Starting phenix.real_space_refine on Sun Jul 5 07:30:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mbm_23738/07_2026/7mbm_23738.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mbm_23738/07_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_23738/07_2026/7mbm_23738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mbm_23738/07_2026/7mbm_23738.map" model { file = "/net/cci-nas-00/data/ceres_data/7mbm_23738/07_2026/7mbm_23738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mbm_23738/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 3.82, per 1000 atoms: 0.19 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: 1.40 Conformation dependent library (CDL) restraints added in 576.1 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: 2.11 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: 3.81 Time building geometry restraints manager: 1.94 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: 27752 2.02 - 4.05: 1412 4.05 - 6.07: 84 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.760 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.520 ------------------------------------------------------------------------------- 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 : 0.930 10.121 29274 Z= 0.702 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 0.92959 / 0.70 (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 : 0.591 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: symmetry clash revert: symmetry clash REVERT: A 148 ASP cc_start: 0.7250 (t0) cc_final: 0.6943 (p0) REVERT: A 245 LEU cc_start: 0.9036 (mt) cc_final: 0.8601 (mt) REVERT: A 248 LEU cc_start: 0.8950 (mt) cc_final: 0.8637 (mt) REVERT: A 250 ASN cc_start: 0.9051 (m-40) cc_final: 0.8544 (p0) REVERT: A 262 ASP cc_start: 0.8125 (p0) cc_final: 0.7768 (p0) REVERT: A 277 TYR cc_start: 0.8073 (m-10) cc_final: 0.7280 (m-80) REVERT: B 53 PHE cc_start: 0.1419 (m-80) cc_final: 0.1178 (p90) REVERT: B 252 TYR cc_start: 0.4022 (m-80) cc_final: 0.2872 (t80) REVERT: C 3823 LEU cc_start: 0.8217 (tp) cc_final: 0.7208 (tp) REVERT: C 3844 PHE cc_start: 0.7844 (m-80) cc_final: 0.7450 (m-80) REVERT: C 3855 VAL cc_start: 0.8449 (t) cc_final: 0.7683 (p) REVERT: C 3867 LEU cc_start: 0.8357 (tp) cc_final: 0.8140 (tp) REVERT: C 3871 ARG cc_start: 0.8453 (mtt-85) cc_final: 0.8209 (mmp-170) REVERT: D 315 MET cc_start: 0.5782 (ttp) cc_final: 0.5146 (ppp) REVERT: D 338 PRO cc_start: 0.6609 (Cg_exo) cc_final: 0.6399 (Cg_endo) REVERT: D 397 ASN cc_start: 0.6647 (t0) cc_final: 0.6358 (t0) REVERT: D 448 ILE cc_start: 0.6713 (mt) cc_final: 0.5891 (mp) REVERT: D 500 MET cc_start: 0.1472 (mmm) cc_final: 0.1176 (mtm) REVERT: G 48 LEU cc_start: 0.9220 (mt) cc_final: 0.8986 (mm) REVERT: G 62 ILE cc_start: 0.9001 (mt) cc_final: 0.8736 (mm) REVERT: G 64 LYS cc_start: 0.9159 (ptpp) cc_final: 0.8556 (mmmm) REVERT: G 65 LEU cc_start: 0.9294 (mp) cc_final: 0.8930 (mm) REVERT: G 68 GLN cc_start: 0.9396 (tt0) cc_final: 0.9119 (pt0) REVERT: G 76 GLN cc_start: 0.8480 (tt0) cc_final: 0.7671 (tp-100) REVERT: G 89 VAL cc_start: 0.9776 (t) cc_final: 0.9470 (t) REVERT: G 99 TYR cc_start: 0.9094 (t80) cc_final: 0.8649 (t80) REVERT: G 105 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8425 (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: 0.6388 (mtp) REVERT: H 49 LEU cc_start: 0.9499 (mt) cc_final: 0.9163 (mt) REVERT: H 64 ASN cc_start: 0.9245 (m-40) cc_final: 0.8951 (t0) REVERT: H 67 ARG cc_start: 0.8647 (ttp-170) cc_final: 0.8411 (tpp-160) REVERT: H 75 HIS cc_start: 0.8717 (t70) cc_final: 0.7912 (t-170) REVERT: H 79 LYS cc_start: 0.8568 (mttt) cc_final: 0.8237 (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: 0.9169 (mm) REVERT: H 98 TYR cc_start: 0.8106 (m-10) cc_final: 0.7261 (m-80) REVERT: I 56 GLU cc_start: 0.8794 (tt0) cc_final: 0.8337 (tm-30) REVERT: I 72 ASP cc_start: 0.8213 (m-30) cc_final: 0.8002 (p0) REVERT: I 73 ASN cc_start: 0.8854 (m-40) cc_final: 0.8640 (p0) REVERT: I 81 ARG cc_start: 0.9289 (tpt-90) cc_final: 0.8906 (tpt170) REVERT: I 85 LEU cc_start: 0.9471 (mt) cc_final: 0.9191 (mm) REVERT: I 89 ASN cc_start: 0.9545 (m-40) cc_final: 0.9176 (m110) REVERT: I 90 ASP cc_start: 0.9163 (t0) cc_final: 0.8910 (p0) REVERT: J 43 LYS cc_start: 0.9102 (mmtp) cc_final: 0.8800 (mmtm) REVERT: J 54 LYS cc_start: 0.9591 (mmmt) cc_final: 0.9357 (mmmt) REVERT: J 59 MET cc_start: 0.9471 (mmm) cc_final: 0.9114 (mmm) REVERT: J 65 ASP cc_start: 0.9270 (t0) cc_final: 0.9067 (t0) REVERT: J 76 ARG cc_start: 0.9379 (ttm110) cc_final: 0.8901 (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: 0.8722 (p) REVERT: J 96 ARG cc_start: 0.9286 (ttm170) cc_final: 0.9038 (ttm170) REVERT: K 48 LEU cc_start: 0.8928 (mt) cc_final: 0.8283 (mm) REVERT: K 100 LEU cc_start: 0.9790 (mt) cc_final: 0.9458 (pp) REVERT: L 27 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8438 (mp10) REVERT: L 53 GLU cc_start: 0.9436 (tp30) cc_final: 0.9048 (tt0) REVERT: L 63 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8170 (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: 0.8648 (tptm) REVERT: M 61 GLU cc_start: 0.9448 (tp30) cc_final: 0.8963 (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: 0.9171 (mttt) REVERT: N 59 MET cc_start: 0.9478 (mmm) cc_final: 0.9081 (mmm) REVERT: N 65 ASP cc_start: 0.8939 (t0) cc_final: 0.8672 (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: 0.9339 (tptt) REVERT: N 87 THR cc_start: 0.7521 (p) cc_final: 0.6417 (p) REVERT: N 90 GLU cc_start: 0.9231 (mp0) cc_final: 0.8520 (mp0) REVERT: N 92 GLN cc_start: 0.9102 (tt0) cc_final: 0.8842 (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: 0.8780 (ttmm) REVERT: N 116 THR cc_start: 0.9573 (m) cc_final: 0.9342 (p) outliers start: 1 outliers final: 1 residues processed: 567 average time/residue: 0.1821 time to fit residues: 144.5012 Evaluate side-chains 289 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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: 9.9990 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 B 214 ASN B 310 HIS C3907 HIS D 320 HIS D 354 GLN D 381 HIS G 68 GLN G 125 GLN I 31 HIS L 64 ASN ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.094358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.068102 restraints weight = 112070.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069907 restraints weight = 63870.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.071103 restraints weight = 42886.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.071886 restraints weight = 32454.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.072368 restraints weight = 26916.920| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 20743 Z= 0.169 Angle : 0.712 8.905 29274 Z= 0.407 Chirality : 0.049 0.352 3285 Planarity : 0.006 0.089 2701 Dihedral : 28.035 168.951 5080 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.40 % Allowed : 2.22 % Favored : 97.38 % 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: -2.70 (0.18), residues: 1717 helix: 0.27 (0.21), residues: 560 sheet: -2.56 (0.32), residues: 227 loop : -3.05 (0.17), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 42 TYR 0.028 0.002 TYR C3942 PHE 0.020 0.001 PHE K 67 TRP 0.011 0.002 TRP B 241 HIS 0.008 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (20743) covalent geometry : angle 0.71229 / 0.41 (29274) hydrogen bonds : bond 0.07123 / 4.77 ( 839) hydrogen bonds : angle 4.35442 / 2.96 ( 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 390 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 384 time to evaluate : 0.445 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: 0.7167 (t0) cc_final: 0.6915 (p0) REVERT: A 184 ASP cc_start: 0.8731 (t0) cc_final: 0.8378 (t0) REVERT: A 186 VAL cc_start: 0.9025 (m) cc_final: 0.7982 (m) REVERT: A 250 ASN cc_start: 0.9370 (m-40) cc_final: 0.8664 (p0) REVERT: A 262 ASP cc_start: 0.8877 (p0) cc_final: 0.7673 (t0) REVERT: A 277 TYR cc_start: 0.8131 (m-10) cc_final: 0.7356 (m-80) REVERT: A 315 SER cc_start: 0.7904 (m) cc_final: 0.7673 (p) REVERT: B 53 PHE cc_start: 0.2213 (m-80) cc_final: 0.1370 (p90) REVERT: B 252 TYR cc_start: 0.4004 (m-80) cc_final: 0.2841 (t80) REVERT: C 3844 PHE cc_start: 0.7887 (m-80) cc_final: 0.7675 (m-80) REVERT: C 3867 LEU cc_start: 0.8517 (tp) cc_final: 0.8178 (tp) REVERT: C 3871 ARG cc_start: 0.8452 (mtt-85) cc_final: 0.8132 (mmp-170) REVERT: C 3897 MET cc_start: 0.4457 (ttm) cc_final: 0.4086 (ptp) REVERT: C 3913 CYS cc_start: 0.9122 (m) cc_final: 0.8873 (p) REVERT: C 3942 TYR cc_start: 0.7213 (t80) cc_final: 0.6303 (t80) REVERT: D 315 MET cc_start: 0.6038 (ttp) cc_final: 0.5353 (ppp) REVERT: D 397 ASN cc_start: 0.6902 (t0) cc_final: 0.6613 (t0) REVERT: D 500 MET cc_start: 0.1386 (mmm) cc_final: 0.1100 (mtm) REVERT: G 50 GLU cc_start: 0.9409 (tp30) cc_final: 0.8698 (tm-30) REVERT: G 60 LEU cc_start: 0.7967 (pt) cc_final: 0.7627 (pt) REVERT: G 64 LYS cc_start: 0.9137 (ptpp) cc_final: 0.8453 (mmtp) REVERT: G 67 PHE cc_start: 0.9326 (t80) cc_final: 0.9082 (t80) REVERT: G 68 GLN cc_start: 0.9297 (tt0) cc_final: 0.9068 (pt0) REVERT: G 76 GLN cc_start: 0.8407 (tt0) cc_final: 0.7621 (tp-100) REVERT: G 93 GLN cc_start: 0.9243 (mt0) cc_final: 0.9021 (mt0) REVERT: G 99 TYR cc_start: 0.8867 (t80) cc_final: 0.8597 (t80) REVERT: G 105 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8488 (mm-30) REVERT: G 119 ILE cc_start: 0.8250 (mt) cc_final: 0.7924 (mt) REVERT: G 120 MET cc_start: 0.7154 (mtt) cc_final: 0.6610 (mtm) REVERT: H 44 LYS cc_start: 0.8675 (tppp) cc_final: 0.8159 (tppt) REVERT: H 75 HIS cc_start: 0.8880 (t70) cc_final: 0.8476 (t70) REVERT: H 79 LYS cc_start: 0.8692 (mttt) cc_final: 0.8159 (ptpp) REVERT: H 93 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8860 (tp40) REVERT: H 97 LEU cc_start: 0.9599 (tp) cc_final: 0.9342 (mm) REVERT: H 98 TYR cc_start: 0.8774 (m-10) cc_final: 0.7915 (m-80) REVERT: I 23 LEU cc_start: 0.9146 (mm) cc_final: 0.8818 (mm) REVERT: I 38 ASN cc_start: 0.7186 (t0) cc_final: 0.6851 (t0) REVERT: I 56 GLU cc_start: 0.8901 (tt0) cc_final: 0.8341 (tm-30) REVERT: I 71 ARG cc_start: 0.9100 (ttp80) cc_final: 0.8884 (ttp80) REVERT: I 72 ASP cc_start: 0.8321 (m-30) cc_final: 0.7978 (p0) REVERT: I 89 ASN cc_start: 0.9551 (m-40) cc_final: 0.9109 (m110) REVERT: I 104 GLN cc_start: 0.8392 (mp10) cc_final: 0.7958 (mp10) REVERT: J 77 LEU cc_start: 0.9515 (mt) cc_final: 0.9225 (mt) REVERT: J 85 THR cc_start: 0.9484 (m) cc_final: 0.9203 (p) REVERT: J 96 ARG cc_start: 0.9309 (ttm170) cc_final: 0.9032 (ttm170) REVERT: K 50 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8856 (mm-30) REVERT: K 105 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8231 (tm-30) REVERT: L 53 GLU cc_start: 0.9517 (tp30) cc_final: 0.8942 (tt0) REVERT: L 64 ASN cc_start: 0.9247 (OUTLIER) cc_final: 0.9028 (t0) REVERT: L 88 TYR cc_start: 0.9458 (m-10) cc_final: 0.8860 (m-80) REVERT: M 61 GLU cc_start: 0.9255 (tp30) cc_final: 0.8996 (tm-30) REVERT: M 72 ASP cc_start: 0.9369 (m-30) cc_final: 0.9100 (t0) REVERT: M 83 LEU cc_start: 0.9428 (mt) cc_final: 0.9178 (mm) REVERT: N 40 LYS cc_start: 0.9617 (mttt) cc_final: 0.9218 (mttt) REVERT: N 56 MET cc_start: 0.8782 (tpp) cc_final: 0.8573 (tpp) REVERT: N 59 MET cc_start: 0.9132 (mmm) cc_final: 0.8799 (mmm) REVERT: N 69 ARG cc_start: 0.9177 (ttm110) cc_final: 0.8962 (ttm110) REVERT: N 73 GLU cc_start: 0.8647 (tp30) cc_final: 0.8410 (tp30) REVERT: N 90 GLU cc_start: 0.9134 (mp0) cc_final: 0.8814 (mp0) REVERT: N 98 LEU cc_start: 0.9289 (tp) cc_final: 0.9052 (tt) outliers start: 6 outliers final: 0 residues processed: 388 average time/residue: 0.1602 time to fit residues: 90.5949 Evaluate side-chains 272 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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: 0.8980 chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 ASN B 100 ASN B 310 HIS C3907 HIS J 46 HIS M 31 HIS M 89 ASN N 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.088203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.062051 restraints weight = 113809.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.063868 restraints weight = 62420.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.065024 restraints weight = 41145.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.065786 restraints weight = 30756.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.066274 restraints weight = 25250.489| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 20743 Z= 0.204 Angle : 0.705 9.644 29274 Z= 0.399 Chirality : 0.046 0.393 3285 Planarity : 0.006 0.091 2701 Dihedral : 27.877 177.603 5080 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % 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: -2.39 (0.19), residues: 1717 helix: 0.60 (0.21), residues: 562 sheet: -2.48 (0.29), residues: 274 loop : -2.87 (0.17), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG K 53 TYR 0.017 0.002 TYR N 118 PHE 0.020 0.002 PHE I 25 TRP 0.017 0.002 TRP A 51 HIS 0.011 0.002 HIS K 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 (20743) covalent geometry : angle 0.70537 / 0.40 (29274) hydrogen bonds : bond 0.07455 / 4.98 ( 839) hydrogen bonds : angle 4.25199 / 2.90 ( 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 343 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 341 time to evaluate : 0.621 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: symmetry clash REVERT: A 148 ASP cc_start: 0.7412 (t0) cc_final: 0.7124 (p0) REVERT: A 184 ASP cc_start: 0.8711 (t0) cc_final: 0.8390 (t0) REVERT: A 186 VAL cc_start: 0.9048 (m) cc_final: 0.8010 (m) REVERT: A 215 ILE cc_start: 0.9286 (pt) cc_final: 0.9067 (pt) REVERT: A 250 ASN cc_start: 0.9538 (m-40) cc_final: 0.8585 (t0) REVERT: A 273 GLN cc_start: 0.8063 (mt0) cc_final: 0.7546 (pm20) REVERT: A 276 LEU cc_start: 0.8487 (mt) cc_final: 0.7930 (tp) REVERT: A 277 TYR cc_start: 0.8209 (m-10) cc_final: 0.7569 (m-80) REVERT: A 279 TRP cc_start: 0.8405 (m-90) cc_final: 0.7539 (m-90) REVERT: B 53 PHE cc_start: 0.2241 (m-80) cc_final: 0.1390 (p90) REVERT: B 100 ASN cc_start: 0.6234 (OUTLIER) cc_final: 0.5855 (t0) REVERT: B 252 TYR cc_start: 0.4336 (m-80) cc_final: 0.2890 (t80) REVERT: C 3897 MET cc_start: 0.4727 (ttm) cc_final: 0.4430 (ptp) REVERT: C 3913 CYS cc_start: 0.8995 (m) cc_final: 0.8765 (p) REVERT: D 315 MET cc_start: 0.6020 (ttp) cc_final: 0.5408 (ppp) REVERT: D 327 TRP cc_start: 0.6504 (m-90) cc_final: 0.5845 (m-90) REVERT: D 397 ASN cc_start: 0.6836 (t0) cc_final: 0.6563 (t0) REVERT: D 500 MET cc_start: 0.1463 (mmm) cc_final: 0.1261 (mpp) REVERT: G 50 GLU cc_start: 0.9339 (tp30) cc_final: 0.8703 (tm-30) REVERT: G 60 LEU cc_start: 0.8010 (pt) cc_final: 0.7392 (pt) REVERT: G 64 LYS cc_start: 0.9208 (ptpp) cc_final: 0.8977 (mmtm) REVERT: G 67 PHE cc_start: 0.9382 (t80) cc_final: 0.9145 (t80) REVERT: G 68 GLN cc_start: 0.9423 (tt0) cc_final: 0.9216 (pt0) REVERT: G 76 GLN cc_start: 0.8443 (tt0) cc_final: 0.7701 (tp-100) REVERT: G 93 GLN cc_start: 0.9342 (mt0) cc_final: 0.9050 (mt0) REVERT: G 94 GLU cc_start: 0.9249 (mm-30) cc_final: 0.9017 (mm-30) REVERT: G 99 TYR cc_start: 0.9078 (t80) cc_final: 0.8515 (t80) REVERT: G 120 MET cc_start: 0.7400 (mtt) cc_final: 0.6688 (mtm) REVERT: H 44 LYS cc_start: 0.8755 (tppp) cc_final: 0.8290 (tppt) REVERT: H 75 HIS cc_start: 0.8833 (t70) cc_final: 0.8606 (t70) REVERT: H 79 LYS cc_start: 0.8848 (mttt) cc_final: 0.8266 (ptpp) REVERT: H 88 TYR cc_start: 0.8670 (m-80) cc_final: 0.8238 (m-80) REVERT: H 97 LEU cc_start: 0.9636 (tp) cc_final: 0.9290 (mm) REVERT: H 98 TYR cc_start: 0.9039 (m-10) cc_final: 0.8195 (m-80) REVERT: I 23 LEU cc_start: 0.9185 (mm) cc_final: 0.8969 (mm) REVERT: I 38 ASN cc_start: 0.7135 (t0) cc_final: 0.6908 (t0) REVERT: I 56 GLU cc_start: 0.8831 (tt0) cc_final: 0.8401 (tm-30) REVERT: I 64 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8861 (tm-30) REVERT: I 104 GLN cc_start: 0.8575 (mp10) cc_final: 0.8152 (mp10) REVERT: J 61 SER cc_start: 0.9381 (m) cc_final: 0.9004 (p) REVERT: J 85 THR cc_start: 0.9477 (m) cc_final: 0.9250 (p) REVERT: J 96 ARG cc_start: 0.9404 (ttm170) cc_final: 0.9000 (ttm170) REVERT: J 102 GLU cc_start: 0.7226 (tp30) cc_final: 0.7023 (tp30) REVERT: K 50 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8203 (tt0) REVERT: K 68 GLN cc_start: 0.9593 (pt0) cc_final: 0.9376 (pt0) REVERT: K 76 GLN cc_start: 0.9135 (tt0) cc_final: 0.8279 (tp-100) REVERT: K 77 ASP cc_start: 0.8865 (m-30) cc_final: 0.8424 (p0) REVERT: K 105 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8547 (tm-30) REVERT: K 106 ASP cc_start: 0.7724 (m-30) cc_final: 0.7159 (m-30) REVERT: K 120 MET cc_start: 0.8429 (mmm) cc_final: 0.8126 (mmp) REVERT: L 53 GLU cc_start: 0.9642 (tp30) cc_final: 0.9418 (tp30) REVERT: L 88 TYR cc_start: 0.9423 (m-10) cc_final: 0.8785 (m-80) REVERT: M 38 ASN cc_start: 0.8724 (p0) cc_final: 0.8184 (p0) REVERT: M 61 GLU cc_start: 0.9288 (tp30) cc_final: 0.9066 (tm-30) REVERT: M 64 GLU cc_start: 0.8985 (tp30) cc_final: 0.8491 (mm-30) REVERT: M 72 ASP cc_start: 0.9376 (m-30) cc_final: 0.9030 (t0) REVERT: M 83 LEU cc_start: 0.9513 (mt) cc_final: 0.9282 (mm) REVERT: N 30 ARG cc_start: 0.7673 (mmm160) cc_final: 0.7294 (tpp-160) REVERT: N 40 LYS cc_start: 0.9636 (mttt) cc_final: 0.9402 (mmtt) REVERT: N 59 MET cc_start: 0.9274 (mmm) cc_final: 0.8871 (mmm) REVERT: N 65 ASP cc_start: 0.9032 (t0) cc_final: 0.8700 (t0) REVERT: N 69 ARG cc_start: 0.9230 (ttm110) cc_final: 0.9018 (ttm110) REVERT: N 73 GLU cc_start: 0.8982 (tp30) cc_final: 0.8718 (tp30) REVERT: N 82 LYS cc_start: 0.9143 (tppt) cc_final: 0.8881 (tppt) REVERT: N 90 GLU cc_start: 0.9162 (mp0) cc_final: 0.8848 (mp0) REVERT: N 98 LEU cc_start: 0.9266 (tp) cc_final: 0.8973 (tt) outliers start: 2 outliers final: 0 residues processed: 342 average time/residue: 0.1637 time to fit residues: 82.2316 Evaluate side-chains 261 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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: 5.9990 chunk 138 optimal weight: 0.6980 chunk 117 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 40 optimal weight: 30.0000 chunk 173 optimal weight: 10.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN A 154 ASN A 274 HIS A 285 ASN B 86 HIS ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 HIS N 79 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.085153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.059177 restraints weight = 115644.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.060943 restraints weight = 63592.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.062077 restraints weight = 42189.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.062829 restraints weight = 31617.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.063287 restraints weight = 26005.747| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 20743 Z= 0.182 Angle : 0.665 10.597 29274 Z= 0.380 Chirality : 0.045 0.393 3285 Planarity : 0.005 0.088 2701 Dihedral : 27.805 179.403 5080 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.07 % Allowed : 3.09 % Favored : 96.84 % 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: -2.04 (0.19), residues: 1717 helix: 0.97 (0.21), residues: 558 sheet: -2.10 (0.31), residues: 244 loop : -2.77 (0.17), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 30 TYR 0.018 0.002 TYR I 50 PHE 0.014 0.001 PHE M 25 TRP 0.013 0.001 TRP D 327 HIS 0.007 0.001 HIS K 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 (20743) covalent geometry : angle 0.66513 / 0.38 (29274) hydrogen bonds : bond 0.06105 / 4.17 ( 839) hydrogen bonds : angle 4.07504 / 2.76 ( 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 327 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 0.512 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: A 148 ASP cc_start: 0.7541 (t0) cc_final: 0.7268 (p0) REVERT: A 184 ASP cc_start: 0.8708 (t0) cc_final: 0.8368 (t0) REVERT: A 186 VAL cc_start: 0.9050 (m) cc_final: 0.7784 (m) REVERT: A 215 ILE cc_start: 0.9321 (pt) cc_final: 0.9068 (pt) REVERT: A 250 ASN cc_start: 0.9598 (m-40) cc_final: 0.8968 (p0) REVERT: A 273 GLN cc_start: 0.8103 (mt0) cc_final: 0.7638 (pm20) REVERT: A 276 LEU cc_start: 0.8586 (mt) cc_final: 0.8093 (tp) REVERT: A 277 TYR cc_start: 0.8165 (m-10) cc_final: 0.7624 (m-80) REVERT: A 279 TRP cc_start: 0.8432 (m-90) cc_final: 0.7525 (m-90) REVERT: A 341 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7289 (mm-30) REVERT: B 53 PHE cc_start: 0.2069 (m-80) cc_final: 0.1327 (p90) REVERT: C 3818 MET cc_start: 0.8831 (mtm) cc_final: 0.8591 (mtm) REVERT: C 3932 ARG cc_start: 0.8535 (mpp-170) cc_final: 0.7911 (ppt170) REVERT: C 3942 TYR cc_start: 0.6255 (t80) cc_final: 0.5819 (t80) REVERT: D 315 MET cc_start: 0.6137 (ttp) cc_final: 0.5511 (ppp) REVERT: D 327 TRP cc_start: 0.6173 (m-90) cc_final: 0.5624 (m-90) REVERT: D 397 ASN cc_start: 0.6840 (t0) cc_final: 0.6567 (t0) REVERT: D 500 MET cc_start: 0.1563 (mmm) cc_final: 0.1299 (mpp) REVERT: G 50 GLU cc_start: 0.9346 (tp30) cc_final: 0.8713 (tm-30) REVERT: G 76 GLN cc_start: 0.8528 (tt0) cc_final: 0.7779 (tp-100) REVERT: G 93 GLN cc_start: 0.9223 (mt0) cc_final: 0.8851 (mt0) REVERT: G 94 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8920 (mm-30) REVERT: G 99 TYR cc_start: 0.8941 (t80) cc_final: 0.8298 (t80) REVERT: G 120 MET cc_start: 0.6986 (mtt) cc_final: 0.6337 (mtm) REVERT: G 122 LYS cc_start: 0.8419 (ptpt) cc_final: 0.8210 (ptpt) REVERT: H 31 LYS cc_start: 0.9248 (tttm) cc_final: 0.8926 (tmtm) REVERT: H 44 LYS cc_start: 0.8802 (tppp) cc_final: 0.8577 (tppt) REVERT: H 61 PHE cc_start: 0.9098 (t80) cc_final: 0.8738 (t80) REVERT: H 67 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.7996 (ttm-80) REVERT: H 75 HIS cc_start: 0.8929 (t70) cc_final: 0.8592 (t70) REVERT: H 79 LYS cc_start: 0.8917 (mttt) cc_final: 0.8336 (ptpp) REVERT: H 84 MET cc_start: 0.8750 (mpp) cc_final: 0.8506 (mpp) REVERT: H 88 TYR cc_start: 0.8969 (m-80) cc_final: 0.8367 (m-80) REVERT: H 95 ARG cc_start: 0.8978 (mmm-85) cc_final: 0.8480 (mtt-85) REVERT: H 98 TYR cc_start: 0.9168 (m-10) cc_final: 0.8489 (m-80) REVERT: I 38 ASN cc_start: 0.7378 (t0) cc_final: 0.6813 (t0) REVERT: I 56 GLU cc_start: 0.8796 (tt0) cc_final: 0.8449 (tm-30) REVERT: I 64 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8878 (tm-30) REVERT: I 74 LYS cc_start: 0.9177 (tttp) cc_final: 0.8519 (tptp) REVERT: J 96 ARG cc_start: 0.9394 (ttm170) cc_final: 0.9039 (ttm170) REVERT: K 76 GLN cc_start: 0.9217 (tt0) cc_final: 0.8546 (tp-100) REVERT: K 79 LYS cc_start: 0.9116 (tptp) cc_final: 0.8818 (tppt) REVERT: K 94 GLU cc_start: 0.9486 (mm-30) cc_final: 0.9006 (mm-30) REVERT: K 105 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8397 (tm-30) REVERT: K 106 ASP cc_start: 0.7849 (m-30) cc_final: 0.7439 (m-30) REVERT: K 120 MET cc_start: 0.8528 (mmm) cc_final: 0.8256 (mmp) REVERT: K 130 ILE cc_start: 0.9666 (mm) cc_final: 0.9410 (tp) REVERT: L 88 TYR cc_start: 0.9486 (m-10) cc_final: 0.8914 (m-80) REVERT: M 38 ASN cc_start: 0.8793 (p0) cc_final: 0.7987 (p0) REVERT: M 64 GLU cc_start: 0.9043 (tp30) cc_final: 0.8542 (mm-30) REVERT: M 72 ASP cc_start: 0.9331 (m-30) cc_final: 0.9086 (t0) REVERT: M 83 LEU cc_start: 0.9567 (mt) cc_final: 0.9347 (mm) REVERT: N 40 LYS cc_start: 0.9651 (mttt) cc_final: 0.9402 (mmtt) REVERT: N 59 MET cc_start: 0.9283 (mmm) cc_final: 0.8816 (mmm) REVERT: N 73 GLU cc_start: 0.9110 (tp30) cc_final: 0.8813 (tp30) REVERT: N 82 LYS cc_start: 0.9142 (tppt) cc_final: 0.8889 (tppt) REVERT: N 90 GLU cc_start: 0.9137 (mp0) cc_final: 0.8674 (mp0) REVERT: N 92 GLN cc_start: 0.8895 (mt0) cc_final: 0.8654 (mt0) outliers start: 1 outliers final: 0 residues processed: 327 average time/residue: 0.1508 time to fit residues: 74.8345 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 : 0.648 ------------------------------------------------------------------------------- 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: 3.9990 chunk 40 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 171 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 142 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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** N 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.083133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.057237 restraints weight = 117086.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.059000 restraints weight = 64491.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.060131 restraints weight = 42574.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.060880 restraints weight = 31928.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.061362 restraints weight = 26308.672| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 20743 Z= 0.170 Angle : 0.648 8.717 29274 Z= 0.369 Chirality : 0.045 0.386 3285 Planarity : 0.005 0.088 2701 Dihedral : 27.693 179.819 5080 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.13 % Allowed : 2.08 % Favored : 97.78 % 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: 0.91 (0.21), residues: 558 sheet: -1.96 (0.31), residues: 257 loop : -2.66 (0.18), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 67 TYR 0.034 0.002 TYR K 54 PHE 0.020 0.002 PHE D 469 TRP 0.011 0.001 TRP D 327 HIS 0.013 0.001 HIS C3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (20743) covalent geometry : angle 0.64760 / 0.37 (29274) hydrogen bonds : bond 0.06158 / 4.17 ( 839) hydrogen bonds : angle 4.00204 / 2.72 ( 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 325 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 323 time to evaluate : 0.649 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: A 148 ASP cc_start: 0.7428 (t0) cc_final: 0.7187 (p0) REVERT: A 184 ASP cc_start: 0.8719 (t0) cc_final: 0.8449 (t0) REVERT: A 186 VAL cc_start: 0.9088 (m) cc_final: 0.8006 (m) REVERT: A 215 ILE cc_start: 0.9316 (pt) cc_final: 0.9060 (pt) REVERT: A 250 ASN cc_start: 0.9613 (m-40) cc_final: 0.8906 (p0) REVERT: A 273 GLN cc_start: 0.8138 (mt0) cc_final: 0.7666 (pm20) REVERT: A 277 TYR cc_start: 0.8251 (m-10) cc_final: 0.7897 (m-80) REVERT: A 279 TRP cc_start: 0.8480 (m-90) cc_final: 0.7662 (m-90) REVERT: B 53 PHE cc_start: 0.2324 (m-80) cc_final: 0.1346 (p90) REVERT: C 3818 MET cc_start: 0.8835 (mtm) cc_final: 0.8562 (mtm) REVERT: C 3822 HIS cc_start: 0.7226 (t-170) cc_final: 0.6968 (t-170) REVERT: C 3897 MET cc_start: 0.4895 (ttm) cc_final: 0.4509 (ptm) REVERT: C 3932 ARG cc_start: 0.8566 (mpp-170) cc_final: 0.7934 (ppt170) REVERT: C 3942 TYR cc_start: 0.6050 (t80) cc_final: 0.5647 (t80) REVERT: D 315 MET cc_start: 0.6221 (ttp) cc_final: 0.5685 (ppp) REVERT: D 327 TRP cc_start: 0.6234 (m-90) cc_final: 0.5663 (m-90) REVERT: D 397 ASN cc_start: 0.6688 (t0) cc_final: 0.6376 (t0) REVERT: G 50 GLU cc_start: 0.9342 (tp30) cc_final: 0.8720 (tm-30) REVERT: G 76 GLN cc_start: 0.8618 (tt0) cc_final: 0.7847 (tp-100) REVERT: G 99 TYR cc_start: 0.8938 (t80) cc_final: 0.8611 (t80) REVERT: G 105 GLU cc_start: 0.9523 (tt0) cc_final: 0.8755 (pp20) REVERT: G 112 ILE cc_start: 0.9272 (mm) cc_final: 0.9066 (mm) REVERT: G 120 MET cc_start: 0.7198 (mtt) cc_final: 0.6491 (mtm) REVERT: H 43 VAL cc_start: 0.9488 (t) cc_final: 0.9166 (p) REVERT: H 75 HIS cc_start: 0.8869 (t70) cc_final: 0.8455 (t70) REVERT: H 79 LYS cc_start: 0.9038 (mttt) cc_final: 0.8500 (ptpp) REVERT: H 95 ARG cc_start: 0.8878 (mmm-85) cc_final: 0.8533 (mtt-85) REVERT: H 100 PHE cc_start: 0.8865 (m-10) cc_final: 0.8660 (m-10) REVERT: I 56 GLU cc_start: 0.8601 (tt0) cc_final: 0.8332 (tm-30) REVERT: I 64 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8852 (tm-30) REVERT: I 72 ASP cc_start: 0.8235 (p0) cc_final: 0.8016 (p0) REVERT: I 74 LYS cc_start: 0.9221 (tttp) cc_final: 0.8592 (tptp) REVERT: J 92 GLN cc_start: 0.9512 (tt0) cc_final: 0.9267 (tt0) REVERT: J 96 ARG cc_start: 0.9440 (ttm170) cc_final: 0.9007 (ttm170) REVERT: J 102 GLU cc_start: 0.6908 (tp30) cc_final: 0.6666 (tp30) REVERT: K 60 LEU cc_start: 0.8666 (mm) cc_final: 0.8273 (mm) REVERT: K 61 LEU cc_start: 0.9603 (mm) cc_final: 0.9394 (mm) REVERT: K 62 ILE cc_start: 0.9036 (mp) cc_final: 0.8640 (mp) REVERT: K 64 LYS cc_start: 0.9577 (mppt) cc_final: 0.9242 (mmtp) REVERT: K 68 GLN cc_start: 0.9505 (pt0) cc_final: 0.9292 (pt0) REVERT: K 76 GLN cc_start: 0.9184 (tt0) cc_final: 0.8606 (tp-100) REVERT: K 94 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9048 (mm-30) REVERT: K 97 GLU cc_start: 0.9279 (mt-10) cc_final: 0.9015 (mp0) REVERT: K 105 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8466 (tm-30) REVERT: K 112 ILE cc_start: 0.9014 (mt) cc_final: 0.8810 (mt) REVERT: K 120 MET cc_start: 0.8535 (mmm) cc_final: 0.8209 (mmp) REVERT: L 52 GLU cc_start: 0.8426 (pp20) cc_final: 0.8213 (pp20) REVERT: L 53 GLU cc_start: 0.9580 (tp30) cc_final: 0.9170 (tp30) REVERT: L 88 TYR cc_start: 0.9498 (m-10) cc_final: 0.8961 (m-80) REVERT: M 61 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8845 (tm-30) REVERT: M 64 GLU cc_start: 0.9051 (tp30) cc_final: 0.8486 (mm-30) REVERT: M 72 ASP cc_start: 0.9313 (m-30) cc_final: 0.9079 (t0) REVERT: N 40 LYS cc_start: 0.9660 (mttt) cc_final: 0.9334 (mmtt) REVERT: N 48 ASP cc_start: 0.8483 (p0) cc_final: 0.8129 (t0) REVERT: N 59 MET cc_start: 0.9247 (mmm) cc_final: 0.8862 (mmm) REVERT: N 73 GLU cc_start: 0.9133 (tp30) cc_final: 0.8916 (tp30) REVERT: N 82 LYS cc_start: 0.9145 (tppt) cc_final: 0.8850 (tppt) REVERT: N 90 GLU cc_start: 0.9095 (mp0) cc_final: 0.8640 (mp0) REVERT: N 92 GLN cc_start: 0.8919 (mt0) cc_final: 0.8641 (mt0) REVERT: N 117 LYS cc_start: 0.8858 (tptt) cc_final: 0.8399 (ptmt) outliers start: 2 outliers final: 0 residues processed: 325 average time/residue: 0.1529 time to fit residues: 74.9364 Evaluate side-chains 251 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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: 0.9980 chunk 128 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 178 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.084041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.058212 restraints weight = 113001.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.059968 restraints weight = 62379.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.061108 restraints weight = 41339.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.061880 restraints weight = 31047.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.062282 restraints weight = 25490.684| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 20743 Z= 0.135 Angle : 0.615 9.207 29274 Z= 0.351 Chirality : 0.045 0.385 3285 Planarity : 0.004 0.091 2701 Dihedral : 27.666 179.565 5080 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.13 % Allowed : 1.08 % Favored : 98.79 % 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: -1.68 (0.19), residues: 1717 helix: 1.23 (0.21), residues: 557 sheet: -1.82 (0.32), residues: 244 loop : -2.54 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 92 TYR 0.016 0.001 TYR D 328 PHE 0.022 0.001 PHE G 67 TRP 0.012 0.001 TRP D 327 HIS 0.009 0.001 HIS C3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (20743) covalent geometry : angle 0.61510 / 0.35 (29274) hydrogen bonds : bond 0.04954 / 3.39 ( 839) hydrogen bonds : angle 3.74746 / 2.56 ( 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 328 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 326 time to evaluate : 0.681 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 148 ASP cc_start: 0.7507 (t0) cc_final: 0.7255 (p0) REVERT: A 184 ASP cc_start: 0.8697 (t0) cc_final: 0.8405 (t0) REVERT: A 186 VAL cc_start: 0.9026 (m) cc_final: 0.8015 (m) REVERT: A 215 ILE cc_start: 0.9305 (pt) cc_final: 0.9058 (pt) REVERT: A 250 ASN cc_start: 0.9583 (m-40) cc_final: 0.8920 (p0) REVERT: A 273 GLN cc_start: 0.8125 (mt0) cc_final: 0.7659 (pm20) REVERT: A 276 LEU cc_start: 0.8505 (mm) cc_final: 0.7858 (tp) REVERT: A 277 TYR cc_start: 0.8222 (m-10) cc_final: 0.7680 (m-80) REVERT: A 279 TRP cc_start: 0.8483 (m-90) cc_final: 0.7745 (m-90) REVERT: B 53 PHE cc_start: 0.2093 (m-80) cc_final: 0.1052 (p90) REVERT: C 3818 MET cc_start: 0.8866 (mtm) cc_final: 0.8619 (mtm) REVERT: C 3897 MET cc_start: 0.4883 (ttm) cc_final: 0.4491 (ptm) REVERT: C 3932 ARG cc_start: 0.8625 (mpp-170) cc_final: 0.7950 (ppt170) REVERT: C 3942 TYR cc_start: 0.5933 (t80) cc_final: 0.5544 (t80) REVERT: D 315 MET cc_start: 0.6261 (ttp) cc_final: 0.5590 (ppp) REVERT: D 397 ASN cc_start: 0.6771 (t0) cc_final: 0.6500 (t0) REVERT: G 50 GLU cc_start: 0.9328 (tp30) cc_final: 0.8686 (tm-30) REVERT: G 67 PHE cc_start: 0.9221 (t80) cc_final: 0.8918 (t80) REVERT: G 76 GLN cc_start: 0.8602 (tt0) cc_final: 0.7853 (tp-100) REVERT: G 99 TYR cc_start: 0.8932 (t80) cc_final: 0.8676 (t80) REVERT: G 112 ILE cc_start: 0.9189 (mm) cc_final: 0.8964 (mm) REVERT: G 119 ILE cc_start: 0.7910 (mt) cc_final: 0.7634 (mt) REVERT: G 120 MET cc_start: 0.6990 (mtt) cc_final: 0.6260 (mtp) REVERT: H 43 VAL cc_start: 0.9454 (t) cc_final: 0.9165 (p) REVERT: H 53 GLU cc_start: 0.9355 (mp0) cc_final: 0.9049 (pt0) REVERT: H 67 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.7802 (tpp-160) REVERT: H 75 HIS cc_start: 0.8820 (t70) cc_final: 0.8480 (t70) REVERT: H 79 LYS cc_start: 0.9085 (mttt) cc_final: 0.8529 (ptpp) REVERT: H 95 ARG cc_start: 0.8807 (mmm-85) cc_final: 0.8515 (mtt-85) REVERT: H 100 PHE cc_start: 0.8935 (m-10) cc_final: 0.8675 (m-10) REVERT: I 56 GLU cc_start: 0.8657 (tt0) cc_final: 0.8328 (tm-30) REVERT: I 64 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8880 (tm-30) REVERT: I 68 ASN cc_start: 0.9404 (t0) cc_final: 0.9168 (t0) REVERT: I 74 LYS cc_start: 0.9183 (tttp) cc_final: 0.8548 (tptp) REVERT: J 61 SER cc_start: 0.9486 (m) cc_final: 0.9131 (p) REVERT: J 62 PHE cc_start: 0.9421 (t80) cc_final: 0.9205 (t80) REVERT: J 76 ARG cc_start: 0.9425 (ttm110) cc_final: 0.9117 (ttm110) REVERT: J 96 ARG cc_start: 0.9379 (ttm170) cc_final: 0.9033 (ttm170) REVERT: K 64 LYS cc_start: 0.9587 (mppt) cc_final: 0.9242 (mmtp) REVERT: K 68 GLN cc_start: 0.9484 (pt0) cc_final: 0.9275 (pt0) REVERT: K 76 GLN cc_start: 0.9149 (tt0) cc_final: 0.8610 (tp-100) REVERT: K 94 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9188 (mm-30) REVERT: K 120 MET cc_start: 0.8502 (mmm) cc_final: 0.8196 (mmp) REVERT: K 130 ILE cc_start: 0.9694 (mm) cc_final: 0.9421 (tp) REVERT: L 53 GLU cc_start: 0.9598 (tp30) cc_final: 0.9264 (tp30) REVERT: L 88 TYR cc_start: 0.9498 (m-10) cc_final: 0.8984 (m-80) REVERT: M 61 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8845 (tm-30) REVERT: M 64 GLU cc_start: 0.9060 (tp30) cc_final: 0.8357 (mm-30) REVERT: N 40 LYS cc_start: 0.9655 (mttt) cc_final: 0.9375 (mmtm) REVERT: N 48 ASP cc_start: 0.8393 (p0) cc_final: 0.8020 (t0) REVERT: N 59 MET cc_start: 0.9259 (mmm) cc_final: 0.8859 (mmm) REVERT: N 82 LYS cc_start: 0.9141 (tppt) cc_final: 0.8877 (tppt) REVERT: N 90 GLU cc_start: 0.9067 (mp0) cc_final: 0.8543 (mp0) REVERT: N 92 GLN cc_start: 0.8892 (mt0) cc_final: 0.8537 (mt0) REVERT: N 117 LYS cc_start: 0.8839 (tptt) cc_final: 0.8392 (ptmt) outliers start: 2 outliers final: 0 residues processed: 328 average time/residue: 0.1572 time to fit residues: 77.8220 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 : 0.659 ------------------------------------------------------------------------------- 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: 9.9990 chunk 126 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 136 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 158 optimal weight: 0.8980 chunk 123 optimal weight: 0.0670 chunk 7 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN B 100 ASN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 ASN N 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.081338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055914 restraints weight = 115741.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.057652 restraints weight = 63144.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.058757 restraints weight = 41500.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.059493 restraints weight = 31077.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.059854 restraints weight = 25550.786| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20743 Z= 0.170 Angle : 0.639 8.744 29274 Z= 0.363 Chirality : 0.044 0.360 3285 Planarity : 0.005 0.087 2701 Dihedral : 27.641 179.827 5080 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.20 % Allowed : 1.21 % Favored : 98.59 % 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: -1.50 (0.20), residues: 1717 helix: 1.36 (0.22), residues: 550 sheet: -1.69 (0.31), residues: 258 loop : -2.41 (0.18), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 42 TYR 0.013 0.001 TYR D 460 PHE 0.029 0.002 PHE G 104 TRP 0.009 0.001 TRP B 330 HIS 0.013 0.001 HIS C3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (20743) covalent geometry : angle 0.63856 / 0.36 (29274) hydrogen bonds : bond 0.06033 / 4.06 ( 839) hydrogen bonds : angle 3.84173 / 2.63 ( 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 307 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 304 time to evaluate : 0.651 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 184 ASP cc_start: 0.8677 (t0) cc_final: 0.8426 (t0) REVERT: A 186 VAL cc_start: 0.9082 (m) cc_final: 0.8003 (m) REVERT: A 215 ILE cc_start: 0.9296 (pt) cc_final: 0.9036 (pt) REVERT: A 250 ASN cc_start: 0.9616 (m-40) cc_final: 0.8931 (p0) REVERT: A 273 GLN cc_start: 0.8258 (mt0) cc_final: 0.7732 (pm20) REVERT: A 276 LEU cc_start: 0.8508 (mm) cc_final: 0.7862 (tp) REVERT: A 277 TYR cc_start: 0.8191 (m-10) cc_final: 0.7702 (m-80) REVERT: A 279 TRP cc_start: 0.8452 (m-90) cc_final: 0.7442 (m-90) REVERT: B 53 PHE cc_start: 0.1541 (m-80) cc_final: 0.0968 (p90) REVERT: C 3818 MET cc_start: 0.8869 (mtm) cc_final: 0.8616 (mtm) REVERT: C 3822 HIS cc_start: 0.7288 (t-170) cc_final: 0.6950 (t-170) REVERT: C 3867 LEU cc_start: 0.8692 (tp) cc_final: 0.8218 (tp) REVERT: C 3871 ARG cc_start: 0.8594 (mtt-85) cc_final: 0.8244 (mmp-170) REVERT: C 3897 MET cc_start: 0.5037 (ttm) cc_final: 0.4458 (ptm) REVERT: C 3942 TYR cc_start: 0.5996 (t80) cc_final: 0.5595 (t80) REVERT: D 315 MET cc_start: 0.6315 (ttp) cc_final: 0.5690 (ppp) REVERT: D 327 TRP cc_start: 0.6467 (t60) cc_final: 0.6110 (m-90) REVERT: D 397 ASN cc_start: 0.6696 (t0) cc_final: 0.6434 (t0) REVERT: G 50 GLU cc_start: 0.9329 (tp30) cc_final: 0.8670 (tm-30) REVERT: G 76 GLN cc_start: 0.8635 (tt0) cc_final: 0.7938 (tp-100) REVERT: G 93 GLN cc_start: 0.9082 (mt0) cc_final: 0.8859 (mt0) REVERT: G 97 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8681 (mm-30) REVERT: G 99 TYR cc_start: 0.8969 (t80) cc_final: 0.8619 (t80) REVERT: G 105 GLU cc_start: 0.9431 (tt0) cc_final: 0.8722 (tp30) REVERT: G 112 ILE cc_start: 0.9225 (mm) cc_final: 0.9023 (mm) REVERT: G 119 ILE cc_start: 0.7877 (mt) cc_final: 0.7569 (mt) REVERT: G 120 MET cc_start: 0.7125 (mtt) cc_final: 0.6457 (mtp) REVERT: H 43 VAL cc_start: 0.9518 (t) cc_final: 0.9253 (p) REVERT: H 53 GLU cc_start: 0.9279 (mp0) cc_final: 0.8990 (pm20) REVERT: H 75 HIS cc_start: 0.8856 (t70) cc_final: 0.8451 (t70) REVERT: H 79 LYS cc_start: 0.9140 (mttt) cc_final: 0.8498 (ptpp) REVERT: H 95 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.8380 (mtt-85) REVERT: I 56 GLU cc_start: 0.8649 (tt0) cc_final: 0.8238 (tm-30) REVERT: I 64 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8899 (tm-30) REVERT: I 68 ASN cc_start: 0.9408 (t0) cc_final: 0.9191 (t0) REVERT: I 74 LYS cc_start: 0.9194 (tttp) cc_final: 0.8563 (tptp) REVERT: J 59 MET cc_start: 0.9468 (mmp) cc_final: 0.9262 (mmm) REVERT: J 61 SER cc_start: 0.9519 (m) cc_final: 0.9123 (p) REVERT: J 62 PHE cc_start: 0.9417 (t80) cc_final: 0.9162 (t80) REVERT: J 76 ARG cc_start: 0.9398 (ttm110) cc_final: 0.8975 (ttm110) REVERT: J 96 ARG cc_start: 0.9355 (ttm170) cc_final: 0.9080 (ttm170) REVERT: K 64 LYS cc_start: 0.9597 (mppt) cc_final: 0.9222 (mmtp) REVERT: K 68 GLN cc_start: 0.9458 (pt0) cc_final: 0.9253 (pt0) REVERT: K 76 GLN cc_start: 0.9165 (tt0) cc_final: 0.8662 (tp-100) REVERT: K 97 GLU cc_start: 0.9281 (mt-10) cc_final: 0.9027 (mt-10) REVERT: K 120 MET cc_start: 0.8584 (mmm) cc_final: 0.8282 (mmp) REVERT: K 130 ILE cc_start: 0.9690 (mm) cc_final: 0.9452 (tp) REVERT: L 39 ARG cc_start: 0.9241 (mmt180) cc_final: 0.8860 (mmm160) REVERT: L 52 GLU cc_start: 0.8412 (pp20) cc_final: 0.8179 (pp20) REVERT: L 53 GLU cc_start: 0.9582 (tp30) cc_final: 0.9145 (tp30) REVERT: L 88 TYR cc_start: 0.9514 (m-10) cc_final: 0.9029 (m-80) REVERT: M 64 GLU cc_start: 0.9061 (tp30) cc_final: 0.8469 (mm-30) REVERT: N 40 LYS cc_start: 0.9648 (mttt) cc_final: 0.9320 (mmtt) REVERT: N 48 ASP cc_start: 0.8506 (p0) cc_final: 0.8146 (t0) REVERT: N 59 MET cc_start: 0.9291 (mmm) cc_final: 0.8893 (mmm) REVERT: N 82 LYS cc_start: 0.9176 (tppt) cc_final: 0.8926 (tppt) REVERT: N 90 GLU cc_start: 0.9093 (mp0) cc_final: 0.8595 (mp0) REVERT: N 92 GLN cc_start: 0.8936 (mt0) cc_final: 0.8613 (mt0) REVERT: N 117 LYS cc_start: 0.8852 (tptt) cc_final: 0.8396 (ptmt) outliers start: 3 outliers final: 0 residues processed: 306 average time/residue: 0.1458 time to fit residues: 68.5128 Evaluate side-chains 240 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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: 10.0000 chunk 91 optimal weight: 0.0270 chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- 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** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 ASN N 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.081784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.056320 restraints weight = 115719.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.058073 restraints weight = 63304.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.059188 restraints weight = 41633.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.059942 restraints weight = 31261.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.060432 restraints weight = 25658.191| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20743 Z= 0.139 Angle : 0.609 9.007 29274 Z= 0.348 Chirality : 0.044 0.352 3285 Planarity : 0.004 0.089 2701 Dihedral : 27.619 179.357 5080 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.13 % Allowed : 0.67 % Favored : 99.19 % 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: -1.43 (0.20), residues: 1717 helix: 1.36 (0.22), residues: 552 sheet: -1.64 (0.33), residues: 245 loop : -2.32 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 67 TYR 0.037 0.001 TYR J 80 PHE 0.024 0.001 PHE G 104 TRP 0.011 0.001 TRP B 330 HIS 0.011 0.001 HIS C3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (20743) covalent geometry : angle 0.60895 / 0.35 (29274) hydrogen bonds : bond 0.05059 / 3.43 ( 839) hydrogen bonds : angle 3.69984 / 2.54 ( 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 306 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 304 time to evaluate : 0.546 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: 0.8636 (t0) cc_final: 0.8405 (t0) REVERT: A 186 VAL cc_start: 0.9072 (m) cc_final: 0.7979 (m) REVERT: A 215 ILE cc_start: 0.9298 (pt) cc_final: 0.9040 (pt) REVERT: A 250 ASN cc_start: 0.9615 (m-40) cc_final: 0.8666 (t0) REVERT: A 273 GLN cc_start: 0.8249 (mt0) cc_final: 0.7662 (pm20) REVERT: A 276 LEU cc_start: 0.8499 (mm) cc_final: 0.7854 (tp) REVERT: A 277 TYR cc_start: 0.8294 (m-10) cc_final: 0.7716 (m-80) REVERT: A 279 TRP cc_start: 0.8483 (m-90) cc_final: 0.7632 (m-90) REVERT: B 53 PHE cc_start: 0.1762 (m-80) cc_final: 0.0938 (p90) REVERT: C 3818 MET cc_start: 0.8889 (mtm) cc_final: 0.8630 (mtm) REVERT: C 3897 MET cc_start: 0.4989 (ttm) cc_final: 0.4582 (ptm) REVERT: C 3942 TYR cc_start: 0.6016 (t80) cc_final: 0.5633 (t80) REVERT: D 315 MET cc_start: 0.6321 (ttp) cc_final: 0.5678 (ppp) REVERT: D 327 TRP cc_start: 0.6556 (t60) cc_final: 0.6108 (m-90) REVERT: D 397 ASN cc_start: 0.6662 (t0) cc_final: 0.6396 (t0) REVERT: D 461 LYS cc_start: 0.4939 (pttm) cc_final: 0.4734 (mptt) REVERT: G 50 GLU cc_start: 0.9319 (tp30) cc_final: 0.8641 (tm-30) REVERT: G 76 GLN cc_start: 0.8679 (tt0) cc_final: 0.7866 (tp-100) REVERT: G 93 GLN cc_start: 0.9028 (mt0) cc_final: 0.8823 (mt0) REVERT: G 99 TYR cc_start: 0.8920 (t80) cc_final: 0.8666 (t80) REVERT: G 105 GLU cc_start: 0.9451 (tt0) cc_final: 0.8724 (tp30) REVERT: G 112 ILE cc_start: 0.9199 (mm) cc_final: 0.8990 (mm) REVERT: G 119 ILE cc_start: 0.7713 (mt) cc_final: 0.7442 (mt) REVERT: G 120 MET cc_start: 0.7109 (mtt) cc_final: 0.6421 (mtp) REVERT: H 53 GLU cc_start: 0.9205 (mp0) cc_final: 0.8962 (mp0) REVERT: H 63 GLU cc_start: 0.8520 (pp20) cc_final: 0.8224 (tt0) REVERT: H 67 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.7952 (tpp-160) REVERT: H 75 HIS cc_start: 0.8782 (t70) cc_final: 0.8518 (t70) REVERT: H 79 LYS cc_start: 0.9164 (mttt) cc_final: 0.8692 (ptpp) REVERT: H 95 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8472 (mtt-85) REVERT: I 56 GLU cc_start: 0.8629 (tt0) cc_final: 0.8257 (tm-30) REVERT: I 64 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8877 (tm-30) REVERT: I 68 ASN cc_start: 0.9417 (t0) cc_final: 0.9184 (t0) REVERT: I 74 LYS cc_start: 0.9199 (tttp) cc_final: 0.8588 (tptp) REVERT: J 59 MET cc_start: 0.9455 (mmp) cc_final: 0.9195 (mmm) REVERT: J 61 SER cc_start: 0.9508 (m) cc_final: 0.9116 (p) REVERT: J 62 PHE cc_start: 0.9373 (t80) cc_final: 0.9136 (t80) REVERT: J 96 ARG cc_start: 0.9367 (ttm170) cc_final: 0.9033 (ttm170) REVERT: K 53 ARG cc_start: 0.9018 (tmm-80) cc_final: 0.8643 (tmm-80) REVERT: K 64 LYS cc_start: 0.9585 (mppt) cc_final: 0.9204 (mmtp) REVERT: K 68 GLN cc_start: 0.9418 (pt0) cc_final: 0.9212 (pt0) REVERT: K 76 GLN cc_start: 0.9131 (tt0) cc_final: 0.8692 (tp-100) REVERT: K 119 ILE cc_start: 0.8833 (mp) cc_final: 0.8613 (mm) REVERT: K 130 ILE cc_start: 0.9686 (mm) cc_final: 0.9459 (tp) REVERT: L 39 ARG cc_start: 0.9240 (mmt180) cc_final: 0.9032 (mmm-85) REVERT: L 52 GLU cc_start: 0.8403 (pp20) cc_final: 0.8171 (pp20) REVERT: L 53 GLU cc_start: 0.9584 (tp30) cc_final: 0.9144 (tp30) REVERT: L 88 TYR cc_start: 0.9477 (m-10) cc_final: 0.8993 (m-80) REVERT: M 64 GLU cc_start: 0.9074 (tp30) cc_final: 0.8413 (mm-30) REVERT: N 40 LYS cc_start: 0.9642 (mttt) cc_final: 0.9367 (mmtm) REVERT: N 48 ASP cc_start: 0.8432 (p0) cc_final: 0.8087 (t0) REVERT: N 59 MET cc_start: 0.9273 (mmm) cc_final: 0.8887 (mmm) REVERT: N 82 LYS cc_start: 0.9154 (tppt) cc_final: 0.8903 (tppt) REVERT: N 90 GLU cc_start: 0.9081 (mp0) cc_final: 0.8538 (mp0) REVERT: N 92 GLN cc_start: 0.8893 (mt0) cc_final: 0.8525 (mt0) REVERT: N 117 LYS cc_start: 0.8847 (tptt) cc_final: 0.8399 (ptmt) outliers start: 2 outliers final: 0 residues processed: 306 average time/residue: 0.1515 time to fit residues: 70.5646 Evaluate side-chains 244 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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: 5.9990 chunk 73 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 HIS A 285 ASN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** 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 = 0.3712 r_free = 0.3712 target = 0.080028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.054676 restraints weight = 115606.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.056399 restraints weight = 63411.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.057510 restraints weight = 41865.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.058228 restraints weight = 31356.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.058750 restraints weight = 25935.453| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20743 Z= 0.159 Angle : 0.637 11.476 29274 Z= 0.359 Chirality : 0.044 0.317 3285 Planarity : 0.004 0.084 2701 Dihedral : 27.547 178.202 5080 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.13 % Allowed : 0.67 % Favored : 99.19 % 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: -1.43 (0.20), residues: 1717 helix: 1.23 (0.21), residues: 553 sheet: -1.63 (0.33), residues: 234 loop : -2.24 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 76 TYR 0.038 0.002 TYR J 80 PHE 0.015 0.001 PHE M 25 TRP 0.011 0.001 TRP B 330 HIS 0.019 0.001 HIS C3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (20743) covalent geometry : angle 0.63743 / 0.36 (29274) hydrogen bonds : bond 0.05869 / 3.95 ( 839) hydrogen bonds : angle 3.75891 / 2.57 ( 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 302 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 300 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: A 186 VAL cc_start: 0.9010 (m) cc_final: 0.7853 (m) REVERT: A 250 ASN cc_start: 0.9622 (m-40) cc_final: 0.8785 (t0) REVERT: A 273 GLN cc_start: 0.8297 (mt0) cc_final: 0.8060 (tt0) REVERT: A 276 LEU cc_start: 0.8530 (mm) cc_final: 0.7844 (tp) REVERT: A 277 TYR cc_start: 0.8336 (m-10) cc_final: 0.7720 (m-80) REVERT: A 279 TRP cc_start: 0.8519 (m-90) cc_final: 0.7482 (m-90) REVERT: B 53 PHE cc_start: 0.1757 (m-80) cc_final: 0.0971 (p90) REVERT: C 3818 MET cc_start: 0.8936 (mtm) cc_final: 0.8677 (mtm) REVERT: C 3822 HIS cc_start: 0.7428 (t-170) cc_final: 0.7181 (t-170) REVERT: C 3897 MET cc_start: 0.5013 (ttm) cc_final: 0.4610 (ptm) REVERT: C 3942 TYR cc_start: 0.6030 (t80) cc_final: 0.5609 (t80) REVERT: D 315 MET cc_start: 0.6408 (ttp) cc_final: 0.5804 (ppp) REVERT: D 327 TRP cc_start: 0.6706 (t60) cc_final: 0.6276 (m-10) REVERT: D 397 ASN cc_start: 0.6725 (t0) cc_final: 0.6403 (t0) REVERT: G 50 GLU cc_start: 0.9331 (tp30) cc_final: 0.8663 (tm-30) REVERT: G 65 LEU cc_start: 0.8887 (mt) cc_final: 0.8487 (mt) REVERT: G 67 PHE cc_start: 0.9281 (t80) cc_final: 0.8917 (t80) REVERT: G 76 GLN cc_start: 0.8699 (tt0) cc_final: 0.7940 (tp-100) REVERT: G 93 GLN cc_start: 0.9069 (mt0) cc_final: 0.8677 (mt0) REVERT: G 97 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8810 (mm-30) REVERT: G 99 TYR cc_start: 0.8885 (t80) cc_final: 0.8142 (t80) REVERT: G 105 GLU cc_start: 0.9561 (tt0) cc_final: 0.8858 (pp20) REVERT: G 112 ILE cc_start: 0.9220 (mm) cc_final: 0.9004 (mm) REVERT: H 43 VAL cc_start: 0.9504 (t) cc_final: 0.9291 (p) REVERT: H 67 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8129 (tpp-160) REVERT: H 75 HIS cc_start: 0.8759 (t70) cc_final: 0.8431 (t70) REVERT: H 95 ARG cc_start: 0.8752 (mmm-85) cc_final: 0.8333 (mtt-85) REVERT: I 41 GLU cc_start: 0.7222 (pm20) cc_final: 0.6869 (pp20) REVERT: I 56 GLU cc_start: 0.8616 (tt0) cc_final: 0.8220 (tm-30) REVERT: I 64 GLU cc_start: 0.9240 (tm-30) cc_final: 0.8904 (tm-30) REVERT: I 68 ASN cc_start: 0.9431 (t0) cc_final: 0.9215 (t0) REVERT: I 74 LYS cc_start: 0.9225 (tttp) cc_final: 0.8607 (tptp) REVERT: I 91 GLU cc_start: 0.8828 (pp20) cc_final: 0.8579 (pp20) REVERT: J 56 MET cc_start: 0.8998 (ptp) cc_final: 0.8765 (pmm) REVERT: J 59 MET cc_start: 0.9468 (mmp) cc_final: 0.9207 (mmm) REVERT: J 61 SER cc_start: 0.9535 (m) cc_final: 0.9189 (p) REVERT: J 96 ARG cc_start: 0.9340 (ttm170) cc_final: 0.9088 (ttm170) REVERT: K 64 LYS cc_start: 0.9664 (mppt) cc_final: 0.9461 (mmtp) REVERT: K 76 GLN cc_start: 0.9154 (tt0) cc_final: 0.8726 (tp-100) REVERT: K 120 MET cc_start: 0.8357 (mmp) cc_final: 0.8070 (mmp) REVERT: K 130 ILE cc_start: 0.9702 (mm) cc_final: 0.9498 (tp) REVERT: L 26 ILE cc_start: 0.8483 (tp) cc_final: 0.8222 (tt) REVERT: L 39 ARG cc_start: 0.9349 (mmt180) cc_final: 0.9022 (mmm-85) REVERT: L 52 GLU cc_start: 0.8360 (pp20) cc_final: 0.8127 (pp20) REVERT: L 53 GLU cc_start: 0.9555 (tp30) cc_final: 0.9132 (tp30) REVERT: L 63 GLU cc_start: 0.8780 (pp20) cc_final: 0.8147 (mt-10) REVERT: L 88 TYR cc_start: 0.9488 (m-10) cc_final: 0.9008 (m-80) REVERT: M 64 GLU cc_start: 0.9081 (tp30) cc_final: 0.8422 (mm-30) REVERT: N 40 LYS cc_start: 0.9628 (mttt) cc_final: 0.9289 (mmtt) REVERT: N 48 ASP cc_start: 0.8549 (p0) cc_final: 0.8184 (t0) REVERT: N 59 MET cc_start: 0.9304 (mmm) cc_final: 0.8881 (mmm) REVERT: N 82 LYS cc_start: 0.9251 (tppt) cc_final: 0.8979 (tppt) REVERT: N 90 GLU cc_start: 0.9106 (mp0) cc_final: 0.8554 (mp0) REVERT: N 92 GLN cc_start: 0.8953 (mt0) cc_final: 0.8571 (mt0) REVERT: N 117 LYS cc_start: 0.8861 (tptt) cc_final: 0.8388 (ptmt) outliers start: 2 outliers final: 0 residues processed: 302 average time/residue: 0.1487 time to fit residues: 68.7644 Evaluate side-chains 245 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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: 0.7980 chunk 14 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 31 optimal weight: 0.0770 chunk 19 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 ASN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** 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 = 0.3734 r_free = 0.3734 target = 0.081155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055877 restraints weight = 115073.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.057625 restraints weight = 63182.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.058695 restraints weight = 41649.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.059513 restraints weight = 31366.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.060023 restraints weight = 25748.632| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.6388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20743 Z= 0.127 Angle : 0.614 9.776 29274 Z= 0.347 Chirality : 0.044 0.305 3285 Planarity : 0.004 0.089 2701 Dihedral : 27.505 176.900 5080 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.13 % Allowed : 0.40 % Favored : 99.46 % 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: -1.29 (0.20), residues: 1717 helix: 1.37 (0.22), residues: 554 sheet: -1.69 (0.34), residues: 229 loop : -2.14 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 76 TYR 0.041 0.001 TYR J 80 PHE 0.034 0.002 PHE G 104 TRP 0.015 0.001 TRP B 273 HIS 0.018 0.001 HIS C3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (20743) covalent geometry : angle 0.61389 / 0.35 (29274) hydrogen bonds : bond 0.04641 / 3.14 ( 839) hydrogen bonds : angle 3.58851 / 2.47 ( 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 312 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 310 time to evaluate : 0.599 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: 0.8936 (m) cc_final: 0.7802 (m) REVERT: A 215 ILE cc_start: 0.9299 (pt) cc_final: 0.9070 (pt) REVERT: A 250 ASN cc_start: 0.9603 (m-40) cc_final: 0.8739 (t0) REVERT: A 273 GLN cc_start: 0.8332 (mt0) cc_final: 0.8100 (tt0) REVERT: A 276 LEU cc_start: 0.8492 (mm) cc_final: 0.7785 (tp) REVERT: A 277 TYR cc_start: 0.8327 (m-10) cc_final: 0.7673 (m-80) REVERT: A 279 TRP cc_start: 0.8524 (m-90) cc_final: 0.7534 (m-90) REVERT: B 53 PHE cc_start: 0.1725 (m-80) cc_final: 0.0952 (p90) REVERT: C 3818 MET cc_start: 0.8958 (mtm) cc_final: 0.8740 (mtm) REVERT: C 3822 HIS cc_start: 0.7330 (t-170) cc_final: 0.7032 (t-170) REVERT: C 3897 MET cc_start: 0.4904 (ttm) cc_final: 0.4512 (ptm) REVERT: C 3942 TYR cc_start: 0.5910 (t80) cc_final: 0.5494 (t80) REVERT: D 315 MET cc_start: 0.6306 (ttp) cc_final: 0.5763 (ppp) REVERT: D 327 TRP cc_start: 0.6694 (t60) cc_final: 0.6270 (m-10) REVERT: D 397 ASN cc_start: 0.6700 (t0) cc_final: 0.6403 (t0) REVERT: D 458 VAL cc_start: 0.8068 (p) cc_final: 0.7747 (p) REVERT: G 50 GLU cc_start: 0.9321 (tp30) cc_final: 0.8620 (tm-30) REVERT: G 65 LEU cc_start: 0.8818 (mt) cc_final: 0.8416 (mt) REVERT: G 67 PHE cc_start: 0.9258 (t80) cc_final: 0.8882 (t80) REVERT: G 76 GLN cc_start: 0.8682 (tt0) cc_final: 0.7886 (tp-100) REVERT: G 93 GLN cc_start: 0.9006 (mt0) cc_final: 0.8637 (mt0) REVERT: G 105 GLU cc_start: 0.9556 (tt0) cc_final: 0.9138 (tp30) REVERT: G 112 ILE cc_start: 0.9164 (mm) cc_final: 0.8950 (mm) REVERT: G 119 ILE cc_start: 0.7798 (mt) cc_final: 0.7546 (mt) REVERT: G 120 MET cc_start: 0.7446 (mtt) cc_final: 0.6704 (mtp) REVERT: H 67 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.8025 (tpp-160) REVERT: H 95 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8185 (mtt-85) REVERT: H 97 LEU cc_start: 0.9713 (tp) cc_final: 0.9235 (mm) REVERT: I 56 GLU cc_start: 0.8944 (tt0) cc_final: 0.8583 (tm-30) REVERT: I 64 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8915 (tm-30) REVERT: I 68 ASN cc_start: 0.9418 (t0) cc_final: 0.9191 (t0) REVERT: I 74 LYS cc_start: 0.9215 (tttp) cc_final: 0.8581 (tptp) REVERT: J 28 LYS cc_start: 0.7139 (pttm) cc_final: 0.6699 (pptt) REVERT: J 56 MET cc_start: 0.9003 (ptp) cc_final: 0.8733 (pmm) REVERT: J 59 MET cc_start: 0.9471 (mmp) cc_final: 0.9237 (mmm) REVERT: J 61 SER cc_start: 0.9513 (m) cc_final: 0.9095 (p) REVERT: J 62 PHE cc_start: 0.9406 (t80) cc_final: 0.9177 (t80) REVERT: J 96 ARG cc_start: 0.9302 (ttm170) cc_final: 0.9027 (ttm170) REVERT: K 76 GLN cc_start: 0.9127 (tt0) cc_final: 0.8721 (tp-100) REVERT: K 112 ILE cc_start: 0.8903 (mt) cc_final: 0.8703 (mt) REVERT: K 120 MET cc_start: 0.8186 (mmp) cc_final: 0.7829 (mmm) REVERT: L 26 ILE cc_start: 0.8343 (tp) cc_final: 0.8089 (tt) REVERT: L 52 GLU cc_start: 0.8355 (pp20) cc_final: 0.8152 (pp20) REVERT: L 53 GLU cc_start: 0.9559 (tp30) cc_final: 0.9186 (tp30) REVERT: L 63 GLU cc_start: 0.8668 (pp20) cc_final: 0.8032 (mt-10) REVERT: L 88 TYR cc_start: 0.9496 (m-10) cc_final: 0.9065 (m-80) REVERT: M 64 GLU cc_start: 0.9051 (tp30) cc_final: 0.8411 (mm-30) REVERT: M 91 GLU cc_start: 0.9198 (pp20) cc_final: 0.8981 (pp20) REVERT: N 36 ILE cc_start: 0.9203 (pt) cc_final: 0.8966 (pt) REVERT: N 40 LYS cc_start: 0.9643 (mttt) cc_final: 0.9265 (mmtt) REVERT: N 48 ASP cc_start: 0.8434 (p0) cc_final: 0.8106 (t0) REVERT: N 59 MET cc_start: 0.9288 (mmm) cc_final: 0.8852 (mmm) REVERT: N 85 THR cc_start: 0.9256 (m) cc_final: 0.8936 (m) REVERT: N 90 GLU cc_start: 0.9090 (mp0) cc_final: 0.8597 (mt-10) REVERT: N 92 GLN cc_start: 0.8871 (mt0) cc_final: 0.8476 (mt0) outliers start: 2 outliers final: 0 residues processed: 312 average time/residue: 0.1451 time to fit residues: 69.9217 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 : 0.565 ------------------------------------------------------------------------------- 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: 6.9990 chunk 153 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 139 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 151 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 ASN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.079621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.054404 restraints weight = 115827.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.056134 restraints weight = 63394.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.057229 restraints weight = 41689.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.057989 restraints weight = 31323.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.058414 restraints weight = 25744.269| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20743 Z= 0.145 Angle : 0.620 10.503 29274 Z= 0.350 Chirality : 0.043 0.282 3285 Planarity : 0.004 0.085 2701 Dihedral : 27.458 176.345 5080 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.07 % Allowed : 0.27 % 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: -1.26 (0.20), residues: 1717 helix: 1.39 (0.22), residues: 554 sheet: -1.63 (0.32), residues: 262 loop : -2.11 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 76 TYR 0.043 0.001 TYR J 80 PHE 0.025 0.002 PHE J 62 TRP 0.010 0.001 TRP B 330 HIS 0.016 0.001 HIS C3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (20743) covalent geometry : angle 0.62034 / 0.35 (29274) hydrogen bonds : bond 0.05520 / 3.70 ( 839) hydrogen bonds : angle 3.60577 / 2.47 ( 2107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3962.56 seconds wall clock time: 69 minutes 8.00 seconds (4148.00 seconds total)