: I 23 LEU cc_start: 0.9158 (mm) cc_final: 0.8917 (mm) REVERT: I 56 GLU cc_start: 0.8584 (tt0) cc_final: 0.8250 (tm-30) REVERT: I 64 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8864 (tm-30) REVERT: I 68 ASN cc_start: 0.9373 (t0) cc_final: 0.9116 (t0) REVERT: I 72 ASP cc_start: 0.8320 (p0) cc_final: 0.8108 (p0) REVERT: I 74 LYS cc_start: 0.9157 (tttp) cc_final: 0.8561 (tptp) REVERT: I 75 LYS cc_start: 0.8154 (tptt) cc_final: 0.7218 (mtpp) REVERT: I 91 GLU cc_start: 0.8695 (pp20) cc_final: 0.8418 (pp20) REVERT: J 31 LYS cc_start: 0.9030 (ptpp) cc_final: 0.8559 (tptp) REVERT: J 61 SER cc_start: 0.9488 (m) cc_final: 0.9124 (p) REVERT: J 62 PHE cc_start: 0.9425 (t80) cc_final: 0.9147 (t80) REVERT: J 76 ARG cc_start: 0.9433 (ttm110) cc_final: 0.9040 (ttm110) REVERT: J 96 ARG cc_start: 0.9326 (ttm170) cc_final: 0.9061 (ttm170) REVERT: J 117 LYS cc_start: 0.9084 (tptt) cc_final: 0.8757 (tppt) REVERT: K 50 GLU cc_start: 0.8664 (tt0) cc_final: 0.8409 (tt0) REVERT: K 61 LEU cc_start: 0.9651 (mm) cc_final: 0.9420 (mm) REVERT: K 76 GLN cc_start: 0.9082 (tt0) cc_final: 0.8576 (tp-100) REVERT: K 79 LYS cc_start: 0.9114 (tptp) cc_final: 0.8883 (tppt) REVERT: K 97 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8992 (mt-10) REVERT: K 120 MET cc_start: 0.8550 (mmm) cc_final: 0.8246 (mmm) REVERT: K 130 ILE cc_start: 0.9650 (mm) cc_final: 0.9411 (tp) REVERT: L 43 VAL cc_start: 0.8987 (t) cc_final: 0.8685 (p) REVERT: L 44 LYS cc_start: 0.9175 (mttm) cc_final: 0.8810 (mttt) REVERT: L 63 GLU cc_start: 0.8772 (pp20) cc_final: 0.8244 (mt-10) REVERT: L 68 ASP cc_start: 0.9321 (m-30) cc_final: 0.8859 (p0) REVERT: L 88 TYR cc_start: 0.9477 (m-10) cc_final: 0.9039 (m-80) REVERT: M 61 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8841 (tm-30) REVERT: M 64 GLU cc_start: 0.9039 (tp30) cc_final: 0.8360 (mm-30) REVERT: N 48 ASP cc_start: 0.8444 (p0) cc_final: 0.8130 (t0) REVERT: N 59 MET cc_start: 0.9250 (mmm) cc_final: 0.8850 (mmm) REVERT: N 90 GLU cc_start: 0.9039 (mp0) cc_final: 0.8566 (mp0) REVERT: N 92 GLN cc_start: 0.8932 (mt0) cc_final: 0.8582 (mt0) REVERT: N 117 LYS cc_start: 0.8860 (tptt) cc_final: 0.8444 (ptmt) outliers start: 2 outliers final: 0 residues processed: 315 average time/residue: 0.1348 time to fit residues: 65.9021 Evaluate side-chains 256 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 59 optimal weight: 8.9990 chunk 91 optimal weight: 0.0980 chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 HIS A 243 GLN A 285 ASN A 342 ASN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3925 HIS ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 ASN N 79 HIS N 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.078857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.053296 restraints weight = 117974.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.054977 restraints weight = 65089.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.056046 restraints weight = 43073.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.056770 restraints weight = 32443.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.057178 restraints weight = 26718.582| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.6250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20743 Z= 0.197 Angle : 0.671 12.866 29274 Z= 0.375 Chirality : 0.045 0.298 3285 Planarity : 0.005 0.088 2701 Dihedral : 27.575 176.137 5080 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.13 % Allowed : 0.81 % Favored : 99.06 % 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: -1.57 (0.19), residues: 1717 helix: 1.09 (0.21), residues: 558 sheet: -1.92 (0.32), residues: 255 loop : -2.26 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 30 TYR 0.029 0.002 TYR G 99 PHE 0.020 0.002 PHE M 25 TRP 0.011 0.001 TRP B 95 HIS 0.007 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.20 (20743) covalent geometry : angle 0.67054 / 0.38 (29274) hydrogen bonds : bond 0.06797 / 4.59 ( 839) hydrogen bonds : angle 3.94596 / 2.71 ( 2107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 314 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 VAL cc_start: 0.9063 (m) cc_final: 0.7958 (m) REVERT: A 215 ILE cc_start: 0.9324 (pt) cc_final: 0.9121 (pt) REVERT: A 250 ASN cc_start: 0.9654 (m-40) cc_final: 0.8587 (t0) REVERT: A 273 GLN cc_start: 0.8325 (mt0) cc_final: 0.7988 (tt0) REVERT: A 276 LEU cc_start: 0.8578 (mm) cc_final: 0.7844 (tp) REVERT: A 277 TYR cc_start: 0.8236 (m-10) cc_final: 0.7427 (m-80) REVERT: A 279 TRP cc_start: 0.8578 (m-90) cc_final: 0.7462 (m-90) REVERT: B 53 PHE cc_start: 0.2168 (m-80) cc_final: 0.0927 (p90) REVERT: C 3897 MET cc_start: 0.5014 (ttm) cc_final: 0.4664 (ptm) REVERT: C 3932 ARG cc_start: 0.8044 (mpp80) cc_final: 0.7641 (ppt170) REVERT: D 315 MET cc_start: 0.6290 (ttp) cc_final: 0.5814 (ppp) REVERT: D 397 ASN cc_start: 0.6730 (t0) cc_final: 0.6444 (t0) REVERT: G 50 GLU cc_start: 0.9358 (tp30) cc_final: 0.8689 (tm-30) REVERT: G 65 LEU cc_start: 0.9161 (mp) cc_final: 0.8777 (mm) REVERT: G 76 GLN cc_start: 0.8775 (tt0) cc_final: 0.7994 (tp-100) REVERT: G 93 GLN cc_start: 0.9246 (mt0) cc_final: 0.8631 (mt0) REVERT: G 97 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8760 (mm-30) REVERT: G 103 LEU cc_start: 0.9587 (tp) cc_final: 0.9373 (tp) REVERT: G 105 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8767 (pp20) REVERT: G 112 ILE cc_start: 0.9261 (mm) cc_final: 0.9053 (mm) REVERT: H 43 VAL cc_start: 0.9527 (t) cc_final: 0.9300 (p) REVERT: H 67 ARG cc_start: 0.8487 (ttm-80) cc_final: 0.8086 (tpp-160) REVERT: H 75 HIS cc_start: 0.8901 (t70) cc_final: 0.8473 (t70) REVERT: H 79 LYS cc_start: 0.9209 (mttt) cc_final: 0.8681 (mtmm) REVERT: H 88 TYR cc_start: 0.9136 (m-10) cc_final: 0.8667 (m-80) REVERT: H 92 ARG cc_start: 0.9122 (ttt-90) cc_final: 0.8902 (ttt180) REVERT: H 100 PHE cc_start: 0.9001 (m-10) cc_final: 0.8414 (m-10) REVERT: I 56 GLU cc_start: 0.8529 (tt0) cc_final: 0.8250 (tm-30) REVERT: I 64 GLU cc_start: 0.9301 (tm-30) cc_final: 0.8956 (tm-30) REVERT: I 68 ASN cc_start: 0.9427 (t0) cc_final: 0.9164 (t0) REVERT: I 72 ASP cc_start: 0.8366 (p0) cc_final: 0.8119 (p0) REVERT: I 74 LYS cc_start: 0.9184 (tttp) cc_final: 0.8581 (tptp) REVERT: I 75 LYS cc_start: 0.8270 (tptt) cc_final: 0.7477 (mtpp) REVERT: J 31 LYS cc_start: 0.9065 (ptpp) cc_final: 0.8641 (tptt) REVERT: J 59 MET cc_start: 0.9519 (mmp) cc_final: 0.9284 (mmm) REVERT: J 61 SER cc_start: 0.9531 (m) cc_final: 0.9179 (p) REVERT: J 62 PHE cc_start: 0.9465 (t80) cc_final: 0.9205 (t80) REVERT: J 96 ARG cc_start: 0.9375 (ttm170) cc_final: 0.9065 (ttm170) REVERT: J 117 LYS cc_start: 0.9156 (tptt) cc_final: 0.8884 (tppt) REVERT: K 50 GLU cc_start: 0.8861 (tt0) cc_final: 0.8477 (tt0) REVERT: K 60 LEU cc_start: 0.8581 (mm) cc_final: 0.8303 (mm) REVERT: K 76 GLN cc_start: 0.9169 (tt0) cc_final: 0.8764 (tp-100) REVERT: K 79 LYS cc_start: 0.9058 (tptp) cc_final: 0.8792 (tppt) REVERT: K 120 MET cc_start: 0.8662 (mmm) cc_final: 0.8274 (mmm) REVERT: K 130 ILE cc_start: 0.9671 (mm) cc_final: 0.9468 (tp) REVERT: L 43 VAL cc_start: 0.9010 (t) cc_final: 0.8738 (p) REVERT: L 44 LYS cc_start: 0.9222 (mttm) cc_final: 0.8839 (mttt) REVERT: L 68 ASP cc_start: 0.9404 (m-30) cc_final: 0.8913 (p0) REVERT: L 88 TYR cc_start: 0.9433 (m-10) cc_final: 0.9062 (m-80) REVERT: M 61 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8847 (tm-30) REVERT: M 64 GLU cc_start: 0.9097 (tp30) cc_final: 0.8377 (mm-30) REVERT: M 83 LEU cc_start: 0.9537 (mm) cc_final: 0.9321 (mm) REVERT: N 48 ASP cc_start: 0.8689 (p0) cc_final: 0.8323 (t0) REVERT: N 59 MET cc_start: 0.9328 (mmm) cc_final: 0.9064 (mmp) REVERT: N 90 GLU cc_start: 0.9118 (mp0) cc_final: 0.8634 (mp0) REVERT: N 92 GLN cc_start: 0.9018 (mt0) cc_final: 0.8678 (mt0) outliers start: 2 outliers final: 0 residues processed: 316 average time/residue: 0.1428 time to fit residues: 69.4374 Evaluate side-chains 249 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 1 optimal weight: 10.0000 chunk 62 optimal weight: 0.0870 chunk 73 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 97 optimal weight: 0.1980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN A 285 ASN A 342 ASN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3925 HIS N 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.080604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.054791 restraints weight = 115051.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.056519 restraints weight = 62982.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.057659 restraints weight = 41468.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.058417 restraints weight = 30897.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.058886 restraints weight = 25246.391| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 20743 Z= 0.133 Angle : 0.623 13.137 29274 Z= 0.350 Chirality : 0.044 0.302 3285 Planarity : 0.004 0.098 2701 Dihedral : 27.533 175.248 5080 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.13 % Allowed : 0.34 % Favored : 99.53 % 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: -1.31 (0.20), residues: 1717 helix: 1.38 (0.22), residues: 557 sheet: -1.83 (0.32), residues: 264 loop : -2.12 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 76 TYR 0.020 0.001 TYR H 51 PHE 0.021 0.002 PHE H 61 TRP 0.010 0.001 TRP A 279 HIS 0.008 0.001 HIS C3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (20743) covalent geometry : angle 0.62340 / 0.35 (29274) hydrogen bonds : bond 0.04993 / 3.40 ( 839) hydrogen bonds : angle 3.60410 / 2.47 ( 2107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 319 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 VAL cc_start: 0.8971 (m) cc_final: 0.7913 (m) REVERT: A 215 ILE cc_start: 0.9324 (pt) cc_final: 0.9117 (pt) REVERT: A 250 ASN cc_start: 0.9640 (m-40) cc_final: 0.8550 (t0) REVERT: A 273 GLN cc_start: 0.8353 (mt0) cc_final: 0.8045 (tt0) REVERT: A 276 LEU cc_start: 0.8513 (mm) cc_final: 0.7800 (tp) REVERT: A 277 TYR cc_start: 0.8226 (m-10) cc_final: 0.7677 (m-80) REVERT: A 279 TRP cc_start: 0.8588 (m-90) cc_final: 0.7693 (m-90) REVERT: A 341 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7996 (mm-30) REVERT: B 53 PHE cc_start: 0.2260 (m-80) cc_final: 0.0918 (p90) REVERT: C 3818 MET cc_start: 0.8447 (mtm) cc_final: 0.8243 (mtm) REVERT: C 3897 MET cc_start: 0.4989 (ttm) cc_final: 0.4614 (ptm) REVERT: C 3932 ARG cc_start: 0.8054 (mpp80) cc_final: 0.7649 (ppt170) REVERT: D 315 MET cc_start: 0.6242 (ttp) cc_final: 0.5754 (ppp) REVERT: D 327 TRP cc_start: 0.6981 (t60) cc_final: 0.6146 (m-90) REVERT: D 397 ASN cc_start: 0.6712 (t0) cc_final: 0.6451 (t0) REVERT: D 461 LYS cc_start: 0.4950 (pttm) cc_final: 0.4542 (ptmt) REVERT: G 50 GLU cc_start: 0.9330 (tp30) cc_final: 0.8684 (tm-30) REVERT: G 56 LYS cc_start: 0.8819 (tppp) cc_final: 0.8550 (tppp) REVERT: G 65 LEU cc_start: 0.9059 (mp) cc_final: 0.8669 (mt) REVERT: G 76 GLN cc_start: 0.8763 (tt0) cc_final: 0.7973 (tp-100) REVERT: G 97 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8738 (mm-30) REVERT: G 112 ILE cc_start: 0.9304 (mm) cc_final: 0.9083 (mm) REVERT: G 122 LYS cc_start: 0.8430 (ptpp) cc_final: 0.8216 (ptpp) REVERT: H 43 VAL cc_start: 0.9478 (t) cc_final: 0.9245 (p) REVERT: H 63 GLU cc_start: 0.8447 (pp20) cc_final: 0.8150 (tt0) REVERT: H 67 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.7951 (tpp-160) REVERT: H 75 HIS cc_start: 0.8840 (t70) cc_final: 0.8529 (t70) REVERT: H 79 LYS cc_start: 0.9218 (mttt) cc_final: 0.8682 (mtmm) REVERT: H 88 TYR cc_start: 0.9143 (m-10) cc_final: 0.8677 (m-80) REVERT: H 100 PHE cc_start: 0.9015 (m-10) cc_final: 0.8424 (m-10) REVERT: I 56 GLU cc_start: 0.8523 (tt0) cc_final: 0.8194 (tm-30) REVERT: I 64 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8879 (tm-30) REVERT: I 68 ASN cc_start: 0.9358 (t0) cc_final: 0.9119 (t0) REVERT: I 74 LYS cc_start: 0.9138 (tttp) cc_final: 0.8520 (tptp) REVERT: I 75 LYS cc_start: 0.8187 (tptt) cc_final: 0.7393 (mtpp) REVERT: J 31 LYS cc_start: 0.9059 (ptpp) cc_final: 0.8595 (tptt) REVERT: J 61 SER cc_start: 0.9518 (m) cc_final: 0.9197 (p) REVERT: J 76 ARG cc_start: 0.9397 (ttm110) cc_final: 0.9046 (ttm110) REVERT: J 96 ARG cc_start: 0.9319 (ttm170) cc_final: 0.9027 (ttm170) REVERT: J 117 LYS cc_start: 0.9106 (tptt) cc_final: 0.8807 (tppt) REVERT: K 68 GLN cc_start: 0.9496 (pt0) cc_final: 0.9277 (pt0) REVERT: K 76 GLN cc_start: 0.9130 (tt0) cc_final: 0.8691 (tp-100) REVERT: K 79 LYS cc_start: 0.9011 (tptp) cc_final: 0.8705 (tppt) REVERT: K 94 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9028 (mt-10) REVERT: K 130 ILE cc_start: 0.9679 (mm) cc_final: 0.9465 (tp) REVERT: L 39 ARG cc_start: 0.9240 (mmt180) cc_final: 0.8957 (mmm-85) REVERT: L 43 VAL cc_start: 0.8888 (t) cc_final: 0.8533 (m) REVERT: L 44 LYS cc_start: 0.9166 (mttm) cc_final: 0.8933 (mttt) REVERT: L 63 GLU cc_start: 0.8740 (pp20) cc_final: 0.8224 (mt-10) REVERT: L 68 ASP cc_start: 0.9379 (m-30) cc_final: 0.8872 (p0) REVERT: L 88 TYR cc_start: 0.9461 (m-10) cc_final: 0.9087 (m-80) REVERT: M 61 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8778 (tm-30) REVERT: M 64 GLU cc_start: 0.9077 (tp30) cc_final: 0.8307 (mm-30) REVERT: M 83 LEU cc_start: 0.9516 (mm) cc_final: 0.9314 (mm) REVERT: N 48 ASP cc_start: 0.8542 (p0) cc_final: 0.8164 (t0) REVERT: N 59 MET cc_start: 0.9289 (mmm) cc_final: 0.8901 (mmm) REVERT: N 90 GLU cc_start: 0.9110 (mp0) cc_final: 0.8546 (mp0) REVERT: N 92 GLN cc_start: 0.8916 (mt0) cc_final: 0.8540 (mt0) REVERT: N 117 LYS cc_start: 0.8873 (tptt) cc_final: 0.8404 (ptmt) outliers start: 2 outliers final: 0 residues processed: 321 average time/residue: 0.1451 time to fit residues: 71.9649 Evaluate side-chains 255 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 179 optimal weight: 20.0000 chunk 167 optimal weight: 0.0980 chunk 14 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 141 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 ASN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN N 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.081076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.055197 restraints weight = 114299.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.056957 restraints weight = 62592.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.058070 restraints weight = 40996.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.058824 restraints weight = 30612.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.059258 restraints weight = 25077.079| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 20743 Z= 0.133 Angle : 0.629 15.348 29274 Z= 0.349 Chirality : 0.044 0.298 3285 Planarity : 0.004 0.095 2701 Dihedral : 27.451 174.823 5080 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.13 % Allowed : 0.13 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.20), residues: 1717 helix: 1.45 (0.22), residues: 558 sheet: -1.78 (0.31), residues: 280 loop : -2.05 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C3819 TYR 0.025 0.001 TYR D 328 PHE 0.035 0.002 PHE D 329 TRP 0.020 0.001 TRP D 327 HIS 0.009 0.001 HIS C3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (20743) covalent geometry : angle 0.62879 / 0.35 (29274) hydrogen bonds : bond 0.04734 / 3.23 ( 839) hydrogen bonds : angle 3.50932 / 2.40 ( 2107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 318 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.8832 (t70) cc_final: 0.8620 (p0) REVERT: A 186 VAL cc_start: 0.9118 (m) cc_final: 0.8202 (m) REVERT: A 250 ASN cc_start: 0.9640 (m-40) cc_final: 0.8942 (p0) REVERT: A 273 GLN cc_start: 0.8352 (mt0) cc_final: 0.8081 (tt0) REVERT: A 276 LEU cc_start: 0.8528 (mm) cc_final: 0.7806 (tp) REVERT: A 277 TYR cc_start: 0.8260 (m-10) cc_final: 0.7660 (m-80) REVERT: A 279 TRP cc_start: 0.8706 (m-90) cc_final: 0.7842 (m-90) REVERT: B 53 PHE cc_start: 0.2114 (m-80) cc_final: 0.0785 (p90) REVERT: B 59 TRP cc_start: 0.7559 (m100) cc_final: 0.7262 (m-10) REVERT: C 3818 MET cc_start: 0.8554 (mtm) cc_final: 0.8184 (mtm) REVERT: C 3897 MET cc_start: 0.4983 (ttm) cc_final: 0.4595 (ptm) REVERT: C 3932 ARG cc_start: 0.8037 (mpp80) cc_final: 0.7641 (ppt170) REVERT: D 315 MET cc_start: 0.6231 (ttp) cc_final: 0.5737 (ppp) REVERT: D 329 PHE cc_start: 0.7499 (m-80) cc_final: 0.6582 (m-10) REVERT: D 397 ASN cc_start: 0.6737 (t0) cc_final: 0.6443 (t0) REVERT: D 461 LYS cc_start: 0.4882 (pttm) cc_final: 0.4467 (ptmt) REVERT: G 50 GLU cc_start: 0.9336 (tp30) cc_final: 0.8671 (tm-30) REVERT: G 56 LYS cc_start: 0.8816 (tppp) cc_final: 0.8545 (tppp) REVERT: G 61 LEU cc_start: 0.8061 (tp) cc_final: 0.7853 (tp) REVERT: G 65 LEU cc_start: 0.9023 (mp) cc_final: 0.8657 (mt) REVERT: G 76 GLN cc_start: 0.8745 (tt0) cc_final: 0.7993 (tp-100) REVERT: G 97 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8704 (mm-30) REVERT: G 103 LEU cc_start: 0.9565 (tp) cc_final: 0.9363 (tp) REVERT: G 112 ILE cc_start: 0.9297 (mm) cc_final: 0.9066 (mm) REVERT: G 122 LYS cc_start: 0.8420 (ptpp) cc_final: 0.8116 (ptpp) REVERT: H 43 VAL cc_start: 0.9455 (t) cc_final: 0.9235 (p) REVERT: H 53 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8865 (pt0) REVERT: H 67 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.8080 (tpp-160) REVERT: H 75 HIS cc_start: 0.8779 (t70) cc_final: 0.8499 (t70) REVERT: H 79 LYS cc_start: 0.9221 (mttt) cc_final: 0.8680 (mtmm) REVERT: H 88 TYR cc_start: 0.9143 (m-10) cc_final: 0.8657 (m-80) REVERT: H 97 LEU cc_start: 0.9746 (tp) cc_final: 0.9197 (mm) REVERT: H 100 PHE cc_start: 0.8978 (m-10) cc_final: 0.8412 (m-10) REVERT: I 23 LEU cc_start: 0.9233 (mm) cc_final: 0.9016 (mm) REVERT: I 56 GLU cc_start: 0.9049 (tt0) cc_final: 0.8713 (tm-30) REVERT: I 64 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8926 (tm-30) REVERT: I 74 LYS cc_start: 0.9137 (tttp) cc_final: 0.8549 (tptp) REVERT: I 75 LYS cc_start: 0.8151 (tptt) cc_final: 0.7358 (mtpp) REVERT: I 83 LEU cc_start: 0.9597 (mp) cc_final: 0.9394 (mm) REVERT: J 31 LYS cc_start: 0.9082 (ptpp) cc_final: 0.8644 (tptt) REVERT: J 61 SER cc_start: 0.9536 (m) cc_final: 0.9212 (p) REVERT: J 62 PHE cc_start: 0.9409 (t80) cc_final: 0.9194 (t80) REVERT: J 76 ARG cc_start: 0.9386 (ttm110) cc_final: 0.9030 (ttm110) REVERT: J 96 ARG cc_start: 0.9312 (ttm170) cc_final: 0.9098 (ttm170) REVERT: J 117 LYS cc_start: 0.9084 (tptt) cc_final: 0.8780 (tppt) REVERT: K 76 GLN cc_start: 0.9112 (tt0) cc_final: 0.8710 (tp-100) REVERT: K 79 LYS cc_start: 0.8987 (tptp) cc_final: 0.8684 (tppt) REVERT: K 94 GLU cc_start: 0.9341 (mm-30) cc_final: 0.9002 (mt-10) REVERT: K 120 MET cc_start: 0.8370 (mmp) cc_final: 0.8145 (mmp) REVERT: K 130 ILE cc_start: 0.9674 (mm) cc_final: 0.9474 (tp) REVERT: L 39 ARG cc_start: 0.9299 (mmt180) cc_final: 0.8967 (mmm-85) REVERT: L 43 VAL cc_start: 0.8901 (t) cc_final: 0.8593 (p) REVERT: L 51 TYR cc_start: 0.8096 (m-80) cc_final: 0.7880 (m-10) REVERT: L 63 GLU cc_start: 0.8759 (pp20) cc_final: 0.8238 (mt-10) REVERT: L 68 ASP cc_start: 0.9395 (m-30) cc_final: 0.8876 (p0) REVERT: L 88 TYR cc_start: 0.9460 (m-10) cc_final: 0.9090 (m-80) REVERT: M 64 GLU cc_start: 0.9074 (tp30) cc_final: 0.8283 (mm-30) REVERT: M 72 ASP cc_start: 0.9597 (t70) cc_final: 0.9387 (t0) REVERT: M 83 LEU cc_start: 0.9533 (mm) cc_final: 0.9331 (mm) REVERT: N 40 LYS cc_start: 0.9640 (mttt) cc_final: 0.9275 (mmtt) REVERT: N 48 ASP cc_start: 0.8500 (p0) cc_final: 0.8162 (t0) REVERT: N 59 MET cc_start: 0.9289 (mmm) cc_final: 0.9003 (mmp) REVERT: N 90 GLU cc_start: 0.9108 (mp0) cc_final: 0.8532 (mp0) REVERT: N 92 GLN cc_start: 0.8908 (mt0) cc_final: 0.8511 (mt0) outliers start: 2 outliers final: 0 residues processed: 320 average time/residue: 0.1403 time to fit residues: 69.8751 Evaluate side-chains 252 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 56 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 139 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 ASN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.080563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054898 restraints weight = 115659.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.056611 restraints weight = 63463.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.057683 restraints weight = 41781.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.058475 restraints weight = 31327.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.059003 restraints weight = 25640.421| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.6611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20743 Z= 0.132 Angle : 0.613 11.870 29274 Z= 0.343 Chirality : 0.043 0.287 3285 Planarity : 0.004 0.093 2701 Dihedral : 27.367 174.615 5080 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.13 % Allowed : 0.20 % Favored : 99.66 % 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: -1.15 (0.20), residues: 1717 helix: 1.47 (0.22), residues: 559 sheet: -1.74 (0.32), residues: 267 loop : -1.99 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 76 TYR 0.016 0.001 TYR G 99 PHE 0.027 0.002 PHE J 62 TRP 0.013 0.001 TRP D 327 HIS 0.007 0.001 HIS D 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 (20743) covalent geometry : angle 0.61273 / 0.34 (29274) hydrogen bonds : bond 0.04942 / 3.35 ( 839) hydrogen bonds : angle 3.45336 / 2.36 ( 2107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3806.05 seconds wall clock time: 66 minutes 15.78 seconds (3975.78 seconds total)