Starting phenix.real_space_refine on Thu Feb 5 10:28:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z03_14403/02_2026/7z03_14403.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z03_14403/02_2026/7z03_14403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z03_14403/02_2026/7z03_14403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z03_14403/02_2026/7z03_14403.map" model { file = "/net/cci-nas-00/data/ceres_data/7z03_14403/02_2026/7z03_14403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z03_14403/02_2026/7z03_14403.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4287 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 82 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 8173 2.51 5 N 2365 2.21 5 O 2736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13396 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2916 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 7, 'TRANS': 366} Chain breaks: 1 Chain: "D" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2914 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 7, 'TRANS': 366} Chain breaks: 1 Chain: "A" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3010 Classifications: {'peptide': 381} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2897 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 20, 'TRANS': 347} Chain breaks: 2 Chain: "E" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 806 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "F" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 793 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 22 residue: pdb=" N GLY A 284 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY A 284 " occ=0.50 residue: pdb=" N ALA A 287 " occ=0.60 ... (3 atoms not shown) pdb=" CB ALA A 287 " occ=0.60 residue: pdb=" N THR A 290 " occ=0.70 ... (5 atoms not shown) pdb=" CG2 THR A 290 " occ=0.70 residue: pdb=" N ALA A 291 " occ=0.60 ... (3 atoms not shown) pdb=" CB ALA A 291 " occ=0.60 residue: pdb=" N GLN A 292 " occ=0.70 ... (7 atoms not shown) pdb=" NE2 GLN A 292 " occ=0.70 residue: pdb=" N LEU A 293 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU A 293 " occ=0.80 residue: pdb=" N PRO A 303 " occ=0.61 ... (5 atoms not shown) pdb=" CD PRO A 303 " occ=0.61 residue: pdb=" N PRO A 304 " occ=0.68 ... (5 atoms not shown) pdb=" CD PRO A 304 " occ=0.68 residue: pdb=" N VAL A 305 " occ=0.88 ... (5 atoms not shown) pdb=" CG2 VAL A 305 " occ=0.88 residue: pdb=" N TRP A 306 " occ=0.97 ... (12 atoms not shown) pdb=" CH2 TRP A 306 " occ=0.97 residue: pdb=" N LEU A 307 " occ=0.87 ... (6 atoms not shown) pdb=" CD2 LEU A 307 " occ=0.87 residue: pdb=" N ILE A 309 " occ=0.89 ... (6 atoms not shown) pdb=" CD1 ILE A 309 " occ=0.89 ... (remaining 10 not shown) Time building chain proxies: 3.11, per 1000 atoms: 0.23 Number of scatterers: 13396 At special positions: 0 Unit cell: (108.018, 118.608, 136.611, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 34 16.00 P 82 15.00 Mg 2 11.99 O 2736 8.00 N 2365 7.00 C 8173 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: 1.12 Conformation dependent library (CDL) restraints added in 426.5 milliseconds 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2812 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 17 sheets defined 43.4% alpha, 17.9% beta 39 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'C' and resid 42 through 56 removed outlier: 3.831A pdb=" N LEU C 47 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 104 Processing helix chain 'C' and resid 128 through 141 Processing helix chain 'C' and resid 143 through 151 removed outlier: 4.345A pdb=" N ARG C 149 " --> pdb=" O GLY C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 164 Processing helix chain 'C' and resid 165 through 178 Processing helix chain 'C' and resid 180 through 201 Processing helix chain 'C' and resid 876 through 887 Processing helix chain 'C' and resid 889 through 891 No H-bonds generated for 'chain 'C' and resid 889 through 891' Processing helix chain 'C' and resid 892 through 900 Processing helix chain 'C' and resid 900 through 919 removed outlier: 3.591A pdb=" N LEU C 910 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 951 removed outlier: 3.544A pdb=" N THR C 950 " --> pdb=" O ASP C 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 951 " --> pdb=" O THR C 948 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 947 through 951' Processing helix chain 'C' and resid 952 through 970 Processing helix chain 'C' and resid 985 through 989 removed outlier: 3.801A pdb=" N THR C 988 " --> pdb=" O GLY C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1006 removed outlier: 3.615A pdb=" N ASP C 995 " --> pdb=" O SER C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1024 Processing helix chain 'C' and resid 1042 through 1046 Processing helix chain 'D' and resid 42 through 56 removed outlier: 3.865A pdb=" N LEU D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 104 Processing helix chain 'D' and resid 128 through 141 Processing helix chain 'D' and resid 143 through 151 removed outlier: 4.263A pdb=" N ARG D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 178 removed outlier: 3.741A pdb=" N LEU D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 199 removed outlier: 3.634A pdb=" N GLN D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 875 through 887 Processing helix chain 'D' and resid 889 through 891 No H-bonds generated for 'chain 'D' and resid 889 through 891' Processing helix chain 'D' and resid 892 through 900 removed outlier: 3.665A pdb=" N ARG D 896 " --> pdb=" O GLY D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 919 removed outlier: 4.507A pdb=" N ARG D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 918 " --> pdb=" O GLN D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 949 through 951 No H-bonds generated for 'chain 'D' and resid 949 through 951' Processing helix chain 'D' and resid 952 through 971 removed outlier: 4.052A pdb=" N VAL D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) Processing helix chain 'D' and resid 990 through 1006 removed outlier: 4.528A pdb=" N THR D 996 " --> pdb=" O GLU D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1018 through 1024 removed outlier: 4.107A pdb=" N GLU D1022 " --> pdb=" O GLU D1018 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG D1023 " --> pdb=" O ALA D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1043 through 1046 Processing helix chain 'A' and resid 20 through 39 Processing helix chain 'A' and resid 56 through 70 Processing helix chain 'A' and resid 86 through 93 removed outlier: 4.365A pdb=" N SER A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 99 removed outlier: 3.836A pdb=" N PHE A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 removed outlier: 3.650A pdb=" N ILE A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 173 removed outlier: 3.598A pdb=" N GLN A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 285 through 294 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 319 through 328 removed outlier: 3.527A pdb=" N LYS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 372 removed outlier: 3.582A pdb=" N LEU A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 394 removed outlier: 3.888A pdb=" N GLN A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ARG A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 39 removed outlier: 3.750A pdb=" N TRP B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 74 removed outlier: 3.573A pdb=" N ARG B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN B 72 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 99 removed outlier: 4.084A pdb=" N PHE B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 154 through 173 Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.744A pdb=" N PHE B 212 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 removed outlier: 3.600A pdb=" N GLU B 248 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS B 249 " --> pdb=" O PHE B 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 249' Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.518A pdb=" N ALA B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 316 through 329 removed outlier: 4.583A pdb=" N ARG B 322 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 373 removed outlier: 3.841A pdb=" N LEU B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 395 removed outlier: 4.529A pdb=" N ARG B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 14 through 21 removed outlier: 6.561A pdb=" N GLY C 16 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU C 84 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU C 6 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU C 82 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU C 8 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU C 80 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASN C 10 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU C 78 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 116 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.522A pdb=" N LEU C 980 " --> pdb=" O GLY C1012 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ILE C1014 " --> pdb=" O LEU C 980 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU C 982 " --> pdb=" O ILE C1014 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 922 through 926 Processing sheet with id=AA4, first strand: chain 'C' and resid 1031 through 1032 Processing sheet with id=AA5, first strand: chain 'D' and resid 14 through 21 removed outlier: 6.610A pdb=" N GLY D 16 " --> pdb=" O ASN D 10 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE D 3 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU D 86 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU D 11 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N GLU D 78 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU D 116 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.132A pdb=" N PHE D 33 " --> pdb=" O VAL D1013 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA D 34 " --> pdb=" O ILE D1028 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL D1030 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR D 36 " --> pdb=" O VAL D1030 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N LYS D1032 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 924 through 926 Processing sheet with id=AA8, first strand: chain 'A' and resid 102 through 105 removed outlier: 6.429A pdb=" N LEU A 77 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL A 105 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 79 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE A 43 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU A 80 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 45 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG A 2 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE A 44 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 4 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ALA A 46 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR A 6 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 255 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASN A 270 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A 257 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL A 268 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR A 259 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 14 through 15 Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AB2, first strand: chain 'A' and resid 180 through 182 removed outlier: 6.827A pdb=" N ALA A 181 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL A 235 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 229 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 279 through 284 removed outlier: 6.754A pdb=" N VAL A 305 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL A 335 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A 307 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 337 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.580A pdb=" N LEU B 77 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL B 105 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL B 79 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 43 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N LEU B 80 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL B 45 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG B 2 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE B 44 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 4 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA B 46 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N THR B 6 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL B 255 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN B 270 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 257 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL B 268 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR B 259 " --> pdb=" O GLU B 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 14 through 15 Processing sheet with id=AB6, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB7, first strand: chain 'B' and resid 180 through 183 removed outlier: 6.518A pdb=" N ALA B 181 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE B 218 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 279 through 284 removed outlier: 3.587A pdb=" N GLY B 284 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N VAL B 305 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N LEU B 337 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU B 307 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG B 339 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE B 309 " --> pdb=" O ARG B 339 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1470 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4039 1.34 - 1.46: 2454 1.46 - 1.57: 7091 1.57 - 1.69: 160 1.69 - 1.81: 52 Bond restraints: 13796 Sorted by residual: bond pdb=" C4 ADP D1101 " pdb=" C5 ADP D1101 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 ADP C1101 " pdb=" C5 ADP C1101 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C5 ADP D1101 " pdb=" C6 ADP D1101 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C5 ADP C1101 " pdb=" C6 ADP C1101 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" N ILE A 223 " pdb=" CA ILE A 223 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 1.01e+01 ... (remaining 13791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 18839 2.69 - 5.37: 182 5.37 - 8.06: 18 8.06 - 10.75: 6 10.75 - 13.44: 4 Bond angle restraints: 19049 Sorted by residual: angle pdb=" C ASN D 12 " pdb=" CA ASN D 12 " pdb=" CB ASN D 12 " ideal model delta sigma weight residual 116.54 109.97 6.57 1.15e+00 7.56e-01 3.26e+01 angle pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" O GLY A 221 " ideal model delta sigma weight residual 121.61 115.82 5.79 1.05e+00 9.07e-01 3.04e+01 angle pdb=" CA GLY B 221 " pdb=" C GLY B 221 " pdb=" O GLY B 221 " ideal model delta sigma weight residual 121.78 117.04 4.74 9.10e-01 1.21e+00 2.71e+01 angle pdb=" PA ADP C1101 " pdb=" O3A ADP C1101 " pdb=" PB ADP C1101 " ideal model delta sigma weight residual 120.50 133.94 -13.44 3.00e+00 1.11e-01 2.01e+01 angle pdb=" PA ADP D1101 " pdb=" O3A ADP D1101 " pdb=" PB ADP D1101 " ideal model delta sigma weight residual 120.50 133.52 -13.02 3.00e+00 1.11e-01 1.88e+01 ... (remaining 19044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.46: 7608 34.46 - 68.93: 442 68.93 - 103.39: 19 103.39 - 137.85: 5 137.85 - 172.32: 2 Dihedral angle restraints: 8076 sinusoidal: 3741 harmonic: 4335 Sorted by residual: dihedral pdb=" C5' ADP D1101 " pdb=" O5' ADP D1101 " pdb=" PA ADP D1101 " pdb=" O2A ADP D1101 " ideal model delta sinusoidal sigma weight residual -60.00 66.10 -126.09 1 2.00e+01 2.50e-03 3.81e+01 dihedral pdb=" O2A ADP D1101 " pdb=" O3A ADP D1101 " pdb=" PA ADP D1101 " pdb=" PB ADP D1101 " ideal model delta sinusoidal sigma weight residual -60.00 65.40 -125.40 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O1B ADP D1101 " pdb=" O3A ADP D1101 " pdb=" PB ADP D1101 " pdb=" PA ADP D1101 " ideal model delta sinusoidal sigma weight residual -60.00 57.79 -117.80 1 2.00e+01 2.50e-03 3.52e+01 ... (remaining 8073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1885 0.058 - 0.115: 277 0.115 - 0.173: 24 0.173 - 0.231: 3 0.231 - 0.288: 4 Chirality restraints: 2193 Sorted by residual: chirality pdb=" CA TYR A 237 " pdb=" N TYR A 237 " pdb=" C TYR A 237 " pdb=" CB TYR A 237 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C3' ADP C1101 " pdb=" C2' ADP C1101 " pdb=" C4' ADP C1101 " pdb=" O3' ADP C1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C3' ADP D1101 " pdb=" C2' ADP D1101 " pdb=" C4' ADP D1101 " pdb=" O3' ADP D1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2190 not shown) Planarity restraints: 2183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 58 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO D 59 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 47 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C GLY A 47 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY A 47 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP A 48 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 41 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C ALA D 41 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA D 41 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY D 42 " 0.008 2.00e-02 2.50e+03 ... (remaining 2180 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 12 2.18 - 2.86: 4464 2.86 - 3.54: 18886 3.54 - 4.22: 31260 4.22 - 4.90: 53778 Nonbonded interactions: 108400 Sorted by model distance: nonbonded pdb=" OD2 ASP A 48 " pdb="MN MN A 501 " model vdw 1.498 2.320 nonbonded pdb=" OD2 ASP A 48 " pdb="MN MN A 502 " model vdw 1.600 2.320 nonbonded pdb=" ND2 ASN A 83 " pdb=" OP2 DC F 55 " model vdw 1.761 3.120 nonbonded pdb=" OD1 ASN B 83 " pdb="MN MN B 502 " model vdw 1.806 2.320 nonbonded pdb=" O3B ADP C1101 " pdb="MG MG C1102 " model vdw 1.816 2.170 ... (remaining 108395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 137 or resid 153 through 343 or resid 356 throug \ h 502)) selection = (chain 'B' and (resid 1 through 189 or resid 204 through 502)) } ncs_group { reference = (chain 'C' and (resid 1 through 200 or resid 875 through 1102)) selection = (chain 'D' and (resid 1 through 200 or resid 875 through 1102)) } 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=0.00 max=1.00 mean=0.99 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: 2.310 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.000 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 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 : 0.004 0.109 13796 Z= 0.241 Angle : 0.699 13.436 19049 Z= 0.396 Chirality : 0.042 0.288 2193 Planarity : 0.003 0.048 2183 Dihedral : 18.983 172.318 5264 Min Nonbonded Distance : 1.498 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.08 % Allowed : 0.31 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.79 (0.23), residues: 1479 helix: 1.66 (0.23), residues: 547 sheet: 0.38 (0.34), residues: 231 loop : -0.29 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 976 TYR 0.014 0.001 TYR C 882 PHE 0.014 0.001 PHE C 895 TRP 0.010 0.001 TRP A 9 HIS 0.009 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00417 (13796) covalent geometry : angle 0.69945 (19049) hydrogen bonds : bond 0.14864 ( 621) hydrogen bonds : angle 5.72061 ( 1674) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 598 time to evaluate : 0.412 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 189 VAL cc_start: 0.8396 (t) cc_final: 0.8007 (t) REVERT: C 193 HIS cc_start: 0.7134 (t70) cc_final: 0.6675 (t70) REVERT: C 1033 ILE cc_start: 0.6499 (mm) cc_final: 0.6246 (mp) REVERT: D 52 LEU cc_start: 0.7449 (tp) cc_final: 0.7076 (tp) REVERT: A 93 SER cc_start: 0.7255 (m) cc_final: 0.6489 (p) REVERT: B 246 PHE cc_start: 0.6214 (m-80) cc_final: 0.5719 (m-10) REVERT: B 306 TRP cc_start: 0.7409 (m-10) cc_final: 0.6825 (m-10) outliers start: 1 outliers final: 1 residues processed: 598 average time/residue: 0.1251 time to fit residues: 105.3789 Evaluate side-chains 394 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 393 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1005 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1016 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN A 256 HIS ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 HIS ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.087545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.058818 restraints weight = 43535.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.061275 restraints weight = 25278.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.062993 restraints weight = 17427.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.064253 restraints weight = 13353.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.065114 restraints weight = 10967.566| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13796 Z= 0.194 Angle : 0.846 15.509 19049 Z= 0.407 Chirality : 0.047 0.235 2193 Planarity : 0.005 0.076 2183 Dihedral : 21.183 174.179 2467 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.30 % Allowed : 18.29 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.42 (0.22), residues: 1479 helix: 1.32 (0.22), residues: 541 sheet: -0.03 (0.31), residues: 276 loop : -0.39 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 102 TYR 0.031 0.003 TYR B 237 PHE 0.039 0.003 PHE C 895 TRP 0.026 0.003 TRP C 880 HIS 0.010 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00421 (13796) covalent geometry : angle 0.84636 (19049) hydrogen bonds : bond 0.04939 ( 621) hydrogen bonds : angle 5.02887 ( 1674) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 451 time to evaluate : 0.476 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: C 3 ILE cc_start: 0.9561 (mm) cc_final: 0.9171 (tp) REVERT: C 12 ASN cc_start: 0.9396 (m-40) cc_final: 0.9100 (t0) REVERT: C 54 LEU cc_start: 0.9760 (mt) cc_final: 0.9544 (mt) REVERT: C 74 ARG cc_start: 0.8868 (mmp80) cc_final: 0.8168 (mmp-170) REVERT: C 82 GLU cc_start: 0.8481 (tt0) cc_final: 0.8262 (tm-30) REVERT: C 85 PHE cc_start: 0.9517 (p90) cc_final: 0.9233 (p90) REVERT: C 95 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8308 (t80) REVERT: C 123 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8397 (pptt) REVERT: C 135 LEU cc_start: 0.9649 (mm) cc_final: 0.9407 (mm) REVERT: C 182 TYR cc_start: 0.8876 (m-80) cc_final: 0.8365 (m-80) REVERT: C 189 VAL cc_start: 0.9474 (t) cc_final: 0.8895 (t) REVERT: C 193 HIS cc_start: 0.8899 (t70) cc_final: 0.8626 (t70) REVERT: C 880 TRP cc_start: 0.9100 (m100) cc_final: 0.8512 (m100) REVERT: C 882 TYR cc_start: 0.8255 (m-80) cc_final: 0.8030 (m-80) REVERT: C 893 ASP cc_start: 0.8597 (m-30) cc_final: 0.8066 (m-30) REVERT: C 895 PHE cc_start: 0.9036 (t80) cc_final: 0.8292 (t80) REVERT: C 902 LEU cc_start: 0.9171 (mm) cc_final: 0.8388 (tp) REVERT: C 906 ASN cc_start: 0.9193 (m110) cc_final: 0.8655 (m110) REVERT: C 955 GLU cc_start: 0.9206 (mp0) cc_final: 0.8949 (mp0) REVERT: C 973 HIS cc_start: 0.9253 (p90) cc_final: 0.8934 (p90) REVERT: C 1016 HIS cc_start: 0.7644 (m170) cc_final: 0.7083 (m170) REVERT: C 1020 MET cc_start: 0.8659 (mmt) cc_final: 0.8310 (mmm) REVERT: C 1045 PHE cc_start: 0.8954 (m-80) cc_final: 0.8142 (m-80) REVERT: D 1 MET cc_start: 0.7753 (tmm) cc_final: 0.7539 (tmm) REVERT: D 12 ASN cc_start: 0.9298 (t0) cc_final: 0.8868 (t0) REVERT: D 55 TYR cc_start: 0.8558 (m-10) cc_final: 0.8011 (m-10) REVERT: D 162 LEU cc_start: 0.9443 (mt) cc_final: 0.9144 (mp) REVERT: D 165 LYS cc_start: 0.9473 (mmmt) cc_final: 0.9251 (mtpt) REVERT: D 188 MET cc_start: 0.9080 (ptp) cc_final: 0.8773 (ptp) REVERT: D 190 PHE cc_start: 0.9165 (t80) cc_final: 0.8904 (t80) REVERT: D 194 LYS cc_start: 0.9557 (tttt) cc_final: 0.9349 (pttp) REVERT: D 896 ARG cc_start: 0.8467 (ttm110) cc_final: 0.7812 (mtm110) REVERT: D 914 GLN cc_start: 0.9502 (tp40) cc_final: 0.9062 (tp-100) REVERT: D 919 HIS cc_start: 0.8167 (t-170) cc_final: 0.7765 (t70) REVERT: D 941 GLN cc_start: 0.9141 (mt0) cc_final: 0.8737 (pt0) REVERT: D 986 PHE cc_start: 0.6946 (m-80) cc_final: 0.6701 (m-80) REVERT: D 989 LEU cc_start: 0.9705 (mt) cc_final: 0.9311 (tp) REVERT: D 1011 ILE cc_start: 0.9470 (OUTLIER) cc_final: 0.8796 (mm) REVERT: A 10 HIS cc_start: 0.9192 (m-70) cc_final: 0.8819 (m-70) REVERT: A 18 LYS cc_start: 0.9220 (mmmt) cc_final: 0.8821 (mmtm) REVERT: A 65 ARG cc_start: 0.9123 (tpm170) cc_final: 0.8864 (tpp-160) REVERT: A 93 SER cc_start: 0.9519 (m) cc_final: 0.8788 (p) REVERT: A 149 LYS cc_start: 0.9662 (mttm) cc_final: 0.9211 (mttt) REVERT: A 212 PHE cc_start: 0.8152 (m-80) cc_final: 0.7800 (m-80) REVERT: A 232 MET cc_start: 0.9187 (mmm) cc_final: 0.8928 (mpp) REVERT: A 242 ILE cc_start: 0.9302 (tp) cc_final: 0.9088 (tp) REVERT: A 244 LEU cc_start: 0.9230 (mt) cc_final: 0.8707 (mt) REVERT: A 253 LYS cc_start: 0.8237 (mmmm) cc_final: 0.7774 (mmmm) REVERT: A 306 TRP cc_start: 0.8852 (m-10) cc_final: 0.8286 (m-10) REVERT: A 318 HIS cc_start: 0.8560 (m170) cc_final: 0.8261 (m90) REVERT: A 339 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8883 (ttp80) REVERT: A 366 PHE cc_start: 0.9041 (t80) cc_final: 0.8620 (t80) REVERT: B 15 PHE cc_start: 0.8748 (t80) cc_final: 0.7943 (t80) REVERT: B 16 TYR cc_start: 0.8312 (m-80) cc_final: 0.8037 (m-10) REVERT: B 18 LYS cc_start: 0.8604 (mtmm) cc_final: 0.8079 (ptpt) REVERT: B 75 CYS cc_start: 0.8088 (m) cc_final: 0.7442 (m) REVERT: B 207 PHE cc_start: 0.8310 (t80) cc_final: 0.7193 (t80) REVERT: B 257 LEU cc_start: 0.8578 (pp) cc_final: 0.8273 (pp) REVERT: B 271 LEU cc_start: 0.9040 (mm) cc_final: 0.8769 (mm) REVERT: B 317 LEU cc_start: 0.9374 (tp) cc_final: 0.8939 (tp) REVERT: B 321 GLN cc_start: 0.9080 (mt0) cc_final: 0.8643 (mt0) REVERT: B 336 LEU cc_start: 0.8381 (mt) cc_final: 0.8076 (mt) REVERT: B 366 PHE cc_start: 0.9216 (t80) cc_final: 0.8901 (t80) REVERT: B 383 LEU cc_start: 0.9320 (mt) cc_final: 0.9068 (mm) REVERT: B 386 LEU cc_start: 0.9497 (mt) cc_final: 0.9083 (pp) outliers start: 42 outliers final: 23 residues processed: 466 average time/residue: 0.1041 time to fit residues: 71.4420 Evaluate side-chains 420 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 393 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 1011 ILE Chi-restraints excluded: chain D residue 1041 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 200 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 50 optimal weight: 0.0870 chunk 88 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 HIS ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.084157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.056798 restraints weight = 44567.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.059119 restraints weight = 25210.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.060710 restraints weight = 17162.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.061872 restraints weight = 13049.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.062659 restraints weight = 10692.582| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13796 Z= 0.157 Angle : 0.808 13.522 19049 Z= 0.385 Chirality : 0.045 0.201 2193 Planarity : 0.005 0.076 2183 Dihedral : 21.154 176.903 2467 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.22 % Allowed : 21.98 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.38 (0.22), residues: 1479 helix: 1.20 (0.22), residues: 539 sheet: 0.20 (0.33), residues: 252 loop : -0.43 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 149 TYR 0.026 0.003 TYR B 217 PHE 0.027 0.003 PHE D 33 TRP 0.023 0.003 TRP B 296 HIS 0.025 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00348 (13796) covalent geometry : angle 0.80774 (19049) hydrogen bonds : bond 0.04444 ( 621) hydrogen bonds : angle 4.83909 ( 1674) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 394 time to evaluate : 0.558 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: C 12 ASN cc_start: 0.9386 (m-40) cc_final: 0.9037 (m-40) REVERT: C 45 THR cc_start: 0.9763 (m) cc_final: 0.9538 (p) REVERT: C 54 LEU cc_start: 0.9763 (mt) cc_final: 0.9524 (mt) REVERT: C 72 MET cc_start: 0.8238 (ppp) cc_final: 0.7478 (ppp) REVERT: C 74 ARG cc_start: 0.8837 (mmp80) cc_final: 0.8482 (mmp80) REVERT: C 123 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8386 (pptt) REVERT: C 135 LEU cc_start: 0.9666 (mm) cc_final: 0.9238 (tp) REVERT: C 182 TYR cc_start: 0.8842 (m-80) cc_final: 0.8243 (m-80) REVERT: C 188 MET cc_start: 0.9174 (mmt) cc_final: 0.8961 (tmm) REVERT: C 189 VAL cc_start: 0.9470 (t) cc_final: 0.9015 (t) REVERT: C 193 HIS cc_start: 0.9037 (t70) cc_final: 0.8737 (t70) REVERT: C 880 TRP cc_start: 0.9088 (m100) cc_final: 0.8544 (m100) REVERT: C 882 TYR cc_start: 0.8278 (m-80) cc_final: 0.8063 (m-80) REVERT: C 893 ASP cc_start: 0.8732 (m-30) cc_final: 0.8355 (m-30) REVERT: C 895 PHE cc_start: 0.9045 (t80) cc_final: 0.8242 (t80) REVERT: C 897 LYS cc_start: 0.9344 (mtmt) cc_final: 0.8932 (mmtp) REVERT: C 902 LEU cc_start: 0.9136 (mm) cc_final: 0.8378 (tp) REVERT: C 906 ASN cc_start: 0.9139 (m110) cc_final: 0.8604 (m110) REVERT: C 940 TRP cc_start: 0.9457 (m-10) cc_final: 0.8828 (m-10) REVERT: C 955 GLU cc_start: 0.9225 (mp0) cc_final: 0.8956 (mp0) REVERT: C 973 HIS cc_start: 0.9212 (p90) cc_final: 0.8922 (p90) REVERT: C 984 GLU cc_start: 0.8584 (tp30) cc_final: 0.7910 (tp30) REVERT: D 12 ASN cc_start: 0.9351 (m-40) cc_final: 0.8780 (t0) REVERT: D 55 TYR cc_start: 0.8675 (m-10) cc_final: 0.8473 (m-10) REVERT: D 92 TYR cc_start: 0.8345 (m-10) cc_final: 0.7098 (m-10) REVERT: D 165 LYS cc_start: 0.9488 (mmmt) cc_final: 0.9126 (mmmm) REVERT: D 188 MET cc_start: 0.9005 (ptp) cc_final: 0.8733 (ttm) REVERT: D 194 LYS cc_start: 0.9559 (tttt) cc_final: 0.9278 (ptpp) REVERT: D 197 ARG cc_start: 0.9476 (tpt90) cc_final: 0.9140 (tpt90) REVERT: D 884 ASN cc_start: 0.8829 (t0) cc_final: 0.8622 (t0) REVERT: D 896 ARG cc_start: 0.8517 (ttm110) cc_final: 0.7840 (mtm110) REVERT: D 914 GLN cc_start: 0.9464 (tp40) cc_final: 0.9079 (tp-100) REVERT: D 919 HIS cc_start: 0.8061 (t-170) cc_final: 0.7656 (t70) REVERT: D 941 GLN cc_start: 0.9195 (mt0) cc_final: 0.8770 (pt0) REVERT: D 989 LEU cc_start: 0.9681 (mt) cc_final: 0.9264 (tp) REVERT: D 1011 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.8757 (mm) REVERT: A 18 LYS cc_start: 0.9336 (mmmt) cc_final: 0.8976 (mmtm) REVERT: A 58 TYR cc_start: 0.9149 (p90) cc_final: 0.8770 (p90) REVERT: A 65 ARG cc_start: 0.9116 (tpm170) cc_final: 0.8812 (tpp-160) REVERT: A 93 SER cc_start: 0.9482 (m) cc_final: 0.8959 (p) REVERT: A 212 PHE cc_start: 0.8162 (m-80) cc_final: 0.7864 (m-80) REVERT: A 244 LEU cc_start: 0.9250 (mt) cc_final: 0.8963 (mt) REVERT: A 246 PHE cc_start: 0.8734 (m-80) cc_final: 0.7541 (m-80) REVERT: A 253 LYS cc_start: 0.8245 (mmmm) cc_final: 0.7731 (mmmm) REVERT: A 306 TRP cc_start: 0.8827 (m-10) cc_final: 0.7967 (m-10) REVERT: A 366 PHE cc_start: 0.9108 (t80) cc_final: 0.8525 (t80) REVERT: B 15 PHE cc_start: 0.8814 (t80) cc_final: 0.7866 (t80) REVERT: B 16 TYR cc_start: 0.8312 (m-80) cc_final: 0.8063 (m-10) REVERT: B 18 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8112 (ptpt) REVERT: B 33 GLU cc_start: 0.9439 (tt0) cc_final: 0.9113 (pt0) REVERT: B 75 CYS cc_start: 0.8179 (m) cc_final: 0.7626 (m) REVERT: B 169 CYS cc_start: 0.9583 (OUTLIER) cc_final: 0.9379 (p) REVERT: B 207 PHE cc_start: 0.9080 (t80) cc_final: 0.8419 (t80) REVERT: B 282 LEU cc_start: 0.8830 (mt) cc_final: 0.8452 (mp) REVERT: B 317 LEU cc_start: 0.9371 (tp) cc_final: 0.8974 (tp) REVERT: B 321 GLN cc_start: 0.9093 (mt0) cc_final: 0.8633 (mt0) REVERT: B 366 PHE cc_start: 0.9288 (t80) cc_final: 0.8902 (t80) REVERT: B 373 GLU cc_start: 0.8906 (tp30) cc_final: 0.8346 (tm-30) outliers start: 41 outliers final: 30 residues processed: 404 average time/residue: 0.1078 time to fit residues: 65.2074 Evaluate side-chains 414 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 381 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 986 PHE Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1011 ILE Chi-restraints excluded: chain D residue 1036 LEU Chi-restraints excluded: chain D residue 1041 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 200 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 77 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 906 ASN ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.083282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055893 restraints weight = 45236.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.058186 restraints weight = 25878.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.059779 restraints weight = 17668.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.060903 restraints weight = 13461.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.061692 restraints weight = 11066.674| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13796 Z= 0.157 Angle : 0.787 13.157 19049 Z= 0.375 Chirality : 0.046 0.441 2193 Planarity : 0.004 0.046 2183 Dihedral : 21.144 178.734 2467 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.61 % Allowed : 22.61 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.41 (0.22), residues: 1479 helix: 1.03 (0.22), residues: 548 sheet: 0.40 (0.34), residues: 242 loop : -0.31 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 74 TYR 0.027 0.002 TYR B 165 PHE 0.025 0.002 PHE C 190 TRP 0.026 0.002 TRP A 296 HIS 0.019 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00339 (13796) covalent geometry : angle 0.78691 (19049) hydrogen bonds : bond 0.04259 ( 621) hydrogen bonds : angle 4.83140 ( 1674) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 390 time to evaluate : 0.492 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: C 12 ASN cc_start: 0.9413 (m-40) cc_final: 0.9000 (m-40) REVERT: C 27 PHE cc_start: 0.9063 (m-10) cc_final: 0.8838 (m-80) REVERT: C 45 THR cc_start: 0.9742 (m) cc_final: 0.9532 (p) REVERT: C 54 LEU cc_start: 0.9753 (mt) cc_final: 0.9496 (mt) REVERT: C 72 MET cc_start: 0.8340 (ppp) cc_final: 0.7505 (ppp) REVERT: C 74 ARG cc_start: 0.8845 (mmp80) cc_final: 0.8429 (mmp80) REVERT: C 95 PHE cc_start: 0.9094 (t80) cc_final: 0.8476 (t80) REVERT: C 135 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8878 (mt) REVERT: C 182 TYR cc_start: 0.8866 (m-80) cc_final: 0.8233 (m-80) REVERT: C 189 VAL cc_start: 0.9446 (t) cc_final: 0.8606 (t) REVERT: C 193 HIS cc_start: 0.9036 (t70) cc_final: 0.7859 (t70) REVERT: C 880 TRP cc_start: 0.8994 (m100) cc_final: 0.8361 (m100) REVERT: C 884 ASN cc_start: 0.8931 (t0) cc_final: 0.8245 (m110) REVERT: C 893 ASP cc_start: 0.8802 (m-30) cc_final: 0.8427 (m-30) REVERT: C 895 PHE cc_start: 0.9095 (t80) cc_final: 0.8443 (t80) REVERT: C 897 LYS cc_start: 0.9347 (mtmt) cc_final: 0.8956 (mmtp) REVERT: C 902 LEU cc_start: 0.9094 (mm) cc_final: 0.8312 (tp) REVERT: C 906 ASN cc_start: 0.9154 (m110) cc_final: 0.8625 (m-40) REVERT: C 955 GLU cc_start: 0.9236 (mp0) cc_final: 0.8936 (mp0) REVERT: C 973 HIS cc_start: 0.9189 (p90) cc_final: 0.8955 (p90) REVERT: C 983 ASP cc_start: 0.7864 (t0) cc_final: 0.6768 (t0) REVERT: C 984 GLU cc_start: 0.8525 (tp30) cc_final: 0.8047 (mm-30) REVERT: C 1014 ILE cc_start: 0.9183 (mm) cc_final: 0.8731 (mm) REVERT: C 1029 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8763 (mppt) REVERT: C 1045 PHE cc_start: 0.9060 (m-80) cc_final: 0.8259 (m-80) REVERT: D 12 ASN cc_start: 0.9329 (m-40) cc_final: 0.8819 (t0) REVERT: D 55 TYR cc_start: 0.8768 (m-10) cc_final: 0.8531 (m-10) REVERT: D 72 MET cc_start: 0.7971 (ttt) cc_final: 0.7246 (tpt) REVERT: D 155 GLN cc_start: 0.8734 (pm20) cc_final: 0.8412 (pm20) REVERT: D 165 LYS cc_start: 0.9482 (mmmt) cc_final: 0.9121 (mmmm) REVERT: D 194 LYS cc_start: 0.9543 (tttt) cc_final: 0.9220 (ptpp) REVERT: D 884 ASN cc_start: 0.8926 (t0) cc_final: 0.8671 (t0) REVERT: D 894 LYS cc_start: 0.9291 (ttpt) cc_final: 0.9049 (ptmt) REVERT: D 896 ARG cc_start: 0.8518 (ttm110) cc_final: 0.7819 (mtm110) REVERT: D 914 GLN cc_start: 0.9440 (tp40) cc_final: 0.9200 (tm-30) REVERT: D 919 HIS cc_start: 0.8136 (t-170) cc_final: 0.7407 (t-170) REVERT: D 983 ASP cc_start: 0.8078 (t0) cc_final: 0.7343 (t0) REVERT: D 989 LEU cc_start: 0.9663 (mt) cc_final: 0.9287 (tp) REVERT: A 18 LYS cc_start: 0.9385 (mmmt) cc_final: 0.9073 (mmtm) REVERT: A 58 TYR cc_start: 0.9207 (p90) cc_final: 0.8845 (p90) REVERT: A 65 ARG cc_start: 0.9120 (tpm170) cc_final: 0.8822 (tpm170) REVERT: A 93 SER cc_start: 0.9516 (m) cc_final: 0.9069 (p) REVERT: A 149 LYS cc_start: 0.9706 (mttm) cc_final: 0.9227 (mttm) REVERT: A 212 PHE cc_start: 0.8171 (m-80) cc_final: 0.7921 (m-80) REVERT: A 232 MET cc_start: 0.9237 (mmm) cc_final: 0.8971 (mpp) REVERT: A 253 LYS cc_start: 0.8232 (mmmm) cc_final: 0.7752 (mmmm) REVERT: A 279 MET cc_start: 0.8641 (mmm) cc_final: 0.7660 (tpt) REVERT: A 360 LEU cc_start: 0.8460 (mm) cc_final: 0.8236 (mm) REVERT: A 366 PHE cc_start: 0.9108 (t80) cc_final: 0.8460 (t80) REVERT: B 15 PHE cc_start: 0.8869 (t80) cc_final: 0.7924 (t80) REVERT: B 16 TYR cc_start: 0.8430 (m-80) cc_final: 0.8124 (m-10) REVERT: B 18 LYS cc_start: 0.8836 (mtmm) cc_final: 0.8482 (ptpt) REVERT: B 33 GLU cc_start: 0.9438 (tt0) cc_final: 0.9160 (pt0) REVERT: B 75 CYS cc_start: 0.8272 (m) cc_final: 0.7989 (m) REVERT: B 207 PHE cc_start: 0.9262 (t80) cc_final: 0.8923 (t80) REVERT: B 218 ILE cc_start: 0.9449 (mm) cc_final: 0.9156 (mp) REVERT: B 271 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8855 (mm) REVERT: B 317 LEU cc_start: 0.9404 (tp) cc_final: 0.8913 (tp) REVERT: B 321 GLN cc_start: 0.9098 (mt0) cc_final: 0.8653 (mt0) REVERT: B 357 LEU cc_start: 0.9365 (tp) cc_final: 0.8851 (tp) REVERT: B 366 PHE cc_start: 0.9278 (t80) cc_final: 0.8840 (t80) outliers start: 46 outliers final: 30 residues processed: 407 average time/residue: 0.1025 time to fit residues: 62.2306 Evaluate side-chains 408 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 375 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1029 LYS Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1014 ILE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 335 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 22 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 96 optimal weight: 0.0270 chunk 111 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 HIS ** B 318 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 = 0.3594 r_free = 0.3594 target = 0.083254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.056202 restraints weight = 45312.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.058508 restraints weight = 25869.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060111 restraints weight = 17644.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.061271 restraints weight = 13415.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062033 restraints weight = 10992.902| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13796 Z= 0.152 Angle : 0.790 14.679 19049 Z= 0.371 Chirality : 0.046 0.440 2193 Planarity : 0.004 0.055 2183 Dihedral : 21.101 179.656 2467 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.08 % Allowed : 23.31 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.40 (0.23), residues: 1479 helix: 0.96 (0.23), residues: 542 sheet: 0.22 (0.33), residues: 251 loop : -0.17 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 74 TYR 0.032 0.002 TYR C 882 PHE 0.029 0.002 PHE B 212 TRP 0.030 0.002 TRP A 296 HIS 0.014 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00331 (13796) covalent geometry : angle 0.78965 (19049) hydrogen bonds : bond 0.04061 ( 621) hydrogen bonds : angle 4.79757 ( 1674) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 385 time to evaluate : 0.516 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: C 12 ASN cc_start: 0.9424 (m-40) cc_final: 0.8979 (m-40) REVERT: C 27 PHE cc_start: 0.9093 (m-10) cc_final: 0.8874 (m-80) REVERT: C 45 THR cc_start: 0.9718 (m) cc_final: 0.9516 (p) REVERT: C 54 LEU cc_start: 0.9736 (mt) cc_final: 0.9439 (mt) REVERT: C 72 MET cc_start: 0.8287 (ppp) cc_final: 0.7514 (ppp) REVERT: C 74 ARG cc_start: 0.8761 (mmp80) cc_final: 0.8384 (mmp80) REVERT: C 82 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7749 (tm-30) REVERT: C 95 PHE cc_start: 0.9123 (t80) cc_final: 0.8511 (t80) REVERT: C 133 LEU cc_start: 0.9687 (mt) cc_final: 0.9456 (pp) REVERT: C 135 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.8889 (mt) REVERT: C 182 TYR cc_start: 0.8883 (m-80) cc_final: 0.8093 (m-80) REVERT: C 189 VAL cc_start: 0.9452 (t) cc_final: 0.8731 (t) REVERT: C 193 HIS cc_start: 0.8968 (t70) cc_final: 0.7766 (t70) REVERT: C 880 TRP cc_start: 0.8942 (m100) cc_final: 0.7912 (m100) REVERT: C 884 ASN cc_start: 0.8933 (t0) cc_final: 0.8006 (m-40) REVERT: C 893 ASP cc_start: 0.8798 (m-30) cc_final: 0.8471 (m-30) REVERT: C 895 PHE cc_start: 0.9121 (t80) cc_final: 0.8413 (t80) REVERT: C 897 LYS cc_start: 0.9347 (mtmt) cc_final: 0.8938 (mmtp) REVERT: C 902 LEU cc_start: 0.9080 (mm) cc_final: 0.8302 (tp) REVERT: C 906 ASN cc_start: 0.9126 (m110) cc_final: 0.8596 (m110) REVERT: C 955 GLU cc_start: 0.9237 (mp0) cc_final: 0.8924 (mp0) REVERT: C 983 ASP cc_start: 0.7875 (t0) cc_final: 0.6841 (t0) REVERT: C 984 GLU cc_start: 0.8338 (tp30) cc_final: 0.7916 (mm-30) REVERT: C 1014 ILE cc_start: 0.9268 (mm) cc_final: 0.8810 (mm) REVERT: C 1029 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8727 (mppt) REVERT: C 1045 PHE cc_start: 0.9133 (m-80) cc_final: 0.8808 (m-80) REVERT: D 12 ASN cc_start: 0.9306 (m-40) cc_final: 0.8808 (t0) REVERT: D 55 TYR cc_start: 0.8786 (m-10) cc_final: 0.8463 (m-10) REVERT: D 72 MET cc_start: 0.7922 (ttt) cc_final: 0.7211 (tpt) REVERT: D 74 ARG cc_start: 0.7362 (tmm-80) cc_final: 0.7097 (tmm-80) REVERT: D 155 GLN cc_start: 0.8751 (pm20) cc_final: 0.8367 (pm20) REVERT: D 194 LYS cc_start: 0.9547 (tttt) cc_final: 0.9253 (ptpp) REVERT: D 884 ASN cc_start: 0.8898 (t0) cc_final: 0.8616 (t0) REVERT: D 896 ARG cc_start: 0.8494 (ttm110) cc_final: 0.7776 (mtm110) REVERT: D 919 HIS cc_start: 0.8043 (t-170) cc_final: 0.7666 (t70) REVERT: D 975 THR cc_start: 0.9093 (m) cc_final: 0.8738 (p) REVERT: D 983 ASP cc_start: 0.8273 (t0) cc_final: 0.7455 (t0) REVERT: D 989 LEU cc_start: 0.9664 (mt) cc_final: 0.9289 (tp) REVERT: A 18 LYS cc_start: 0.9478 (mmmt) cc_final: 0.9227 (mmtm) REVERT: A 58 TYR cc_start: 0.9241 (p90) cc_final: 0.8899 (p90) REVERT: A 65 ARG cc_start: 0.9138 (tpm170) cc_final: 0.8849 (tpm170) REVERT: A 93 SER cc_start: 0.9521 (m) cc_final: 0.9094 (p) REVERT: A 149 LYS cc_start: 0.9706 (mttm) cc_final: 0.9231 (mttm) REVERT: A 212 PHE cc_start: 0.8188 (m-80) cc_final: 0.7910 (m-80) REVERT: A 232 MET cc_start: 0.9242 (mmm) cc_final: 0.8996 (mpp) REVERT: A 296 TRP cc_start: 0.9346 (m100) cc_final: 0.9035 (m100) REVERT: A 360 LEU cc_start: 0.8550 (mm) cc_final: 0.8307 (mm) REVERT: A 366 PHE cc_start: 0.9092 (t80) cc_final: 0.8222 (t80) REVERT: A 387 PHE cc_start: 0.9480 (t80) cc_final: 0.9242 (t80) REVERT: B 15 PHE cc_start: 0.8894 (t80) cc_final: 0.7876 (t80) REVERT: B 16 TYR cc_start: 0.8535 (m-80) cc_final: 0.8126 (m-10) REVERT: B 18 LYS cc_start: 0.8872 (mtmm) cc_final: 0.8486 (ptpt) REVERT: B 33 GLU cc_start: 0.9424 (tt0) cc_final: 0.9144 (pt0) REVERT: B 75 CYS cc_start: 0.8323 (m) cc_final: 0.8070 (m) REVERT: B 113 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8557 (tm-30) REVERT: B 207 PHE cc_start: 0.9190 (t80) cc_final: 0.8821 (t80) REVERT: B 223 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7640 (mm) REVERT: B 249 CYS cc_start: 0.8228 (m) cc_final: 0.7037 (m) REVERT: B 271 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8841 (mm) REVERT: B 279 MET cc_start: 0.8819 (mpp) cc_final: 0.7676 (ppp) REVERT: B 317 LEU cc_start: 0.9404 (tp) cc_final: 0.8924 (tp) REVERT: B 321 GLN cc_start: 0.9074 (mt0) cc_final: 0.8642 (mt0) REVERT: B 357 LEU cc_start: 0.9456 (tp) cc_final: 0.8900 (tp) REVERT: B 366 PHE cc_start: 0.9274 (t80) cc_final: 0.8824 (t80) outliers start: 52 outliers final: 37 residues processed: 404 average time/residue: 0.1027 time to fit residues: 61.6669 Evaluate side-chains 414 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 373 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1029 LYS Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1011 ILE Chi-restraints excluded: chain D residue 1014 ILE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 335 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 129 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.083444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.056399 restraints weight = 45121.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.058695 restraints weight = 25841.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.060295 restraints weight = 17642.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.061467 restraints weight = 13435.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.062275 restraints weight = 10990.921| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13796 Z= 0.143 Angle : 0.788 13.991 19049 Z= 0.368 Chirality : 0.045 0.388 2193 Planarity : 0.004 0.049 2183 Dihedral : 21.061 178.778 2467 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.85 % Allowed : 25.51 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.35 (0.23), residues: 1479 helix: 0.89 (0.23), residues: 542 sheet: 0.17 (0.33), residues: 258 loop : -0.17 (0.25), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 149 TYR 0.022 0.002 TYR B 217 PHE 0.024 0.002 PHE B 131 TRP 0.019 0.002 TRP D 96 HIS 0.010 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00311 (13796) covalent geometry : angle 0.78849 (19049) hydrogen bonds : bond 0.03909 ( 621) hydrogen bonds : angle 4.79380 ( 1674) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 385 time to evaluate : 0.530 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: C 12 ASN cc_start: 0.9432 (m-40) cc_final: 0.8992 (m-40) REVERT: C 27 PHE cc_start: 0.9158 (m-10) cc_final: 0.8944 (m-80) REVERT: C 54 LEU cc_start: 0.9733 (mt) cc_final: 0.9502 (mt) REVERT: C 82 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7762 (tm-30) REVERT: C 95 PHE cc_start: 0.9142 (t80) cc_final: 0.8544 (t80) REVERT: C 135 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.8913 (mt) REVERT: C 182 TYR cc_start: 0.8926 (m-80) cc_final: 0.8275 (m-80) REVERT: C 189 VAL cc_start: 0.9510 (t) cc_final: 0.8688 (t) REVERT: C 193 HIS cc_start: 0.8925 (t70) cc_final: 0.7972 (t-170) REVERT: C 880 TRP cc_start: 0.8947 (m100) cc_final: 0.8104 (m100) REVERT: C 884 ASN cc_start: 0.8916 (t0) cc_final: 0.8054 (m110) REVERT: C 893 ASP cc_start: 0.8946 (m-30) cc_final: 0.8462 (m-30) REVERT: C 895 PHE cc_start: 0.9157 (t80) cc_final: 0.8418 (t80) REVERT: C 897 LYS cc_start: 0.9331 (mtmt) cc_final: 0.8937 (mmtp) REVERT: C 902 LEU cc_start: 0.9052 (mm) cc_final: 0.8241 (tp) REVERT: C 906 ASN cc_start: 0.9135 (m110) cc_final: 0.8586 (m110) REVERT: C 919 HIS cc_start: 0.8097 (t70) cc_final: 0.7629 (t70) REVERT: C 940 TRP cc_start: 0.9441 (m-10) cc_final: 0.8807 (m-10) REVERT: C 955 GLU cc_start: 0.9279 (mp0) cc_final: 0.8941 (mp0) REVERT: C 1045 PHE cc_start: 0.9131 (m-80) cc_final: 0.8873 (m-80) REVERT: D 12 ASN cc_start: 0.9304 (m-40) cc_final: 0.8800 (t0) REVERT: D 55 TYR cc_start: 0.8732 (m-10) cc_final: 0.8354 (m-10) REVERT: D 72 MET cc_start: 0.7906 (ttt) cc_final: 0.7198 (tpt) REVERT: D 155 GLN cc_start: 0.8845 (pm20) cc_final: 0.8468 (pm20) REVERT: D 194 LYS cc_start: 0.9518 (tttt) cc_final: 0.8620 (ptpp) REVERT: D 894 LYS cc_start: 0.9311 (ttmt) cc_final: 0.9086 (ptmt) REVERT: D 896 ARG cc_start: 0.8462 (ttm110) cc_final: 0.7792 (mtm110) REVERT: D 919 HIS cc_start: 0.7977 (t-170) cc_final: 0.7587 (t70) REVERT: D 949 ARG cc_start: 0.8910 (mmm160) cc_final: 0.8622 (mmp80) REVERT: D 975 THR cc_start: 0.9124 (m) cc_final: 0.8763 (p) REVERT: D 989 LEU cc_start: 0.9653 (mt) cc_final: 0.9287 (tp) REVERT: A 58 TYR cc_start: 0.9248 (p90) cc_final: 0.8916 (p90) REVERT: A 65 ARG cc_start: 0.9146 (tpm170) cc_final: 0.8858 (tpm170) REVERT: A 93 SER cc_start: 0.9533 (m) cc_final: 0.9175 (p) REVERT: A 149 LYS cc_start: 0.9711 (mttm) cc_final: 0.9223 (mttm) REVERT: A 212 PHE cc_start: 0.8193 (m-80) cc_final: 0.7949 (m-80) REVERT: A 253 LYS cc_start: 0.8156 (mmmm) cc_final: 0.7763 (mmmm) REVERT: A 296 TRP cc_start: 0.9355 (m100) cc_final: 0.9010 (m100) REVERT: A 360 LEU cc_start: 0.8636 (mm) cc_final: 0.8391 (mm) REVERT: A 366 PHE cc_start: 0.9087 (t80) cc_final: 0.8205 (t80) REVERT: A 387 PHE cc_start: 0.9445 (t80) cc_final: 0.9166 (t80) REVERT: B 15 PHE cc_start: 0.8902 (t80) cc_final: 0.7846 (t80) REVERT: B 16 TYR cc_start: 0.8560 (m-80) cc_final: 0.8153 (m-10) REVERT: B 18 LYS cc_start: 0.8871 (mtmm) cc_final: 0.8469 (ptpt) REVERT: B 33 GLU cc_start: 0.9413 (tt0) cc_final: 0.9130 (pt0) REVERT: B 97 MET cc_start: 0.9236 (mmm) cc_final: 0.8923 (ppp) REVERT: B 207 PHE cc_start: 0.9207 (t80) cc_final: 0.8815 (t80) REVERT: B 223 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7534 (mm) REVERT: B 253 LYS cc_start: 0.8227 (mmmt) cc_final: 0.7794 (mmtp) REVERT: B 271 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8887 (mm) REVERT: B 317 LEU cc_start: 0.9379 (tp) cc_final: 0.8907 (tp) REVERT: B 321 GLN cc_start: 0.9015 (mt0) cc_final: 0.8574 (mt0) REVERT: B 357 LEU cc_start: 0.9472 (tp) cc_final: 0.8853 (pp) REVERT: B 366 PHE cc_start: 0.9274 (t80) cc_final: 0.8485 (t80) REVERT: B 387 PHE cc_start: 0.9423 (t80) cc_final: 0.9172 (t80) outliers start: 49 outliers final: 38 residues processed: 401 average time/residue: 0.1076 time to fit residues: 64.7834 Evaluate side-chains 408 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 367 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1014 ILE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 335 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 134 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 105 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 131 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 HIS B 318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.083929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.056600 restraints weight = 45227.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.058895 restraints weight = 26063.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.060502 restraints weight = 17886.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.061619 restraints weight = 13692.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.062402 restraints weight = 11293.072| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13796 Z= 0.139 Angle : 0.801 14.551 19049 Z= 0.371 Chirality : 0.046 0.407 2193 Planarity : 0.004 0.054 2183 Dihedral : 21.039 178.578 2467 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.53 % Allowed : 26.84 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.42 (0.23), residues: 1479 helix: 0.84 (0.23), residues: 543 sheet: 0.34 (0.33), residues: 260 loop : -0.08 (0.26), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 74 TYR 0.019 0.002 TYR C 55 PHE 0.017 0.002 PHE C 957 TRP 0.021 0.002 TRP C 96 HIS 0.008 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00305 (13796) covalent geometry : angle 0.80101 (19049) hydrogen bonds : bond 0.03837 ( 621) hydrogen bonds : angle 4.76117 ( 1674) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 387 time to evaluate : 0.492 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: C 12 ASN cc_start: 0.9346 (m-40) cc_final: 0.8966 (t0) REVERT: C 27 PHE cc_start: 0.9149 (m-10) cc_final: 0.8915 (m-80) REVERT: C 54 LEU cc_start: 0.9681 (mt) cc_final: 0.9322 (mt) REVERT: C 55 TYR cc_start: 0.8744 (m-80) cc_final: 0.8475 (m-10) REVERT: C 95 PHE cc_start: 0.9162 (t80) cc_final: 0.8568 (t80) REVERT: C 127 ASP cc_start: 0.8922 (p0) cc_final: 0.8333 (m-30) REVERT: C 133 LEU cc_start: 0.9682 (mt) cc_final: 0.9453 (pp) REVERT: C 135 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.8902 (mt) REVERT: C 155 GLN cc_start: 0.8073 (pm20) cc_final: 0.7497 (pm20) REVERT: C 182 TYR cc_start: 0.8918 (m-80) cc_final: 0.8258 (m-80) REVERT: C 189 VAL cc_start: 0.9514 (t) cc_final: 0.8682 (t) REVERT: C 193 HIS cc_start: 0.8942 (t70) cc_final: 0.7951 (t-170) REVERT: C 880 TRP cc_start: 0.9017 (m100) cc_final: 0.8220 (m100) REVERT: C 884 ASN cc_start: 0.8860 (t0) cc_final: 0.7883 (m110) REVERT: C 893 ASP cc_start: 0.8882 (m-30) cc_final: 0.8451 (m-30) REVERT: C 895 PHE cc_start: 0.9208 (t80) cc_final: 0.8566 (t80) REVERT: C 897 LYS cc_start: 0.9331 (mtmt) cc_final: 0.8900 (mmtp) REVERT: C 902 LEU cc_start: 0.9034 (mm) cc_final: 0.8304 (tp) REVERT: C 904 LEU cc_start: 0.9750 (tp) cc_final: 0.9472 (pp) REVERT: C 906 ASN cc_start: 0.9090 (m110) cc_final: 0.8613 (m110) REVERT: C 940 TRP cc_start: 0.9436 (m-10) cc_final: 0.8752 (m-10) REVERT: C 955 GLU cc_start: 0.9269 (mp0) cc_final: 0.8985 (mp0) REVERT: C 983 ASP cc_start: 0.7923 (t0) cc_final: 0.7108 (t0) REVERT: C 1045 PHE cc_start: 0.9159 (m-80) cc_final: 0.8867 (m-80) REVERT: D 12 ASN cc_start: 0.9311 (m-40) cc_final: 0.8982 (t0) REVERT: D 55 TYR cc_start: 0.8742 (m-80) cc_final: 0.8299 (m-10) REVERT: D 72 MET cc_start: 0.7846 (ttt) cc_final: 0.6267 (tpt) REVERT: D 95 PHE cc_start: 0.8994 (t80) cc_final: 0.8658 (t80) REVERT: D 155 GLN cc_start: 0.8858 (pm20) cc_final: 0.8552 (pm20) REVERT: D 890 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8270 (ttpt) REVERT: D 894 LYS cc_start: 0.9232 (ttmt) cc_final: 0.9016 (ptpt) REVERT: D 896 ARG cc_start: 0.8428 (ttm110) cc_final: 0.8057 (ttp-110) REVERT: D 919 HIS cc_start: 0.7950 (t-170) cc_final: 0.7218 (t70) REVERT: D 949 ARG cc_start: 0.8911 (mmm160) cc_final: 0.8605 (mmp80) REVERT: D 975 THR cc_start: 0.9176 (m) cc_final: 0.8790 (p) REVERT: D 986 PHE cc_start: 0.8024 (m-80) cc_final: 0.7774 (m-80) REVERT: D 989 LEU cc_start: 0.9654 (mt) cc_final: 0.9251 (tp) REVERT: D 1045 PHE cc_start: 0.8949 (m-80) cc_final: 0.8588 (m-80) REVERT: A 40 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8271 (p) REVERT: A 58 TYR cc_start: 0.9228 (p90) cc_final: 0.8894 (p90) REVERT: A 65 ARG cc_start: 0.9158 (tpm170) cc_final: 0.8867 (tpm170) REVERT: A 93 SER cc_start: 0.9516 (m) cc_final: 0.9222 (p) REVERT: A 149 LYS cc_start: 0.9721 (mttm) cc_final: 0.9231 (mttm) REVERT: A 212 PHE cc_start: 0.8279 (m-80) cc_final: 0.8040 (m-80) REVERT: A 253 LYS cc_start: 0.8071 (mmmm) cc_final: 0.7635 (mmmm) REVERT: A 296 TRP cc_start: 0.9348 (m100) cc_final: 0.8993 (m100) REVERT: A 360 LEU cc_start: 0.8658 (mm) cc_final: 0.8418 (mm) REVERT: A 366 PHE cc_start: 0.9115 (t80) cc_final: 0.8253 (t80) REVERT: A 387 PHE cc_start: 0.9415 (t80) cc_final: 0.9126 (t80) REVERT: B 15 PHE cc_start: 0.8896 (t80) cc_final: 0.7759 (t80) REVERT: B 16 TYR cc_start: 0.8533 (m-80) cc_final: 0.8067 (m-10) REVERT: B 33 GLU cc_start: 0.9404 (tt0) cc_final: 0.9119 (pt0) REVERT: B 50 PHE cc_start: 0.8268 (m-10) cc_final: 0.7968 (m-80) REVERT: B 165 TYR cc_start: 0.9480 (t80) cc_final: 0.9233 (t80) REVERT: B 207 PHE cc_start: 0.9198 (t80) cc_final: 0.8787 (t80) REVERT: B 271 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8921 (mm) REVERT: B 317 LEU cc_start: 0.9409 (tp) cc_final: 0.8958 (tp) REVERT: B 321 GLN cc_start: 0.9043 (mt0) cc_final: 0.8569 (mt0) REVERT: B 357 LEU cc_start: 0.9478 (tp) cc_final: 0.8853 (pp) REVERT: B 366 PHE cc_start: 0.9290 (t80) cc_final: 0.8486 (t80) REVERT: B 387 PHE cc_start: 0.9432 (t80) cc_final: 0.9172 (t80) outliers start: 45 outliers final: 33 residues processed: 403 average time/residue: 0.1054 time to fit residues: 63.7580 Evaluate side-chains 404 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 367 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 890 LYS Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 133 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 919 HIS ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 GLN ** B 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.081861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.055102 restraints weight = 46456.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.057304 restraints weight = 27369.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.058838 restraints weight = 18969.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.059888 restraints weight = 14603.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.060655 restraints weight = 12122.444| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13796 Z= 0.237 Angle : 0.807 14.626 19049 Z= 0.393 Chirality : 0.047 0.402 2193 Planarity : 0.004 0.054 2183 Dihedral : 21.073 179.480 2467 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.85 % Allowed : 27.24 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.40 (0.23), residues: 1479 helix: 0.88 (0.23), residues: 546 sheet: 0.17 (0.31), residues: 284 loop : -0.08 (0.27), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 74 TYR 0.014 0.002 TYR A 160 PHE 0.033 0.003 PHE A 131 TRP 0.019 0.002 TRP D 96 HIS 0.034 0.002 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00480 (13796) covalent geometry : angle 0.80692 (19049) hydrogen bonds : bond 0.04252 ( 621) hydrogen bonds : angle 4.91799 ( 1674) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 357 time to evaluate : 0.514 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: C 27 PHE cc_start: 0.9242 (m-80) cc_final: 0.8996 (m-10) REVERT: C 54 LEU cc_start: 0.9693 (mt) cc_final: 0.9362 (mt) REVERT: C 55 TYR cc_start: 0.8822 (m-80) cc_final: 0.8546 (m-10) REVERT: C 95 PHE cc_start: 0.9139 (t80) cc_final: 0.8889 (t80) REVERT: C 127 ASP cc_start: 0.8964 (p0) cc_final: 0.8419 (m-30) REVERT: C 133 LEU cc_start: 0.9696 (mt) cc_final: 0.9444 (pp) REVERT: C 135 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.8923 (mm) REVERT: C 155 GLN cc_start: 0.8177 (pm20) cc_final: 0.7589 (pm20) REVERT: C 182 TYR cc_start: 0.8958 (m-80) cc_final: 0.8296 (m-80) REVERT: C 189 VAL cc_start: 0.9497 (t) cc_final: 0.8712 (t) REVERT: C 193 HIS cc_start: 0.8979 (t70) cc_final: 0.8120 (t-170) REVERT: C 880 TRP cc_start: 0.9051 (m100) cc_final: 0.8254 (m100) REVERT: C 884 ASN cc_start: 0.8877 (t0) cc_final: 0.7925 (m110) REVERT: C 893 ASP cc_start: 0.8898 (m-30) cc_final: 0.8533 (m-30) REVERT: C 895 PHE cc_start: 0.9178 (t80) cc_final: 0.8502 (t80) REVERT: C 897 LYS cc_start: 0.9378 (mtmt) cc_final: 0.8947 (mmtp) REVERT: C 902 LEU cc_start: 0.9053 (mm) cc_final: 0.8226 (tp) REVERT: C 906 ASN cc_start: 0.9175 (m110) cc_final: 0.8617 (m110) REVERT: C 955 GLU cc_start: 0.9258 (mp0) cc_final: 0.8942 (mp0) REVERT: C 983 ASP cc_start: 0.8111 (t0) cc_final: 0.7358 (t0) REVERT: C 1045 PHE cc_start: 0.9290 (m-80) cc_final: 0.8932 (m-80) REVERT: D 12 ASN cc_start: 0.9280 (m-40) cc_final: 0.8985 (t0) REVERT: D 142 LEU cc_start: 0.9095 (pt) cc_final: 0.8502 (pp) REVERT: D 155 GLN cc_start: 0.8938 (pm20) cc_final: 0.8698 (pm20) REVERT: D 194 LYS cc_start: 0.9511 (tttt) cc_final: 0.9277 (ptpt) REVERT: D 896 ARG cc_start: 0.8560 (ttm110) cc_final: 0.8194 (ttp-110) REVERT: D 919 HIS cc_start: 0.8196 (t-170) cc_final: 0.7540 (t70) REVERT: D 923 LEU cc_start: 0.9651 (mm) cc_final: 0.9367 (tp) REVERT: D 949 ARG cc_start: 0.8931 (mmm160) cc_final: 0.8660 (mmp80) REVERT: D 983 ASP cc_start: 0.8119 (t0) cc_final: 0.7218 (t70) REVERT: D 989 LEU cc_start: 0.9687 (mt) cc_final: 0.9287 (tp) REVERT: D 993 THR cc_start: 0.9679 (OUTLIER) cc_final: 0.9450 (p) REVERT: A 58 TYR cc_start: 0.9273 (p90) cc_final: 0.8957 (p90) REVERT: A 65 ARG cc_start: 0.9169 (tpm170) cc_final: 0.8882 (tpm170) REVERT: A 93 SER cc_start: 0.9539 (m) cc_final: 0.9297 (p) REVERT: A 212 PHE cc_start: 0.8358 (m-80) cc_final: 0.8104 (m-80) REVERT: A 253 LYS cc_start: 0.8143 (mmmm) cc_final: 0.7708 (mmmm) REVERT: A 296 TRP cc_start: 0.9388 (m100) cc_final: 0.8962 (m100) REVERT: A 366 PHE cc_start: 0.9077 (t80) cc_final: 0.8244 (t80) REVERT: A 385 HIS cc_start: 0.9298 (m-70) cc_final: 0.8879 (m-70) REVERT: A 387 PHE cc_start: 0.9388 (t80) cc_final: 0.9068 (t80) REVERT: B 15 PHE cc_start: 0.8975 (t80) cc_final: 0.7919 (t80) REVERT: B 18 LYS cc_start: 0.8828 (mtmm) cc_final: 0.8488 (ptpt) REVERT: B 33 GLU cc_start: 0.9415 (tt0) cc_final: 0.9177 (pt0) REVERT: B 75 CYS cc_start: 0.8461 (m) cc_final: 0.7909 (m) REVERT: B 97 MET cc_start: 0.9228 (mmm) cc_final: 0.8962 (ppp) REVERT: B 99 PHE cc_start: 0.8928 (m-80) cc_final: 0.8678 (m-80) REVERT: B 165 TYR cc_start: 0.9484 (t80) cc_final: 0.9258 (t80) REVERT: B 260 PHE cc_start: 0.8836 (m-80) cc_final: 0.8393 (m-80) REVERT: B 271 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8920 (mm) REVERT: B 279 MET cc_start: 0.8902 (mpp) cc_final: 0.8555 (mmt) REVERT: B 317 LEU cc_start: 0.9413 (tp) cc_final: 0.9048 (tp) REVERT: B 321 GLN cc_start: 0.9042 (mt0) cc_final: 0.8482 (mt0) REVERT: B 357 LEU cc_start: 0.9545 (tp) cc_final: 0.9014 (pp) REVERT: B 366 PHE cc_start: 0.9286 (t80) cc_final: 0.8518 (t80) REVERT: B 387 PHE cc_start: 0.9416 (t80) cc_final: 0.9065 (t80) outliers start: 49 outliers final: 36 residues processed: 377 average time/residue: 0.1101 time to fit residues: 61.1576 Evaluate side-chains 388 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 349 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 1011 ILE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 70 optimal weight: 0.1980 chunk 148 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.081395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.054454 restraints weight = 46787.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.056671 restraints weight = 27309.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058245 restraints weight = 18900.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.059343 restraints weight = 14503.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060103 restraints weight = 11984.086| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13796 Z= 0.198 Angle : 0.820 14.129 19049 Z= 0.394 Chirality : 0.047 0.392 2193 Planarity : 0.004 0.054 2183 Dihedral : 21.097 179.611 2467 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.14 % Allowed : 28.65 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.42 (0.23), residues: 1479 helix: 0.89 (0.23), residues: 542 sheet: 0.11 (0.31), residues: 293 loop : -0.01 (0.28), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 197 TYR 0.020 0.002 TYR A 16 PHE 0.030 0.003 PHE A 15 TRP 0.023 0.002 TRP C 96 HIS 0.006 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00416 (13796) covalent geometry : angle 0.82037 (19049) hydrogen bonds : bond 0.04026 ( 621) hydrogen bonds : angle 4.88973 ( 1674) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 357 time to evaluate : 0.487 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: C 27 PHE cc_start: 0.9241 (m-80) cc_final: 0.9012 (m-10) REVERT: C 54 LEU cc_start: 0.9691 (mt) cc_final: 0.9363 (mt) REVERT: C 55 TYR cc_start: 0.8741 (m-80) cc_final: 0.8476 (m-10) REVERT: C 95 PHE cc_start: 0.9106 (t80) cc_final: 0.8820 (t80) REVERT: C 127 ASP cc_start: 0.8942 (p0) cc_final: 0.8474 (m-30) REVERT: C 133 LEU cc_start: 0.9704 (mt) cc_final: 0.9457 (pp) REVERT: C 135 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8881 (mt) REVERT: C 155 GLN cc_start: 0.8170 (pm20) cc_final: 0.7724 (pm20) REVERT: C 158 PHE cc_start: 0.9225 (p90) cc_final: 0.8486 (m-80) REVERT: C 182 TYR cc_start: 0.8945 (m-80) cc_final: 0.8344 (m-80) REVERT: C 189 VAL cc_start: 0.9495 (t) cc_final: 0.8697 (t) REVERT: C 193 HIS cc_start: 0.9069 (t70) cc_final: 0.8277 (t-170) REVERT: C 880 TRP cc_start: 0.9071 (m100) cc_final: 0.8275 (m100) REVERT: C 884 ASN cc_start: 0.8890 (t0) cc_final: 0.7933 (m110) REVERT: C 893 ASP cc_start: 0.8881 (m-30) cc_final: 0.8510 (m-30) REVERT: C 895 PHE cc_start: 0.9202 (t80) cc_final: 0.8480 (t80) REVERT: C 897 LYS cc_start: 0.9379 (mtmt) cc_final: 0.8971 (mmtp) REVERT: C 902 LEU cc_start: 0.9044 (mm) cc_final: 0.8225 (tp) REVERT: C 906 ASN cc_start: 0.9150 (m110) cc_final: 0.8577 (m110) REVERT: C 955 GLU cc_start: 0.9261 (mp0) cc_final: 0.8927 (mp0) REVERT: C 1016 HIS cc_start: 0.7142 (m170) cc_final: 0.6885 (m170) REVERT: C 1045 PHE cc_start: 0.9261 (m-80) cc_final: 0.8951 (m-80) REVERT: D 12 ASN cc_start: 0.9225 (m-40) cc_final: 0.8977 (t0) REVERT: D 55 TYR cc_start: 0.8692 (m-10) cc_final: 0.8408 (m-10) REVERT: D 72 MET cc_start: 0.7656 (ttt) cc_final: 0.6992 (tpt) REVERT: D 113 ARG cc_start: 0.7897 (tpt90) cc_final: 0.7520 (tpt90) REVERT: D 142 LEU cc_start: 0.9109 (pt) cc_final: 0.8826 (pt) REVERT: D 155 GLN cc_start: 0.8920 (pm20) cc_final: 0.8588 (pm20) REVERT: D 894 LYS cc_start: 0.9069 (ptpt) cc_final: 0.8840 (ptmt) REVERT: D 896 ARG cc_start: 0.8458 (ttm110) cc_final: 0.8086 (ttp-110) REVERT: D 919 HIS cc_start: 0.8223 (t-170) cc_final: 0.7542 (t-90) REVERT: D 983 ASP cc_start: 0.8203 (t0) cc_final: 0.7152 (t0) REVERT: D 989 LEU cc_start: 0.9678 (mt) cc_final: 0.9163 (tp) REVERT: A 58 TYR cc_start: 0.9232 (p90) cc_final: 0.8927 (p90) REVERT: A 65 ARG cc_start: 0.9146 (tpm170) cc_final: 0.8864 (tpm170) REVERT: A 149 LYS cc_start: 0.9664 (mttm) cc_final: 0.9348 (mttm) REVERT: A 212 PHE cc_start: 0.8434 (m-80) cc_final: 0.8232 (m-80) REVERT: A 232 MET cc_start: 0.9281 (mmm) cc_final: 0.8916 (mpp) REVERT: A 253 LYS cc_start: 0.8115 (mmmm) cc_final: 0.7666 (mmmm) REVERT: A 296 TRP cc_start: 0.9380 (m100) cc_final: 0.8960 (m100) REVERT: A 366 PHE cc_start: 0.9071 (t80) cc_final: 0.8221 (t80) REVERT: A 385 HIS cc_start: 0.9312 (m-70) cc_final: 0.8898 (m-70) REVERT: A 387 PHE cc_start: 0.9348 (t80) cc_final: 0.9013 (t80) REVERT: B 15 PHE cc_start: 0.8984 (t80) cc_final: 0.7956 (t80) REVERT: B 18 LYS cc_start: 0.8843 (mtmm) cc_final: 0.8513 (ptpt) REVERT: B 33 GLU cc_start: 0.9405 (tt0) cc_final: 0.9159 (pt0) REVERT: B 75 CYS cc_start: 0.8433 (m) cc_final: 0.8099 (m) REVERT: B 94 ARG cc_start: 0.9389 (ttp-110) cc_final: 0.9115 (ptm160) REVERT: B 99 PHE cc_start: 0.8932 (m-80) cc_final: 0.8682 (m-80) REVERT: B 165 TYR cc_start: 0.9471 (t80) cc_final: 0.9255 (t80) REVERT: B 271 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8953 (mm) REVERT: B 279 MET cc_start: 0.8890 (mpp) cc_final: 0.8597 (mmt) REVERT: B 317 LEU cc_start: 0.9418 (tp) cc_final: 0.9079 (tp) REVERT: B 321 GLN cc_start: 0.9027 (mt0) cc_final: 0.8456 (mt0) REVERT: B 357 LEU cc_start: 0.9549 (tp) cc_final: 0.9023 (pp) REVERT: B 366 PHE cc_start: 0.9236 (t80) cc_final: 0.8468 (t80) REVERT: B 387 PHE cc_start: 0.9340 (t80) cc_final: 0.9039 (t80) outliers start: 40 outliers final: 34 residues processed: 374 average time/residue: 0.1062 time to fit residues: 58.7089 Evaluate side-chains 378 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 342 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 275 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 119 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN ** B 5 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 = 0.3571 r_free = 0.3571 target = 0.081728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055654 restraints weight = 44881.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.057920 restraints weight = 26435.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.059526 restraints weight = 18290.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.060682 restraints weight = 13967.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.061501 restraints weight = 11410.212| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13796 Z= 0.172 Angle : 0.855 17.208 19049 Z= 0.398 Chirality : 0.048 0.410 2193 Planarity : 0.004 0.056 2183 Dihedral : 21.094 179.324 2467 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.90 % Allowed : 29.91 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.40 (0.23), residues: 1479 helix: 0.91 (0.23), residues: 542 sheet: 0.02 (0.30), residues: 300 loop : -0.01 (0.28), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 197 TYR 0.022 0.002 TYR A 16 PHE 0.054 0.003 PHE B 27 TRP 0.023 0.002 TRP D 96 HIS 0.007 0.001 HIS C 919 Details of bonding type rmsd covalent geometry : bond 0.00375 (13796) covalent geometry : angle 0.85511 (19049) hydrogen bonds : bond 0.03937 ( 621) hydrogen bonds : angle 4.87384 ( 1674) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 354 time to evaluate : 0.346 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: C 12 ASN cc_start: 0.9127 (m-40) cc_final: 0.8802 (t0) REVERT: C 27 PHE cc_start: 0.9242 (m-80) cc_final: 0.9028 (m-10) REVERT: C 55 TYR cc_start: 0.8767 (m-80) cc_final: 0.8464 (m-10) REVERT: C 95 PHE cc_start: 0.9110 (t80) cc_final: 0.8898 (t80) REVERT: C 127 ASP cc_start: 0.8918 (p0) cc_final: 0.8452 (m-30) REVERT: C 133 LEU cc_start: 0.9697 (mt) cc_final: 0.9420 (pp) REVERT: C 135 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8901 (mt) REVERT: C 158 PHE cc_start: 0.9229 (p90) cc_final: 0.8547 (m-80) REVERT: C 182 TYR cc_start: 0.8945 (m-80) cc_final: 0.8279 (m-80) REVERT: C 189 VAL cc_start: 0.9501 (t) cc_final: 0.8689 (t) REVERT: C 190 PHE cc_start: 0.8811 (t80) cc_final: 0.8551 (t80) REVERT: C 193 HIS cc_start: 0.9056 (t70) cc_final: 0.8304 (t-170) REVERT: C 197 ARG cc_start: 0.9326 (ptp-170) cc_final: 0.9061 (ptp-170) REVERT: C 880 TRP cc_start: 0.9079 (m100) cc_final: 0.8298 (m100) REVERT: C 884 ASN cc_start: 0.8916 (t0) cc_final: 0.7923 (m110) REVERT: C 893 ASP cc_start: 0.8841 (m-30) cc_final: 0.8373 (m-30) REVERT: C 895 PHE cc_start: 0.9208 (t80) cc_final: 0.8470 (t80) REVERT: C 897 LYS cc_start: 0.9369 (mtmt) cc_final: 0.8946 (mmtp) REVERT: C 902 LEU cc_start: 0.9030 (mm) cc_final: 0.8160 (tp) REVERT: C 906 ASN cc_start: 0.9162 (m110) cc_final: 0.8611 (m110) REVERT: C 919 HIS cc_start: 0.8394 (t70) cc_final: 0.8151 (t70) REVERT: C 955 GLU cc_start: 0.9283 (mp0) cc_final: 0.8960 (mp0) REVERT: C 1016 HIS cc_start: 0.7061 (m170) cc_final: 0.6769 (m170) REVERT: D 12 ASN cc_start: 0.9142 (m-40) cc_final: 0.8926 (t0) REVERT: D 113 ARG cc_start: 0.7921 (tpt90) cc_final: 0.7536 (tpt90) REVERT: D 142 LEU cc_start: 0.9053 (pt) cc_final: 0.8749 (pt) REVERT: D 155 GLN cc_start: 0.8891 (pm20) cc_final: 0.8653 (pm20) REVERT: D 896 ARG cc_start: 0.8384 (ttm110) cc_final: 0.8019 (ttp-110) REVERT: D 919 HIS cc_start: 0.8213 (t-170) cc_final: 0.7471 (t-90) REVERT: D 949 ARG cc_start: 0.8942 (mmm160) cc_final: 0.8652 (mmp80) REVERT: D 983 ASP cc_start: 0.8252 (t0) cc_final: 0.7194 (t70) REVERT: D 989 LEU cc_start: 0.9668 (mt) cc_final: 0.9148 (tp) REVERT: A 58 TYR cc_start: 0.9227 (p90) cc_final: 0.8922 (p90) REVERT: A 65 ARG cc_start: 0.9155 (tpm170) cc_final: 0.8875 (tpm170) REVERT: A 232 MET cc_start: 0.9310 (mmm) cc_final: 0.8837 (mpp) REVERT: A 253 LYS cc_start: 0.8065 (mmmm) cc_final: 0.7605 (mmmm) REVERT: A 296 TRP cc_start: 0.9366 (m100) cc_final: 0.8941 (m100) REVERT: A 366 PHE cc_start: 0.9064 (t80) cc_final: 0.8212 (t80) REVERT: A 385 HIS cc_start: 0.9306 (m-70) cc_final: 0.8893 (m-70) REVERT: A 387 PHE cc_start: 0.9335 (t80) cc_final: 0.8991 (t80) REVERT: B 15 PHE cc_start: 0.9000 (t80) cc_final: 0.7977 (t80) REVERT: B 18 LYS cc_start: 0.8846 (mtmm) cc_final: 0.8515 (ptpt) REVERT: B 75 CYS cc_start: 0.8425 (m) cc_final: 0.8088 (m) REVERT: B 94 ARG cc_start: 0.9384 (ttp-110) cc_final: 0.9080 (ptm160) REVERT: B 99 PHE cc_start: 0.8939 (m-80) cc_final: 0.8676 (m-80) REVERT: B 165 TYR cc_start: 0.9445 (t80) cc_final: 0.9215 (t80) REVERT: B 207 PHE cc_start: 0.9255 (t80) cc_final: 0.8849 (t80) REVERT: B 260 PHE cc_start: 0.8598 (m-80) cc_final: 0.8229 (m-80) REVERT: B 271 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8962 (mm) REVERT: B 279 MET cc_start: 0.8859 (mpp) cc_final: 0.8571 (mmt) REVERT: B 317 LEU cc_start: 0.9409 (tp) cc_final: 0.9078 (tp) REVERT: B 321 GLN cc_start: 0.9043 (mt0) cc_final: 0.8472 (mt0) REVERT: B 357 LEU cc_start: 0.9537 (tp) cc_final: 0.9008 (pp) REVERT: B 366 PHE cc_start: 0.9206 (t80) cc_final: 0.8419 (t80) REVERT: B 387 PHE cc_start: 0.9322 (t80) cc_final: 0.9019 (t80) outliers start: 37 outliers final: 32 residues processed: 369 average time/residue: 0.1035 time to fit residues: 55.8696 Evaluate side-chains 378 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 344 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 1011 ILE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 275 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 884 ASN ** A 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 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 = 0.3583 r_free = 0.3583 target = 0.082806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055841 restraints weight = 46349.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.058070 restraints weight = 27263.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.059632 restraints weight = 18938.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.060746 restraints weight = 14528.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.061524 restraints weight = 11961.276| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13796 Z= 0.149 Angle : 0.872 16.967 19049 Z= 0.403 Chirality : 0.048 0.419 2193 Planarity : 0.004 0.105 2183 Dihedral : 21.069 179.854 2467 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.06 % Allowed : 29.83 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.37 (0.23), residues: 1479 helix: 0.84 (0.23), residues: 540 sheet: 0.03 (0.30), residues: 300 loop : -0.01 (0.28), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 102 TYR 0.023 0.002 TYR A 16 PHE 0.031 0.002 PHE B 27 TRP 0.025 0.002 TRP C 96 HIS 0.006 0.001 HIS C 919 Details of bonding type rmsd covalent geometry : bond 0.00333 (13796) covalent geometry : angle 0.87213 (19049) hydrogen bonds : bond 0.03793 ( 621) hydrogen bonds : angle 4.81822 ( 1674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2695.10 seconds wall clock time: 47 minutes 19.07 seconds (2839.07 seconds total)