Starting phenix.real_space_refine on Fri Jul 3 23:32:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z03_14403/07_2026/7z03_14403.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z03_14403/07_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_14403/07_2026/7z03_14403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z03_14403/07_2026/7z03_14403.map" model { file = "/net/cci-nas-00/data/ceres_data/7z03_14403/07_2026/7z03_14403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z03_14403/07_2026/7z03_14403.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z03_14403/07_2026/7z03_14403.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z03_14403/07_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-dev-6108/lib/python3.11/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: 2.90, per 1000 atoms: 0.22 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: 1.21 Conformation dependent library (CDL) restraints added in 708.2 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: 1.74 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: 2.58 Time building geometry restraints manager: 1.64 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: 18826 2.69 - 5.37: 195 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=" N3 DT F 33 " pdb=" C4 DT F 33 " pdb=" O4 DT F 33 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.17e+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 ... (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: 1822 0.058 - 0.115: 335 0.115 - 0.173: 29 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.060 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 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 : 0.005 0.109 13796 Z= 0.334 Angle : 0.738 13.436 19049 Z= 0.479 Chirality : 0.045 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/Z covalent geometry : bond 0.00467 / 0.33 (13796) covalent geometry : angle 0.73820 / 0.48 (19049) hydrogen bonds : bond 0.14864 / 9.65 ( 621) hydrogen bonds : angle 5.72061 / 4.00 ( 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 : 0.482 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: 0.1292 time to fit residues: 109.5920 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 : 0.529 ------------------------------------------------------------------------------- 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: 10.0000 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1005 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.087003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.059203 restraints weight = 43217.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.061576 restraints weight = 25317.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.063238 restraints weight = 17547.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.064449 restraints weight = 13471.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.065279 restraints weight = 11062.293| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 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 = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 15 (20 function evaluations) r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13796 Z= 0.203 Angle : 0.877 17.327 19049 Z= 0.428 Chirality : 0.051 0.307 2193 Planarity : 0.005 0.096 2183 Dihedral : 21.335 177.104 2467 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.38 % Allowed : 18.76 % Favored : 77.86 % 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 (0.22), residues: 1479 helix: 1.21 (0.22), residues: 541 sheet: 0.05 (0.32), residues: 267 loop : -0.43 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 102 TYR 0.034 0.004 TYR B 237 PHE 0.035 0.003 PHE C 895 TRP 0.035 0.003 TRP C 880 HIS 0.010 0.002 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (13796) covalent geometry : angle 0.87675 / 0.43 (19049) hydrogen bonds : bond 0.05399 / 3.53 ( 621) hydrogen bonds : angle 5.08838 / 3.49 ( 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 483 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 440 time to evaluate : 0.619 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: 0.9362 (m-40) cc_final: 0.9102 (t0) REVERT: C 54 LEU cc_start: 0.9744 (mt) cc_final: 0.9543 (mt) REVERT: C 74 ARG cc_start: 0.8881 (mmp80) cc_final: 0.8139 (mmp-170) REVERT: C 82 GLU cc_start: 0.8494 (tt0) cc_final: 0.8257 (tm-30) REVERT: C 85 PHE cc_start: 0.9517 (p90) cc_final: 0.9202 (p90) REVERT: C 95 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8218 (t80) REVERT: C 135 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9376 (mm) REVERT: C 189 VAL cc_start: 0.9530 (t) cc_final: 0.8801 (t) REVERT: C 193 HIS cc_start: 0.8835 (t70) cc_final: 0.8591 (t70) REVERT: C 880 TRP cc_start: 0.9124 (m100) cc_final: 0.8149 (m100) REVERT: C 882 TYR cc_start: 0.8273 (m-80) cc_final: 0.8064 (m-80) REVERT: C 895 PHE cc_start: 0.9021 (t80) cc_final: 0.8299 (t80) REVERT: C 902 LEU cc_start: 0.9206 (mm) cc_final: 0.8474 (tp) REVERT: C 904 LEU cc_start: 0.9778 (tp) cc_final: 0.9537 (pp) REVERT: C 906 ASN cc_start: 0.9171 (m110) cc_final: 0.8643 (m-40) REVERT: C 921 ARG cc_start: 0.8621 (ttt180) cc_final: 0.7890 (ttt-90) REVERT: C 922 TYR cc_start: 0.8908 (m-80) cc_final: 0.8374 (m-80) REVERT: C 932 LEU cc_start: 0.8723 (mt) cc_final: 0.8378 (mm) REVERT: C 955 GLU cc_start: 0.9205 (mp0) cc_final: 0.8849 (mp0) REVERT: C 973 HIS cc_start: 0.9241 (p90) cc_final: 0.8949 (p90) REVERT: C 984 GLU cc_start: 0.8258 (tp30) cc_final: 0.7715 (tp30) REVERT: C 1045 PHE cc_start: 0.8890 (m-80) cc_final: 0.8130 (m-80) REVERT: D 1 MET cc_start: 0.7793 (tmm) cc_final: 0.7592 (tmm) REVERT: D 12 ASN cc_start: 0.9248 (m-40) cc_final: 0.8817 (t0) REVERT: D 55 TYR cc_start: 0.8511 (m-10) cc_final: 0.7862 (m-10) REVERT: D 72 MET cc_start: 0.7656 (ttm) cc_final: 0.7203 (ttt) REVERT: D 74 ARG cc_start: 0.8472 (mmp80) cc_final: 0.8256 (mmp80) REVERT: D 84 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8646 (mm-30) REVERT: D 92 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7719 (m-10) REVERT: D 165 LYS cc_start: 0.9475 (mmmt) cc_final: 0.9156 (mmmm) REVERT: D 184 GLN cc_start: 0.9295 (mp10) cc_final: 0.8872 (mp10) REVERT: D 188 MET cc_start: 0.9054 (ptp) cc_final: 0.8749 (ttm) REVERT: D 896 ARG cc_start: 0.8412 (ttm110) cc_final: 0.7751 (mtm110) REVERT: D 914 GLN cc_start: 0.9494 (tp40) cc_final: 0.9059 (tp-100) REVERT: D 919 HIS cc_start: 0.8116 (t-170) cc_final: 0.7831 (t70) REVERT: D 941 GLN cc_start: 0.9117 (mt0) cc_final: 0.8735 (pt0) REVERT: D 989 LEU cc_start: 0.9699 (mt) cc_final: 0.9310 (tp) REVERT: D 1011 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.8815 (mm) REVERT: D 1016 HIS cc_start: 0.7950 (m-70) cc_final: 0.7731 (m170) REVERT: A 9 TRP cc_start: 0.9658 (m-10) cc_final: 0.9402 (m-10) REVERT: A 10 HIS cc_start: 0.9187 (m-70) cc_final: 0.8744 (m-70) REVERT: A 18 LYS cc_start: 0.9204 (mmmt) cc_final: 0.8721 (mmtm) REVERT: A 65 ARG cc_start: 0.9129 (tpm170) cc_final: 0.8867 (tpp-160) REVERT: A 93 SER cc_start: 0.9522 (m) cc_final: 0.8844 (p) REVERT: A 149 LYS cc_start: 0.9679 (mttm) cc_final: 0.9225 (mttt) REVERT: A 212 PHE cc_start: 0.8154 (m-80) cc_final: 0.7820 (m-80) REVERT: A 232 MET cc_start: 0.9165 (mmm) cc_final: 0.8904 (mpp) REVERT: A 253 LYS cc_start: 0.8253 (mmmm) cc_final: 0.7810 (mmmm) REVERT: A 366 PHE cc_start: 0.9047 (t80) cc_final: 0.8626 (t80) REVERT: B 15 PHE cc_start: 0.8752 (t80) cc_final: 0.8056 (t80) REVERT: B 16 TYR cc_start: 0.8314 (m-80) cc_final: 0.7980 (m-10) REVERT: B 62 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9245 (mm) REVERT: B 65 ARG cc_start: 0.9358 (mtp85) cc_final: 0.9019 (ptp-110) REVERT: B 75 CYS cc_start: 0.8144 (m) cc_final: 0.7643 (m) REVERT: B 154 LEU cc_start: 0.8680 (pt) cc_final: 0.8299 (pt) REVERT: B 207 PHE cc_start: 0.8244 (t80) cc_final: 0.7162 (t80) REVERT: B 225 ARG cc_start: 0.8917 (ttm170) cc_final: 0.8425 (ttm110) REVERT: B 271 LEU cc_start: 0.9047 (mm) cc_final: 0.8797 (mm) REVERT: B 282 LEU cc_start: 0.8601 (mt) cc_final: 0.8250 (mt) REVERT: B 317 LEU cc_start: 0.9326 (tp) cc_final: 0.8875 (tp) REVERT: B 321 GLN cc_start: 0.9093 (mt0) cc_final: 0.8667 (mt0) REVERT: B 366 PHE cc_start: 0.9231 (t80) cc_final: 0.8938 (t80) outliers start: 43 outliers final: 22 residues processed: 453 average time/residue: 0.1129 time to fit residues: 75.7069 Evaluate side-chains 416 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 389 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 92 TYR 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 B residue 43 ILE Chi-restraints excluded: chain B residue 62 LEU 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: 6.9990 chunk 123 optimal weight: 3.9990 chunk 78 optimal weight: 0.0070 chunk 74 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.084406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.057231 restraints weight = 44283.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.059484 restraints weight = 25438.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061067 restraints weight = 17485.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062183 restraints weight = 13343.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.062969 restraints weight = 10957.252| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (15 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13796 Z= 0.187 Angle : 0.847 14.869 19049 Z= 0.411 Chirality : 0.050 0.474 2193 Planarity : 0.004 0.052 2183 Dihedral : 21.318 178.440 2467 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.85 % Allowed : 22.37 % 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: 0.21 (0.22), residues: 1479 helix: 1.08 (0.22), residues: 542 sheet: -0.13 (0.31), residues: 279 loop : -0.44 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 197 TYR 0.030 0.003 TYR B 217 PHE 0.027 0.003 PHE C 895 TRP 0.026 0.002 TRP B 296 HIS 0.025 0.002 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 (13796) covalent geometry : angle 0.84712 / 0.41 (19049) hydrogen bonds : bond 0.04955 / 3.29 ( 621) hydrogen bonds : angle 4.94826 / 3.39 ( 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 448 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 399 time to evaluate : 0.496 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: 0.9397 (m-40) cc_final: 0.9091 (m-40) REVERT: C 45 THR cc_start: 0.9774 (m) cc_final: 0.9546 (p) REVERT: C 54 LEU cc_start: 0.9763 (mt) cc_final: 0.9535 (mt) REVERT: C 72 MET cc_start: 0.8287 (ppp) cc_final: 0.7499 (ppp) REVERT: C 74 ARG cc_start: 0.8796 (mmp80) cc_final: 0.8455 (mmp80) REVERT: C 85 PHE cc_start: 0.9526 (p90) cc_final: 0.9323 (p90) REVERT: C 95 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8410 (t80) REVERT: C 135 LEU cc_start: 0.9638 (mm) cc_final: 0.9432 (mm) REVERT: C 189 VAL cc_start: 0.9511 (t) cc_final: 0.9291 (t) REVERT: C 193 HIS cc_start: 0.9110 (t70) cc_final: 0.8033 (t70) REVERT: C 880 TRP cc_start: 0.8987 (m100) cc_final: 0.8651 (m100) REVERT: C 884 ASN cc_start: 0.8987 (t0) cc_final: 0.8346 (m110) REVERT: C 895 PHE cc_start: 0.9051 (t80) cc_final: 0.8449 (t80) REVERT: C 897 LYS cc_start: 0.9385 (mtmt) cc_final: 0.8866 (mmtp) REVERT: C 902 LEU cc_start: 0.9163 (mm) cc_final: 0.8410 (tp) REVERT: C 906 ASN cc_start: 0.9195 (m110) cc_final: 0.8673 (m110) REVERT: C 921 ARG cc_start: 0.8658 (ttt180) cc_final: 0.7826 (ttt-90) REVERT: C 922 TYR cc_start: 0.8919 (m-80) cc_final: 0.8053 (m-10) REVERT: C 955 GLU cc_start: 0.9204 (mp0) cc_final: 0.9004 (mp0) REVERT: C 973 HIS cc_start: 0.9224 (p90) cc_final: 0.8976 (p90) REVERT: D 4 LEU cc_start: 0.9107 (pp) cc_final: 0.8690 (mp) REVERT: D 12 ASN cc_start: 0.9327 (m-40) cc_final: 0.8921 (t0) REVERT: D 92 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8152 (m-10) REVERT: D 165 LYS cc_start: 0.9490 (mmmt) cc_final: 0.9140 (mmmm) REVERT: D 184 GLN cc_start: 0.9313 (mp10) cc_final: 0.8870 (mp10) REVERT: D 188 MET cc_start: 0.9050 (ptp) cc_final: 0.8783 (ttm) REVERT: D 197 ARG cc_start: 0.9451 (tpt90) cc_final: 0.9080 (tpt90) REVERT: D 914 GLN cc_start: 0.9473 (tp40) cc_final: 0.9114 (tp-100) REVERT: D 919 HIS cc_start: 0.8203 (t-170) cc_final: 0.7870 (t70) REVERT: D 941 GLN cc_start: 0.9165 (mt0) cc_final: 0.8756 (pt0) REVERT: D 989 LEU cc_start: 0.9693 (mt) cc_final: 0.9272 (tp) REVERT: D 1016 HIS cc_start: 0.7953 (m-70) cc_final: 0.7706 (m170) REVERT: D 1038 TYR cc_start: 0.8687 (m-10) cc_final: 0.8228 (m-10) REVERT: A 18 LYS cc_start: 0.9286 (mmmt) cc_final: 0.8893 (mmtm) REVERT: A 58 TYR cc_start: 0.9170 (p90) cc_final: 0.8785 (p90) REVERT: A 65 ARG cc_start: 0.9120 (tpm170) cc_final: 0.8835 (tpp-160) REVERT: A 93 SER cc_start: 0.9529 (m) cc_final: 0.8994 (p) REVERT: A 149 LYS cc_start: 0.9706 (mttm) cc_final: 0.9201 (mttm) REVERT: A 212 PHE cc_start: 0.8199 (m-80) cc_final: 0.7904 (m-80) REVERT: A 244 LEU cc_start: 0.9245 (mt) cc_final: 0.8964 (mt) REVERT: A 246 PHE cc_start: 0.8778 (m-80) cc_final: 0.7523 (m-80) REVERT: A 253 LYS cc_start: 0.8246 (mmmm) cc_final: 0.7761 (mmmm) REVERT: A 357 LEU cc_start: 0.9254 (mp) cc_final: 0.9028 (mp) REVERT: A 366 PHE cc_start: 0.9080 (t80) cc_final: 0.8528 (t80) REVERT: B 15 PHE cc_start: 0.8813 (t80) cc_final: 0.7804 (t80) REVERT: B 16 TYR cc_start: 0.8239 (m-80) cc_final: 0.8036 (m-10) REVERT: B 33 GLU cc_start: 0.9453 (tt0) cc_final: 0.9187 (mt-10) REVERT: B 62 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9072 (mm) REVERT: B 65 ARG cc_start: 0.9351 (mtp85) cc_final: 0.9098 (ptp-110) REVERT: B 75 CYS cc_start: 0.8176 (m) cc_final: 0.7631 (m) REVERT: B 169 CYS cc_start: 0.9564 (OUTLIER) cc_final: 0.9319 (p) REVERT: B 207 PHE cc_start: 0.9126 (t80) cc_final: 0.8254 (t80) REVERT: B 279 MET cc_start: 0.7672 (ppp) cc_final: 0.6841 (ppp) REVERT: B 282 LEU cc_start: 0.8814 (mt) cc_final: 0.8562 (mp) REVERT: B 321 GLN cc_start: 0.9120 (mt0) cc_final: 0.8389 (tp-100) REVERT: B 366 PHE cc_start: 0.9253 (t80) cc_final: 0.8900 (t80) outliers start: 49 outliers final: 34 residues processed: 418 average time/residue: 0.1096 time to fit residues: 68.2001 Evaluate side-chains 421 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 383 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 LEU 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 976 ARG Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 986 PHE 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 92 TYR Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 149 ARG Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 906 ASN Chi-restraints excluded: chain D residue 993 THR 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 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 62 LEU 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 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: 3.9990 chunk 65 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1016 HIS A 110 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 = 0.3556 r_free = 0.3556 target = 0.081354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.054391 restraints weight = 46703.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.056571 restraints weight = 27000.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058070 restraints weight = 18601.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059149 restraints weight = 14298.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.059900 restraints weight = 11821.423| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 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 = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13796 Z= 0.260 Angle : 0.835 14.301 19049 Z= 0.416 Chirality : 0.049 0.528 2193 Planarity : 0.005 0.056 2183 Dihedral : 21.357 174.770 2467 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.18 % Allowed : 21.98 % Favored : 72.84 % 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: 0.19 (0.22), residues: 1479 helix: 0.92 (0.22), residues: 548 sheet: -0.02 (0.32), residues: 277 loop : -0.39 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 896 TYR 0.036 0.003 TYR C 882 PHE 0.026 0.003 PHE A 260 TRP 0.025 0.002 TRP B 296 HIS 0.018 0.002 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.26 (13796) covalent geometry : angle 0.83545 / 0.42 (19049) hydrogen bonds : bond 0.05009 / 3.35 ( 621) hydrogen bonds : angle 5.05738 / 3.49 ( 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 453 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 387 time to evaluate : 0.508 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: 0.9398 (m-40) cc_final: 0.8920 (t0) REVERT: C 27 PHE cc_start: 0.9114 (m-10) cc_final: 0.8858 (m-80) REVERT: C 45 THR cc_start: 0.9716 (m) cc_final: 0.9475 (p) REVERT: C 54 LEU cc_start: 0.9755 (mt) cc_final: 0.9481 (mt) REVERT: C 82 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7821 (tm-30) REVERT: C 135 LEU cc_start: 0.9710 (mm) cc_final: 0.9425 (mm) REVERT: C 188 MET cc_start: 0.8919 (tmm) cc_final: 0.8669 (tmm) REVERT: C 189 VAL cc_start: 0.9563 (t) cc_final: 0.9051 (t) REVERT: C 190 PHE cc_start: 0.8841 (t80) cc_final: 0.8311 (t80) REVERT: C 880 TRP cc_start: 0.8915 (m100) cc_final: 0.8427 (m100) REVERT: C 895 PHE cc_start: 0.9139 (t80) cc_final: 0.8397 (t80) REVERT: C 897 LYS cc_start: 0.9396 (mtmt) cc_final: 0.8996 (mmtp) REVERT: C 902 LEU cc_start: 0.9160 (mm) cc_final: 0.8399 (tp) REVERT: C 906 ASN cc_start: 0.9241 (m110) cc_final: 0.8710 (m110) REVERT: C 921 ARG cc_start: 0.8699 (ttt180) cc_final: 0.8217 (ttt-90) REVERT: C 984 GLU cc_start: 0.8270 (tp30) cc_final: 0.7638 (tp30) REVERT: C 1045 PHE cc_start: 0.9111 (m-80) cc_final: 0.8286 (m-80) REVERT: D 12 ASN cc_start: 0.9294 (m-40) cc_final: 0.8769 (t0) REVERT: D 72 MET cc_start: 0.8106 (ttm) cc_final: 0.7772 (ttt) REVERT: D 139 LEU cc_start: 0.9477 (mm) cc_final: 0.9257 (mm) REVERT: D 155 GLN cc_start: 0.8789 (pm20) cc_final: 0.8469 (pm20) REVERT: D 165 LYS cc_start: 0.9490 (mmmt) cc_final: 0.9151 (mmmm) REVERT: D 184 GLN cc_start: 0.9305 (mp10) cc_final: 0.9069 (mt0) REVERT: D 188 MET cc_start: 0.9063 (ptp) cc_final: 0.8791 (ttm) REVERT: D 896 ARG cc_start: 0.8600 (ttm110) cc_final: 0.7868 (mtm110) REVERT: D 914 GLN cc_start: 0.9440 (tp40) cc_final: 0.9100 (tm-30) REVERT: D 919 HIS cc_start: 0.8383 (t-170) cc_final: 0.7920 (t70) REVERT: D 941 GLN cc_start: 0.9204 (mt0) cc_final: 0.8653 (mm-40) REVERT: D 975 THR cc_start: 0.9146 (m) cc_final: 0.8785 (p) REVERT: D 983 ASP cc_start: 0.8088 (t0) cc_final: 0.7252 (t0) REVERT: D 989 LEU cc_start: 0.9662 (mt) cc_final: 0.9361 (tp) REVERT: A 18 LYS cc_start: 0.9403 (mmmt) cc_final: 0.9026 (mmtm) REVERT: A 58 TYR cc_start: 0.9256 (p90) cc_final: 0.8906 (p90) REVERT: A 65 ARG cc_start: 0.9138 (tpm170) cc_final: 0.8863 (tpm170) REVERT: A 93 SER cc_start: 0.9549 (m) cc_final: 0.9012 (p) REVERT: A 149 LYS cc_start: 0.9710 (mttm) cc_final: 0.9281 (mttm) REVERT: A 212 PHE cc_start: 0.8148 (m-80) cc_final: 0.7862 (m-80) REVERT: A 232 MET cc_start: 0.9274 (mmm) cc_final: 0.8971 (mpp) REVERT: A 244 LEU cc_start: 0.9302 (mt) cc_final: 0.9023 (mt) REVERT: A 360 LEU cc_start: 0.8543 (mm) cc_final: 0.8323 (mm) REVERT: A 366 PHE cc_start: 0.9065 (t80) cc_final: 0.8413 (t80) REVERT: B 15 PHE cc_start: 0.8852 (t80) cc_final: 0.7917 (t80) REVERT: B 16 TYR cc_start: 0.8406 (m-80) cc_final: 0.8071 (m-10) REVERT: B 33 GLU cc_start: 0.9450 (tt0) cc_final: 0.9192 (mt-10) REVERT: B 62 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9115 (mm) REVERT: B 65 ARG cc_start: 0.9355 (mtp85) cc_final: 0.9008 (ptp-110) REVERT: B 75 CYS cc_start: 0.8355 (m) cc_final: 0.8092 (m) REVERT: B 127 CYS cc_start: 0.8802 (m) cc_final: 0.8550 (m) REVERT: B 131 PHE cc_start: 0.7475 (t80) cc_final: 0.6924 (t80) REVERT: B 132 LEU cc_start: 0.9039 (tp) cc_final: 0.8593 (tt) REVERT: B 165 TYR cc_start: 0.9573 (t80) cc_final: 0.9353 (t80) REVERT: B 220 LEU cc_start: 0.9435 (mt) cc_final: 0.9213 (mt) REVERT: B 279 MET cc_start: 0.7703 (ppp) cc_final: 0.6917 (ppp) REVERT: B 282 LEU cc_start: 0.8865 (mt) cc_final: 0.8556 (mp) REVERT: B 321 GLN cc_start: 0.9153 (mt0) cc_final: 0.8678 (mt0) REVERT: B 357 LEU cc_start: 0.9414 (tp) cc_final: 0.8896 (pp) REVERT: B 366 PHE cc_start: 0.9289 (t80) cc_final: 0.8876 (t80) REVERT: B 373 GLU cc_start: 0.8920 (tp30) cc_final: 0.8598 (tp30) outliers start: 66 outliers final: 48 residues processed: 407 average time/residue: 0.1134 time to fit residues: 68.6419 Evaluate side-chains 410 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 361 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 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 200 LEU Chi-restraints excluded: chain C residue 893 ASP Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 986 PHE Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 56 HIS 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 149 ARG Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 906 ASN Chi-restraints excluded: chain D residue 982 LEU 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 1030 VAL Chi-restraints excluded: chain D residue 1036 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 SER 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 335 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 62 LEU 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 114 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 200 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1016 HIS A 379 GLN ** 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 = 0.3603 r_free = 0.3603 target = 0.083587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.056387 restraints weight = 45822.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.058680 restraints weight = 26113.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.060277 restraints weight = 17858.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.061406 restraints weight = 13627.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.062206 restraints weight = 11215.652| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 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 = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13796 Z= 0.159 Angle : 0.857 14.812 19049 Z= 0.405 Chirality : 0.049 0.502 2193 Planarity : 0.004 0.087 2183 Dihedral : 21.306 169.623 2467 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.24 % Allowed : 25.04 % Favored : 70.72 % 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: 0.16 (0.22), residues: 1479 helix: 0.78 (0.22), residues: 548 sheet: 0.11 (0.32), residues: 272 loop : -0.36 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 197 TYR 0.035 0.002 TYR D 55 PHE 0.020 0.002 PHE C 190 TRP 0.024 0.002 TRP A 296 HIS 0.014 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (13796) covalent geometry : angle 0.85715 / 0.40 (19049) hydrogen bonds : bond 0.04632 / 3.09 ( 621) hydrogen bonds : angle 4.85672 / 3.34 ( 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 436 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 382 time to evaluate : 0.513 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: 0.9395 (m-40) cc_final: 0.8999 (m-40) REVERT: C 27 PHE cc_start: 0.9109 (m-10) cc_final: 0.8842 (m-80) REVERT: C 45 THR cc_start: 0.9717 (m) cc_final: 0.9500 (p) REVERT: C 54 LEU cc_start: 0.9747 (mt) cc_final: 0.9490 (mt) REVERT: C 82 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7807 (tm-30) REVERT: C 135 LEU cc_start: 0.9703 (mm) cc_final: 0.8224 (mm) REVERT: C 189 VAL cc_start: 0.9499 (t) cc_final: 0.8895 (t) REVERT: C 190 PHE cc_start: 0.8757 (t80) cc_final: 0.8245 (t80) REVERT: C 193 HIS cc_start: 0.9067 (t70) cc_final: 0.8587 (t-170) REVERT: C 197 ARG cc_start: 0.9191 (ptp-170) cc_final: 0.8434 (ptt180) REVERT: C 880 TRP cc_start: 0.8910 (m100) cc_final: 0.8465 (m100) REVERT: C 891 GLU cc_start: 0.9204 (pm20) cc_final: 0.8918 (pm20) REVERT: C 895 PHE cc_start: 0.9060 (t80) cc_final: 0.8289 (t80) REVERT: C 897 LYS cc_start: 0.9302 (mtmt) cc_final: 0.8900 (mmtp) REVERT: C 902 LEU cc_start: 0.9123 (mm) cc_final: 0.8344 (tp) REVERT: C 906 ASN cc_start: 0.9171 (m110) cc_final: 0.8659 (m110) REVERT: C 921 ARG cc_start: 0.8422 (ttt180) cc_final: 0.7975 (ttt-90) REVERT: C 984 GLU cc_start: 0.8161 (tp30) cc_final: 0.7606 (tp30) REVERT: C 1045 PHE cc_start: 0.9091 (m-80) cc_final: 0.8728 (m-80) REVERT: D 12 ASN cc_start: 0.9259 (m-40) cc_final: 0.8723 (t0) REVERT: D 74 ARG cc_start: 0.7396 (tmm-80) cc_final: 0.7114 (tmm-80) REVERT: D 155 GLN cc_start: 0.8778 (pm20) cc_final: 0.8442 (pm20) REVERT: D 165 LYS cc_start: 0.9494 (mmmt) cc_final: 0.9147 (mmmm) REVERT: D 184 GLN cc_start: 0.9333 (mp10) cc_final: 0.9107 (mt0) REVERT: D 188 MET cc_start: 0.9010 (ptp) cc_final: 0.8801 (ttm) REVERT: D 896 ARG cc_start: 0.8513 (ttm110) cc_final: 0.7766 (mtm110) REVERT: D 910 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9345 (mp) REVERT: D 914 GLN cc_start: 0.9438 (tp40) cc_final: 0.9200 (tm-30) REVERT: D 919 HIS cc_start: 0.8118 (t-170) cc_final: 0.7671 (t70) REVERT: D 941 GLN cc_start: 0.9115 (mt0) cc_final: 0.8887 (mm-40) REVERT: D 983 ASP cc_start: 0.8227 (t0) cc_final: 0.7373 (t0) REVERT: D 989 LEU cc_start: 0.9657 (mt) cc_final: 0.9306 (tp) REVERT: D 1017 VAL cc_start: 0.9516 (m) cc_final: 0.9274 (p) REVERT: A 18 LYS cc_start: 0.9399 (mmmt) cc_final: 0.9031 (mmtm) REVERT: A 58 TYR cc_start: 0.9245 (p90) cc_final: 0.8919 (p90) REVERT: A 65 ARG cc_start: 0.9133 (tpm170) cc_final: 0.8833 (tpm170) REVERT: A 93 SER cc_start: 0.9543 (m) cc_final: 0.9124 (p) REVERT: A 149 LYS cc_start: 0.9682 (mttm) cc_final: 0.9232 (mttm) REVERT: A 212 PHE cc_start: 0.8220 (m-80) cc_final: 0.7943 (m-80) REVERT: A 244 LEU cc_start: 0.9302 (mt) cc_final: 0.9033 (mt) REVERT: A 279 MET cc_start: 0.8667 (mmm) cc_final: 0.7700 (tpt) REVERT: A 286 LEU cc_start: 0.9802 (pt) cc_final: 0.9584 (tt) REVERT: A 360 LEU cc_start: 0.8616 (mm) cc_final: 0.8411 (mm) REVERT: A 366 PHE cc_start: 0.9015 (t80) cc_final: 0.8362 (t80) REVERT: B 15 PHE cc_start: 0.8870 (t80) cc_final: 0.7877 (t80) REVERT: B 16 TYR cc_start: 0.8421 (m-80) cc_final: 0.8039 (m-10) REVERT: B 33 GLU cc_start: 0.9428 (tt0) cc_final: 0.8826 (tm-30) REVERT: B 65 ARG cc_start: 0.9308 (mtp85) cc_final: 0.9014 (mtm-85) REVERT: B 75 CYS cc_start: 0.8342 (m) cc_final: 0.8067 (m) REVERT: B 127 CYS cc_start: 0.8748 (m) cc_final: 0.8505 (m) REVERT: B 207 PHE cc_start: 0.9184 (t80) cc_final: 0.8977 (t80) REVERT: B 218 ILE cc_start: 0.9475 (mm) cc_final: 0.9239 (mp) REVERT: B 271 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8844 (mm) REVERT: B 279 MET cc_start: 0.7546 (ppp) cc_final: 0.6768 (ppp) REVERT: B 321 GLN cc_start: 0.9062 (mt0) cc_final: 0.8620 (mt0) REVERT: B 357 LEU cc_start: 0.9356 (tp) cc_final: 0.8865 (pp) REVERT: B 366 PHE cc_start: 0.9238 (t80) cc_final: 0.8514 (t80) REVERT: B 387 PHE cc_start: 0.9457 (t80) cc_final: 0.9178 (t80) outliers start: 54 outliers final: 38 residues processed: 401 average time/residue: 0.1096 time to fit residues: 65.9156 Evaluate side-chains 410 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 370 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 123 LYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 893 ASP 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 1020 MET 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 189 VAL Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 906 ASN Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 1014 ILE Chi-restraints excluded: chain D residue 1036 LEU Chi-restraints excluded: chain A residue 96 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 129 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN B 277 GLN ** 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 = 0.3552 r_free = 0.3552 target = 0.081358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054423 restraints weight = 46726.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.056616 restraints weight = 27008.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.058134 restraints weight = 18630.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.059238 restraints weight = 14321.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060003 restraints weight = 11844.455| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13796 Z= 0.234 Angle : 0.825 15.514 19049 Z= 0.405 Chirality : 0.048 0.416 2193 Planarity : 0.004 0.052 2183 Dihedral : 21.287 166.723 2467 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.34 % Allowed : 25.90 % Favored : 68.76 % 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: 0.17 (0.22), residues: 1479 helix: 0.70 (0.22), residues: 548 sheet: 0.17 (0.32), residues: 278 loop : -0.30 (0.26), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 197 TYR 0.021 0.002 TYR B 217 PHE 0.027 0.003 PHE B 27 TRP 0.047 0.003 TRP B 306 HIS 0.011 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.23 (13796) covalent geometry : angle 0.82517 / 0.41 (19049) hydrogen bonds : bond 0.04808 / 3.24 ( 621) hydrogen bonds : angle 5.00923 / 3.45 ( 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 442 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 374 time to evaluate : 0.482 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: 0.9428 (m-40) cc_final: 0.8896 (t0) REVERT: C 27 PHE cc_start: 0.9191 (m-10) cc_final: 0.8970 (m-10) REVERT: C 54 LEU cc_start: 0.9763 (mt) cc_final: 0.9475 (mt) REVERT: C 76 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8253 (p) REVERT: C 82 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7765 (tm-30) REVERT: C 135 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.8866 (mt) REVERT: C 142 LEU cc_start: 0.9122 (pp) cc_final: 0.8692 (tt) REVERT: C 155 GLN cc_start: 0.8260 (pm20) cc_final: 0.7660 (pm20) REVERT: C 189 VAL cc_start: 0.9480 (t) cc_final: 0.8829 (t) REVERT: C 193 HIS cc_start: 0.9073 (t70) cc_final: 0.8065 (t70) REVERT: C 880 TRP cc_start: 0.8973 (m100) cc_final: 0.8092 (m100) REVERT: C 884 ASN cc_start: 0.8927 (t0) cc_final: 0.8141 (m110) REVERT: C 895 PHE cc_start: 0.9160 (t80) cc_final: 0.8315 (t80) REVERT: C 897 LYS cc_start: 0.9342 (mtmt) cc_final: 0.8936 (mmtm) REVERT: C 902 LEU cc_start: 0.9107 (mm) cc_final: 0.8323 (tp) REVERT: C 906 ASN cc_start: 0.9215 (m110) cc_final: 0.8695 (m110) REVERT: C 919 HIS cc_start: 0.8543 (t70) cc_final: 0.8338 (t70) REVERT: C 983 ASP cc_start: 0.8128 (t0) cc_final: 0.7592 (t0) REVERT: C 984 GLU cc_start: 0.8088 (tp30) cc_final: 0.7492 (tp30) REVERT: C 1036 LEU cc_start: 0.9218 (mp) cc_final: 0.8891 (mt) REVERT: C 1045 PHE cc_start: 0.9164 (m-80) cc_final: 0.8810 (m-80) REVERT: D 12 ASN cc_start: 0.9237 (m-40) cc_final: 0.8692 (t0) REVERT: D 74 ARG cc_start: 0.7468 (tmm-80) cc_final: 0.7169 (tmm-80) REVERT: D 142 LEU cc_start: 0.8921 (pt) cc_final: 0.8524 (pt) REVERT: D 155 GLN cc_start: 0.8803 (pm20) cc_final: 0.8429 (pm20) REVERT: D 165 LYS cc_start: 0.9490 (mmmt) cc_final: 0.9147 (mmmm) REVERT: D 184 GLN cc_start: 0.9337 (mp10) cc_final: 0.9133 (mt0) REVERT: D 188 MET cc_start: 0.9009 (ptp) cc_final: 0.8762 (ttm) REVERT: D 896 ARG cc_start: 0.8541 (ttm110) cc_final: 0.7747 (mtm110) REVERT: D 919 HIS cc_start: 0.8206 (t-170) cc_final: 0.7834 (t70) REVERT: D 983 ASP cc_start: 0.8203 (t0) cc_final: 0.7156 (t0) REVERT: D 989 LEU cc_start: 0.9652 (mt) cc_final: 0.9335 (tp) REVERT: D 1016 HIS cc_start: 0.7845 (m-70) cc_final: 0.7499 (m170) REVERT: A 58 TYR cc_start: 0.9234 (p90) cc_final: 0.8931 (p90) REVERT: A 65 ARG cc_start: 0.9156 (tpm170) cc_final: 0.8863 (tpm170) REVERT: A 93 SER cc_start: 0.9562 (m) cc_final: 0.9230 (p) REVERT: A 180 ILE cc_start: 0.9673 (OUTLIER) cc_final: 0.9442 (tp) REVERT: A 212 PHE cc_start: 0.8238 (m-80) cc_final: 0.7999 (m-80) REVERT: A 232 MET cc_start: 0.9252 (mmm) cc_final: 0.8874 (mpp) REVERT: A 244 LEU cc_start: 0.9327 (mt) cc_final: 0.9115 (mt) REVERT: A 279 MET cc_start: 0.8645 (mmm) cc_final: 0.7709 (tpp) REVERT: A 360 LEU cc_start: 0.8707 (mm) cc_final: 0.8495 (mm) REVERT: A 366 PHE cc_start: 0.9034 (t80) cc_final: 0.8342 (t80) REVERT: B 15 PHE cc_start: 0.8707 (t80) cc_final: 0.7811 (t80) REVERT: B 18 LYS cc_start: 0.9034 (pttt) cc_final: 0.8458 (pttt) REVERT: B 33 GLU cc_start: 0.9427 (tt0) cc_final: 0.9194 (pt0) REVERT: B 62 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.8958 (mm) REVERT: B 65 ARG cc_start: 0.9304 (mtp85) cc_final: 0.9094 (ptp-110) REVERT: B 75 CYS cc_start: 0.8452 (m) cc_final: 0.8168 (m) REVERT: B 127 CYS cc_start: 0.8820 (m) cc_final: 0.8582 (m) REVERT: B 271 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8880 (mm) REVERT: B 279 MET cc_start: 0.7537 (ppp) cc_final: 0.6752 (ppp) REVERT: B 321 GLN cc_start: 0.9055 (mt0) cc_final: 0.8580 (mt0) REVERT: B 357 LEU cc_start: 0.9449 (tp) cc_final: 0.9008 (pp) REVERT: B 366 PHE cc_start: 0.9258 (t80) cc_final: 0.8499 (t80) REVERT: B 387 PHE cc_start: 0.9428 (t80) cc_final: 0.9147 (t80) outliers start: 68 outliers final: 46 residues processed: 399 average time/residue: 0.1075 time to fit residues: 64.5983 Evaluate side-chains 397 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 346 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 76 THR Chi-restraints excluded: chain C residue 80 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 135 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 893 ASP Chi-restraints excluded: chain C residue 965 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 998 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 189 VAL Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 906 ASN 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 1030 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 127 CYS 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 44 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 78 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 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 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: 2.9990 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 131 optimal weight: 0.0980 chunk 61 optimal weight: 0.9980 chunk 153 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 HIS B 39 GLN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3579 r_free = 0.3579 target = 0.083215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.054809 restraints weight = 46965.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.057093 restraints weight = 27151.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.058669 restraints weight = 18808.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.059799 restraints weight = 14499.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.060579 restraints weight = 12009.046| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5479 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= 0.179 Angle : 0.832 13.563 19049 Z= 0.400 Chirality : 0.050 0.491 2193 Planarity : 0.004 0.054 2183 Dihedral : 21.247 163.390 2467 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.08 % Allowed : 28.34 % Favored : 67.58 % 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: 0.22 (0.22), residues: 1479 helix: 0.70 (0.22), residues: 542 sheet: 0.15 (0.31), residues: 288 loop : -0.19 (0.27), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 197 TYR 0.021 0.002 TYR B 217 PHE 0.037 0.003 PHE C 190 TRP 0.057 0.003 TRP B 306 HIS 0.010 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (13796) covalent geometry : angle 0.83210 / 0.40 (19049) hydrogen bonds : bond 0.04539 / 3.03 ( 621) hydrogen bonds : angle 4.91356 / 3.40 ( 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 427 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 375 time to evaluate : 0.508 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: 0.9391 (m-40) cc_final: 0.8998 (t0) REVERT: C 27 PHE cc_start: 0.9212 (m-80) cc_final: 0.8894 (m-80) REVERT: C 54 LEU cc_start: 0.9729 (mt) cc_final: 0.9479 (mt) REVERT: C 82 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7774 (tm-30) REVERT: C 127 ASP cc_start: 0.8989 (p0) cc_final: 0.8458 (m-30) REVERT: C 135 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8889 (mt) REVERT: C 144 TYR cc_start: 0.9008 (t80) cc_final: 0.8789 (t80) REVERT: C 155 GLN cc_start: 0.8314 (pm20) cc_final: 0.7798 (pm20) REVERT: C 188 MET cc_start: 0.9002 (tmm) cc_final: 0.8776 (ppp) REVERT: C 189 VAL cc_start: 0.9548 (t) cc_final: 0.8939 (t) REVERT: C 193 HIS cc_start: 0.9042 (t70) cc_final: 0.8033 (t70) REVERT: C 880 TRP cc_start: 0.8964 (m100) cc_final: 0.8205 (m100) REVERT: C 884 ASN cc_start: 0.8869 (t0) cc_final: 0.8063 (m110) REVERT: C 891 GLU cc_start: 0.9203 (pm20) cc_final: 0.8970 (pm20) REVERT: C 895 PHE cc_start: 0.9069 (t80) cc_final: 0.8322 (t80) REVERT: C 897 LYS cc_start: 0.9323 (mtmt) cc_final: 0.8913 (mmtm) REVERT: C 902 LEU cc_start: 0.9061 (mm) cc_final: 0.8267 (tp) REVERT: C 906 ASN cc_start: 0.9195 (m110) cc_final: 0.8671 (m110) REVERT: C 919 HIS cc_start: 0.8548 (t70) cc_final: 0.8267 (t70) REVERT: C 983 ASP cc_start: 0.7933 (t0) cc_final: 0.7439 (t0) REVERT: C 984 GLU cc_start: 0.8082 (tp30) cc_final: 0.7495 (tp30) REVERT: C 1045 PHE cc_start: 0.9193 (m-80) cc_final: 0.8791 (m-80) REVERT: D 12 ASN cc_start: 0.9227 (m-40) cc_final: 0.8673 (t0) REVERT: D 72 MET cc_start: 0.7895 (ttt) cc_final: 0.7347 (tpt) REVERT: D 74 ARG cc_start: 0.7427 (tmm-80) cc_final: 0.7162 (tmm-80) REVERT: D 155 GLN cc_start: 0.8797 (pm20) cc_final: 0.8412 (pm20) REVERT: D 165 LYS cc_start: 0.9492 (mmmt) cc_final: 0.9147 (mmmm) REVERT: D 188 MET cc_start: 0.8946 (ptp) cc_final: 0.8734 (ttm) REVERT: D 896 ARG cc_start: 0.8481 (ttm110) cc_final: 0.7709 (mtm110) REVERT: D 919 HIS cc_start: 0.8161 (t-170) cc_final: 0.7813 (t70) REVERT: D 983 ASP cc_start: 0.8232 (t0) cc_final: 0.7132 (t0) REVERT: D 989 LEU cc_start: 0.9644 (mt) cc_final: 0.9288 (tp) REVERT: A 18 LYS cc_start: 0.9436 (mmmt) cc_final: 0.9168 (mmtm) REVERT: A 58 TYR cc_start: 0.9215 (p90) cc_final: 0.8917 (p90) REVERT: A 65 ARG cc_start: 0.9136 (tpm170) cc_final: 0.8849 (tpm170) REVERT: A 93 SER cc_start: 0.9518 (m) cc_final: 0.9229 (p) REVERT: A 180 ILE cc_start: 0.9677 (OUTLIER) cc_final: 0.9439 (tp) REVERT: A 212 PHE cc_start: 0.8274 (m-80) cc_final: 0.8052 (m-80) REVERT: A 232 MET cc_start: 0.9237 (mmm) cc_final: 0.8847 (mpp) REVERT: A 244 LEU cc_start: 0.9414 (mt) cc_final: 0.9146 (mt) REVERT: A 253 LYS cc_start: 0.8116 (mmmm) cc_final: 0.7467 (mtpt) REVERT: A 279 MET cc_start: 0.8667 (mmm) cc_final: 0.7698 (tpp) REVERT: A 283 LYS cc_start: 0.9624 (mmtm) cc_final: 0.9351 (tptp) REVERT: A 360 LEU cc_start: 0.8702 (mm) cc_final: 0.8495 (mm) REVERT: A 366 PHE cc_start: 0.9050 (t80) cc_final: 0.8386 (t80) REVERT: B 15 PHE cc_start: 0.8643 (t80) cc_final: 0.7786 (t80) REVERT: B 33 GLU cc_start: 0.9414 (tt0) cc_final: 0.9178 (pt0) REVERT: B 62 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.8945 (mm) REVERT: B 65 ARG cc_start: 0.9282 (mtp85) cc_final: 0.9078 (ptp-110) REVERT: B 75 CYS cc_start: 0.8463 (m) cc_final: 0.7117 (t) REVERT: B 102 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8840 (t) REVERT: B 127 CYS cc_start: 0.8799 (m) cc_final: 0.8570 (m) REVERT: B 271 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8907 (mm) REVERT: B 279 MET cc_start: 0.7516 (ppp) cc_final: 0.6684 (ppp) REVERT: B 321 GLN cc_start: 0.9063 (mt0) cc_final: 0.8515 (mt0) REVERT: B 325 GLN cc_start: 0.9370 (mt0) cc_final: 0.8921 (tm-30) REVERT: B 357 LEU cc_start: 0.9468 (tp) cc_final: 0.9019 (pp) REVERT: B 366 PHE cc_start: 0.9250 (t80) cc_final: 0.8518 (t80) REVERT: B 387 PHE cc_start: 0.9447 (t80) cc_final: 0.9107 (t80) outliers start: 52 outliers final: 41 residues processed: 392 average time/residue: 0.1087 time to fit residues: 64.1682 Evaluate side-chains 402 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 356 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 123 LYS 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 893 ASP 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 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 189 VAL Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 906 ASN Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 1011 ILE Chi-restraints excluded: chain D residue 1014 ILE 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 132 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 HIS 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 B residue 39 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 157 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 Chi-restraints excluded: chain B residue 335 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 133 optimal weight: 10.0000 chunk 139 optimal weight: 0.0670 chunk 49 optimal weight: 0.0050 chunk 145 optimal weight: 6.9990 chunk 32 optimal weight: 0.3980 chunk 114 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.4932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 919 HIS D 184 GLN ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 HIS ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.083118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.055954 restraints weight = 45833.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.058250 restraints weight = 26155.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.059836 restraints weight = 17906.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.060965 restraints weight = 13676.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.061732 restraints weight = 11262.015| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13796 Z= 0.144 Angle : 0.857 15.329 19049 Z= 0.400 Chirality : 0.050 0.458 2193 Planarity : 0.004 0.059 2183 Dihedral : 21.208 162.147 2467 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.32 % Allowed : 28.89 % Favored : 66.80 % 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: 0.24 (0.23), residues: 1479 helix: 0.75 (0.22), residues: 540 sheet: 0.08 (0.31), residues: 284 loop : -0.16 (0.27), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 197 TYR 0.022 0.002 TYR B 217 PHE 0.030 0.002 PHE C 898 TRP 0.037 0.003 TRP B 306 HIS 0.025 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (13796) covalent geometry : angle 0.85659 / 0.40 (19049) hydrogen bonds : bond 0.04412 / 2.94 ( 621) hydrogen bonds : angle 4.84188 / 3.35 ( 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 419 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 364 time to evaluate : 0.510 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: 0.9170 (m-80) cc_final: 0.8863 (m-80) REVERT: C 54 LEU cc_start: 0.9730 (mt) cc_final: 0.9489 (mt) REVERT: C 76 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8305 (p) REVERT: C 127 ASP cc_start: 0.8995 (p0) cc_final: 0.8409 (m-30) REVERT: C 135 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.8886 (mt) REVERT: C 144 TYR cc_start: 0.9128 (t80) cc_final: 0.8884 (t80) REVERT: C 155 GLN cc_start: 0.8234 (pm20) cc_final: 0.7703 (pm20) REVERT: C 189 VAL cc_start: 0.9544 (t) cc_final: 0.8898 (t) REVERT: C 193 HIS cc_start: 0.9041 (t70) cc_final: 0.8016 (t70) REVERT: C 880 TRP cc_start: 0.8929 (m100) cc_final: 0.8131 (m100) REVERT: C 884 ASN cc_start: 0.8882 (t0) cc_final: 0.8050 (m110) REVERT: C 895 PHE cc_start: 0.9149 (t80) cc_final: 0.8353 (t80) REVERT: C 897 LYS cc_start: 0.9315 (mtmt) cc_final: 0.8882 (mmtm) REVERT: C 902 LEU cc_start: 0.9044 (mm) cc_final: 0.8334 (tp) REVERT: C 904 LEU cc_start: 0.9758 (tp) cc_final: 0.9474 (pp) REVERT: C 906 ASN cc_start: 0.9122 (m110) cc_final: 0.8558 (m110) REVERT: C 983 ASP cc_start: 0.7668 (t0) cc_final: 0.7183 (t0) REVERT: C 984 GLU cc_start: 0.8028 (tp30) cc_final: 0.7456 (tp30) REVERT: C 1045 PHE cc_start: 0.9174 (m-80) cc_final: 0.8790 (m-80) REVERT: D 12 ASN cc_start: 0.9212 (m-40) cc_final: 0.8721 (t0) REVERT: D 72 MET cc_start: 0.7750 (ttt) cc_final: 0.7271 (tpt) REVERT: D 74 ARG cc_start: 0.7454 (tmm-80) cc_final: 0.7178 (tmm-80) REVERT: D 155 GLN cc_start: 0.8760 (pm20) cc_final: 0.8494 (pm20) REVERT: D 165 LYS cc_start: 0.9491 (mmmt) cc_final: 0.9136 (mmmm) REVERT: D 890 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8345 (ttpt) REVERT: D 919 HIS cc_start: 0.8111 (t-170) cc_final: 0.7737 (t70) REVERT: D 983 ASP cc_start: 0.8205 (t0) cc_final: 0.7049 (t70) REVERT: D 989 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9271 (tp) REVERT: A 58 TYR cc_start: 0.9204 (p90) cc_final: 0.8915 (p90) REVERT: A 65 ARG cc_start: 0.9123 (tpm170) cc_final: 0.8829 (tpm170) REVERT: A 93 SER cc_start: 0.9506 (m) cc_final: 0.9267 (p) REVERT: A 180 ILE cc_start: 0.9683 (OUTLIER) cc_final: 0.9445 (tp) REVERT: A 212 PHE cc_start: 0.8287 (m-80) cc_final: 0.8064 (m-80) REVERT: A 232 MET cc_start: 0.9251 (mmm) cc_final: 0.8855 (mpp) REVERT: A 244 LEU cc_start: 0.9401 (mt) cc_final: 0.9140 (mt) REVERT: A 253 LYS cc_start: 0.8064 (mmmm) cc_final: 0.7568 (mmmm) REVERT: A 279 MET cc_start: 0.8636 (mmm) cc_final: 0.7607 (tpp) REVERT: A 360 LEU cc_start: 0.8732 (mm) cc_final: 0.8515 (mm) REVERT: A 366 PHE cc_start: 0.9045 (t80) cc_final: 0.8355 (t80) REVERT: B 15 PHE cc_start: 0.8635 (t80) cc_final: 0.7733 (t80) REVERT: B 16 TYR cc_start: 0.8408 (m-10) cc_final: 0.8020 (m-10) REVERT: B 33 GLU cc_start: 0.9412 (tt0) cc_final: 0.8874 (tm-30) REVERT: B 62 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.8967 (mm) REVERT: B 65 ARG cc_start: 0.9278 (mtp85) cc_final: 0.8945 (ptp-110) REVERT: B 75 CYS cc_start: 0.8506 (m) cc_final: 0.7278 (t) REVERT: B 127 CYS cc_start: 0.8782 (m) cc_final: 0.8557 (m) REVERT: B 271 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8937 (mm) REVERT: B 279 MET cc_start: 0.7399 (ppp) cc_final: 0.6589 (ppp) REVERT: B 321 GLN cc_start: 0.9013 (mt0) cc_final: 0.8052 (mt0) REVERT: B 325 GLN cc_start: 0.9340 (mt0) cc_final: 0.9033 (pt0) REVERT: B 357 LEU cc_start: 0.9418 (tp) cc_final: 0.9013 (pp) REVERT: B 366 PHE cc_start: 0.9262 (t80) cc_final: 0.8487 (t80) REVERT: B 387 PHE cc_start: 0.9424 (t80) cc_final: 0.9133 (t80) outliers start: 55 outliers final: 42 residues processed: 383 average time/residue: 0.1125 time to fit residues: 64.1052 Evaluate side-chains 396 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 347 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 123 LYS 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 893 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 998 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 189 VAL Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 890 LYS Chi-restraints excluded: chain D residue 989 LEU Chi-restraints excluded: chain D residue 1014 ILE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1026 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 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 B residue 44 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 157 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 Chi-restraints excluded: chain B residue 335 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 70 optimal weight: 10.0000 chunk 148 optimal weight: 50.0000 chunk 152 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 125 optimal weight: 0.1980 chunk 77 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** 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 = 0.3576 r_free = 0.3576 target = 0.083162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.055264 restraints weight = 46997.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.057554 restraints weight = 27174.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.059160 restraints weight = 18735.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.060300 restraints weight = 14369.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.061100 restraints weight = 11849.033| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13796 Z= 0.168 Angle : 0.841 14.518 19049 Z= 0.400 Chirality : 0.049 0.440 2193 Planarity : 0.004 0.083 2183 Dihedral : 21.198 162.386 2467 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.24 % Allowed : 28.81 % Favored : 66.95 % 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: 0.25 (0.23), residues: 1479 helix: 0.74 (0.22), residues: 534 sheet: 0.00 (0.31), residues: 289 loop : -0.08 (0.27), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 20 TYR 0.018 0.002 TYR B 217 PHE 0.042 0.003 PHE B 27 TRP 0.042 0.003 TRP A 296 HIS 0.010 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (13796) covalent geometry : angle 0.84102 / 0.40 (19049) hydrogen bonds : bond 0.04367 / 2.92 ( 621) hydrogen bonds : angle 4.91255 / 3.41 ( 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 407 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 353 time to evaluate : 0.510 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: C 2 LYS cc_start: 0.9334 (tppp) cc_final: 0.9101 (tppt) REVERT: C 27 PHE cc_start: 0.9211 (m-80) cc_final: 0.8980 (m-10) REVERT: C 54 LEU cc_start: 0.9696 (mt) cc_final: 0.9442 (mt) REVERT: C 76 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8285 (p) REVERT: C 82 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7705 (tm-30) REVERT: C 127 ASP cc_start: 0.8992 (p0) cc_final: 0.8551 (m-30) REVERT: C 131 ASP cc_start: 0.8708 (t0) cc_final: 0.8112 (t0) REVERT: C 135 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.8790 (mt) REVERT: C 144 TYR cc_start: 0.9210 (t80) cc_final: 0.8883 (t80) REVERT: C 155 GLN cc_start: 0.8276 (pm20) cc_final: 0.7717 (pm20) REVERT: C 189 VAL cc_start: 0.9535 (t) cc_final: 0.8927 (t) REVERT: C 193 HIS cc_start: 0.9053 (t70) cc_final: 0.8048 (t70) REVERT: C 880 TRP cc_start: 0.9002 (m100) cc_final: 0.8253 (m100) REVERT: C 884 ASN cc_start: 0.8849 (t0) cc_final: 0.8031 (m110) REVERT: C 895 PHE cc_start: 0.9150 (t80) cc_final: 0.8419 (t80) REVERT: C 897 LYS cc_start: 0.9328 (mtmt) cc_final: 0.8871 (mmtp) REVERT: C 902 LEU cc_start: 0.9031 (mm) cc_final: 0.8196 (tp) REVERT: C 906 ASN cc_start: 0.9127 (m110) cc_final: 0.8548 (m110) REVERT: C 983 ASP cc_start: 0.7766 (t0) cc_final: 0.7260 (t0) REVERT: C 984 GLU cc_start: 0.8049 (tp30) cc_final: 0.7454 (tp30) REVERT: C 1045 PHE cc_start: 0.9228 (m-80) cc_final: 0.8931 (m-80) REVERT: D 12 ASN cc_start: 0.9204 (m-40) cc_final: 0.8807 (t0) REVERT: D 72 MET cc_start: 0.7814 (ttt) cc_final: 0.7295 (tpt) REVERT: D 74 ARG cc_start: 0.7479 (tmm-80) cc_final: 0.7243 (tmm-80) REVERT: D 155 GLN cc_start: 0.8809 (pm20) cc_final: 0.8543 (pm20) REVERT: D 165 LYS cc_start: 0.9484 (mmmt) cc_final: 0.9147 (mmmm) REVERT: D 188 MET cc_start: 0.8975 (ttm) cc_final: 0.8448 (tmm) REVERT: D 890 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8347 (ttpt) REVERT: D 919 HIS cc_start: 0.8246 (t-170) cc_final: 0.7834 (t70) REVERT: D 983 ASP cc_start: 0.8258 (t0) cc_final: 0.7177 (t70) REVERT: D 989 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9286 (tp) REVERT: D 1020 MET cc_start: 0.9209 (pmm) cc_final: 0.9002 (pmm) REVERT: A 58 TYR cc_start: 0.9223 (p90) cc_final: 0.8936 (p90) REVERT: A 65 ARG cc_start: 0.9145 (tpm170) cc_final: 0.8855 (tpm170) REVERT: A 93 SER cc_start: 0.9516 (m) cc_final: 0.9303 (p) REVERT: A 180 ILE cc_start: 0.9672 (OUTLIER) cc_final: 0.9423 (tp) REVERT: A 212 PHE cc_start: 0.8318 (m-80) cc_final: 0.8106 (m-80) REVERT: A 232 MET cc_start: 0.9310 (mmm) cc_final: 0.8926 (mpp) REVERT: A 244 LEU cc_start: 0.9429 (mt) cc_final: 0.9184 (mt) REVERT: A 253 LYS cc_start: 0.8016 (mmmm) cc_final: 0.7679 (mmmm) REVERT: A 279 MET cc_start: 0.8646 (mmm) cc_final: 0.7671 (tpp) REVERT: A 283 LYS cc_start: 0.9626 (mmtm) cc_final: 0.9367 (tptt) REVERT: A 360 LEU cc_start: 0.8750 (mm) cc_final: 0.8536 (mm) REVERT: A 366 PHE cc_start: 0.9061 (t80) cc_final: 0.8371 (t80) REVERT: B 15 PHE cc_start: 0.8496 (t80) cc_final: 0.7963 (t80) REVERT: B 16 TYR cc_start: 0.8432 (m-10) cc_final: 0.8021 (m-10) REVERT: B 27 PHE cc_start: 0.9652 (t80) cc_final: 0.9425 (t80) REVERT: B 33 GLU cc_start: 0.9404 (tt0) cc_final: 0.8873 (tm-30) REVERT: B 62 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.8926 (mm) REVERT: B 65 ARG cc_start: 0.9278 (mtp85) cc_final: 0.9044 (ptp-110) REVERT: B 75 CYS cc_start: 0.8532 (m) cc_final: 0.7312 (t) REVERT: B 99 PHE cc_start: 0.8916 (m-80) cc_final: 0.8673 (m-80) REVERT: B 127 CYS cc_start: 0.8847 (m) cc_final: 0.8618 (m) REVERT: B 165 TYR cc_start: 0.9454 (t80) cc_final: 0.9181 (t80) REVERT: B 271 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8939 (mm) REVERT: B 279 MET cc_start: 0.7381 (ppp) cc_final: 0.6543 (ppp) REVERT: B 321 GLN cc_start: 0.9027 (mt0) cc_final: 0.8467 (mt0) REVERT: B 357 LEU cc_start: 0.9494 (tp) cc_final: 0.9095 (pp) REVERT: B 366 PHE cc_start: 0.9290 (t80) cc_final: 0.8525 (t80) REVERT: B 387 PHE cc_start: 0.9421 (t80) cc_final: 0.9071 (t80) outliers start: 54 outliers final: 42 residues processed: 375 average time/residue: 0.1129 time to fit residues: 63.2994 Evaluate side-chains 393 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 344 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 123 LYS 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 893 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 998 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 154 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 890 LYS Chi-restraints excluded: chain D residue 989 LEU Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 1014 ILE Chi-restraints excluded: chain D residue 1024 ILE Chi-restraints excluded: chain D residue 1026 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 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 B residue 44 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 157 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 Chi-restraints excluded: chain B residue 335 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: 0.5980 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 63 ASN C 919 HIS ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3590 r_free = 0.3590 target = 0.084067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.055769 restraints weight = 45992.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058125 restraints weight = 26532.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.059765 restraints weight = 18261.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.060899 restraints weight = 13985.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.061735 restraints weight = 11538.055| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13796 Z= 0.150 Angle : 0.866 14.611 19049 Z= 0.403 Chirality : 0.050 0.432 2193 Planarity : 0.004 0.054 2183 Dihedral : 21.179 162.615 2467 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.85 % Allowed : 29.36 % Favored : 66.80 % 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: 0.27 (0.23), residues: 1479 helix: 0.75 (0.22), residues: 533 sheet: 0.04 (0.31), residues: 291 loop : -0.09 (0.27), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 347 TYR 0.026 0.002 TYR A 160 PHE 0.036 0.002 PHE C 898 TRP 0.052 0.003 TRP A 296 HIS 0.008 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (13796) covalent geometry : angle 0.86610 / 0.40 (19049) hydrogen bonds : bond 0.04236 / 2.84 ( 621) hydrogen bonds : angle 4.88769 / 3.38 ( 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 406 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 357 time to evaluate : 0.503 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: 0.9141 (m-40) cc_final: 0.8769 (t0) REVERT: C 27 PHE cc_start: 0.9202 (m-80) cc_final: 0.8994 (m-10) REVERT: C 54 LEU cc_start: 0.9688 (mt) cc_final: 0.9362 (mt) REVERT: C 55 TYR cc_start: 0.8814 (m-10) cc_final: 0.8601 (m-10) REVERT: C 76 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8323 (p) REVERT: C 123 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8460 (pptt) REVERT: C 127 ASP cc_start: 0.8976 (p0) cc_final: 0.8541 (m-30) REVERT: C 131 ASP cc_start: 0.8655 (t0) cc_final: 0.8063 (t0) REVERT: C 135 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8924 (mt) REVERT: C 144 TYR cc_start: 0.9173 (t80) cc_final: 0.8926 (t80) REVERT: C 155 GLN cc_start: 0.8200 (pm20) cc_final: 0.7658 (pm20) REVERT: C 189 VAL cc_start: 0.9550 (t) cc_final: 0.8958 (t) REVERT: C 193 HIS cc_start: 0.9056 (t70) cc_final: 0.8053 (t70) REVERT: C 880 TRP cc_start: 0.9040 (m100) cc_final: 0.8207 (m100) REVERT: C 884 ASN cc_start: 0.8827 (t0) cc_final: 0.8004 (m110) REVERT: C 895 PHE cc_start: 0.9144 (t80) cc_final: 0.8402 (t80) REVERT: C 897 LYS cc_start: 0.9322 (mtmt) cc_final: 0.8875 (mmtp) REVERT: C 902 LEU cc_start: 0.9013 (mm) cc_final: 0.8262 (tp) REVERT: C 904 LEU cc_start: 0.9752 (tp) cc_final: 0.9491 (pp) REVERT: C 906 ASN cc_start: 0.9116 (m110) cc_final: 0.8557 (m110) REVERT: C 983 ASP cc_start: 0.7744 (t0) cc_final: 0.7285 (t0) REVERT: C 984 GLU cc_start: 0.7923 (tp30) cc_final: 0.7340 (tp30) REVERT: D 12 ASN cc_start: 0.9301 (m-40) cc_final: 0.8907 (t0) REVERT: D 72 MET cc_start: 0.7733 (ttt) cc_final: 0.7172 (tpt) REVERT: D 74 ARG cc_start: 0.7551 (tmm-80) cc_final: 0.7326 (tmm-80) REVERT: D 142 LEU cc_start: 0.8873 (pt) cc_final: 0.8511 (pt) REVERT: D 155 GLN cc_start: 0.8812 (pm20) cc_final: 0.8581 (pm20) REVERT: D 165 LYS cc_start: 0.9491 (mmmt) cc_final: 0.9154 (mmmm) REVERT: D 188 MET cc_start: 0.9006 (ttm) cc_final: 0.8478 (tmm) REVERT: D 890 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8338 (ttpt) REVERT: D 919 HIS cc_start: 0.8223 (t-170) cc_final: 0.7808 (t70) REVERT: D 983 ASP cc_start: 0.8236 (t0) cc_final: 0.7125 (t70) REVERT: D 989 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9271 (tp) REVERT: D 1016 HIS cc_start: 0.7900 (m-70) cc_final: 0.7555 (m170) REVERT: D 1020 MET cc_start: 0.9183 (pmm) cc_final: 0.8917 (pmm) REVERT: A 1 MET cc_start: 0.8117 (tmm) cc_final: 0.7752 (tpp) REVERT: A 58 TYR cc_start: 0.9204 (p90) cc_final: 0.8910 (p90) REVERT: A 65 ARG cc_start: 0.9139 (tpm170) cc_final: 0.8843 (tpm170) REVERT: A 149 LYS cc_start: 0.9664 (mttm) cc_final: 0.9304 (mttm) REVERT: A 180 ILE cc_start: 0.9673 (OUTLIER) cc_final: 0.9418 (tp) REVERT: A 212 PHE cc_start: 0.8343 (m-80) cc_final: 0.8114 (m-80) REVERT: A 232 MET cc_start: 0.9319 (mmm) cc_final: 0.8934 (mpp) REVERT: A 244 LEU cc_start: 0.9437 (mt) cc_final: 0.9204 (mt) REVERT: A 253 LYS cc_start: 0.7968 (mmmm) cc_final: 0.7622 (mmmm) REVERT: A 279 MET cc_start: 0.8611 (mmm) cc_final: 0.7611 (tpp) REVERT: A 286 LEU cc_start: 0.9807 (pt) cc_final: 0.9596 (tp) REVERT: A 366 PHE cc_start: 0.9060 (t80) cc_final: 0.8362 (t80) REVERT: B 1 MET cc_start: 0.7796 (tpp) cc_final: 0.7516 (tpt) REVERT: B 15 PHE cc_start: 0.8526 (t80) cc_final: 0.7969 (t80) REVERT: B 16 TYR cc_start: 0.8399 (m-10) cc_final: 0.7992 (m-10) REVERT: B 33 GLU cc_start: 0.9398 (tt0) cc_final: 0.9158 (pt0) REVERT: B 62 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.8954 (mm) REVERT: B 65 ARG cc_start: 0.9276 (mtp85) cc_final: 0.8942 (ptp-110) REVERT: B 75 CYS cc_start: 0.8528 (m) cc_final: 0.7276 (t) REVERT: B 99 PHE cc_start: 0.8918 (m-80) cc_final: 0.8663 (m-80) REVERT: B 127 CYS cc_start: 0.8807 (m) cc_final: 0.8569 (m) REVERT: B 165 TYR cc_start: 0.9446 (t80) cc_final: 0.9174 (t80) REVERT: B 260 PHE cc_start: 0.8944 (m-10) cc_final: 0.8653 (m-80) REVERT: B 271 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8942 (mm) REVERT: B 279 MET cc_start: 0.7350 (ppp) cc_final: 0.6551 (ppp) REVERT: B 321 GLN cc_start: 0.9015 (mt0) cc_final: 0.8444 (mt0) REVERT: B 357 LEU cc_start: 0.9489 (tp) cc_final: 0.9091 (pp) REVERT: B 366 PHE cc_start: 0.9281 (t80) cc_final: 0.8503 (t80) REVERT: B 387 PHE cc_start: 0.9397 (t80) cc_final: 0.9046 (t80) outliers start: 49 outliers final: 36 residues processed: 378 average time/residue: 0.1096 time to fit residues: 62.3283 Evaluate side-chains 389 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 345 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 123 LYS 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 893 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 976 ARG 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 154 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 890 LYS Chi-restraints excluded: chain D residue 989 LEU Chi-restraints excluded: chain D residue 1014 ILE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1026 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 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 B residue 44 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 157 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 Chi-restraints excluded: chain B residue 335 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** 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 = 0.3578 r_free = 0.3578 target = 0.083347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.055262 restraints weight = 46700.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.057605 restraints weight = 27219.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.059210 restraints weight = 18725.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.060339 restraints weight = 14376.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.061074 restraints weight = 11899.413| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13796 Z= 0.166 Angle : 0.860 15.833 19049 Z= 0.402 Chirality : 0.050 0.435 2193 Planarity : 0.004 0.053 2183 Dihedral : 21.221 163.324 2467 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.85 % Allowed : 29.83 % Favored : 66.33 % 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: 0.29 (0.23), residues: 1479 helix: 0.82 (0.23), residues: 533 sheet: 0.04 (0.31), residues: 290 loop : -0.12 (0.27), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 197 TYR 0.020 0.002 TYR B 160 PHE 0.055 0.003 PHE B 27 TRP 0.046 0.003 TRP A 296 HIS 0.007 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (13796) covalent geometry : angle 0.85963 / 0.40 (19049) hydrogen bonds : bond 0.04187 / 2.80 ( 621) hydrogen bonds : angle 4.90353 / 3.38 ( 1674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2949.54 seconds wall clock time: 51 minutes 54.68 seconds (3114.68 seconds total)