Starting phenix.real_space_refine on Sun Jun 15 04:16:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z03_14403/06_2025/7z03_14403.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z03_14403/06_2025/7z03_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_14403/06_2025/7z03_14403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z03_14403/06_2025/7z03_14403.map" model { file = "/net/cci-nas-00/data/ceres_data/7z03_14403/06_2025/7z03_14403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z03_14403/06_2025/7z03_14403.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.21, per 1000 atoms: 0.69 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: 3.68 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 5.32 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: 5.13 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4039 1.34 - 1.46: 2454 1.46 - 1.57: 7091 1.57 - 1.69: 160 1.69 - 1.81: 52 Bond restraints: 13796 Sorted by residual: bond pdb=" C4 ADP D1101 " pdb=" C5 ADP D1101 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 ADP C1101 " pdb=" C5 ADP C1101 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C5 ADP D1101 " pdb=" C6 ADP D1101 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C5 ADP C1101 " pdb=" C6 ADP C1101 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" N ILE A 223 " pdb=" CA ILE A 223 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 1.01e+01 ... (remaining 13791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 18839 2.69 - 5.37: 182 5.37 - 8.06: 18 8.06 - 10.75: 6 10.75 - 13.44: 4 Bond angle restraints: 19049 Sorted by residual: angle pdb=" C ASN D 12 " pdb=" CA ASN D 12 " pdb=" CB ASN D 12 " ideal model delta sigma weight residual 116.54 109.97 6.57 1.15e+00 7.56e-01 3.26e+01 angle pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" O GLY A 221 " ideal model delta sigma weight residual 121.61 115.82 5.79 1.05e+00 9.07e-01 3.04e+01 angle pdb=" CA GLY B 221 " pdb=" C GLY B 221 " pdb=" O GLY B 221 " ideal model delta sigma weight residual 121.78 117.04 4.74 9.10e-01 1.21e+00 2.71e+01 angle pdb=" PA ADP C1101 " pdb=" O3A ADP C1101 " pdb=" PB ADP C1101 " ideal model delta sigma weight residual 120.50 133.94 -13.44 3.00e+00 1.11e-01 2.01e+01 angle pdb=" PA ADP D1101 " pdb=" O3A ADP D1101 " pdb=" PB ADP D1101 " ideal model delta sigma weight residual 120.50 133.52 -13.02 3.00e+00 1.11e-01 1.88e+01 ... (remaining 19044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.46: 7608 34.46 - 68.93: 442 68.93 - 103.39: 19 103.39 - 137.85: 5 137.85 - 172.32: 2 Dihedral angle restraints: 8076 sinusoidal: 3741 harmonic: 4335 Sorted by residual: dihedral pdb=" C5' ADP D1101 " pdb=" O5' ADP D1101 " pdb=" PA ADP D1101 " pdb=" O2A ADP D1101 " ideal model delta sinusoidal sigma weight residual -60.00 66.10 -126.09 1 2.00e+01 2.50e-03 3.81e+01 dihedral pdb=" O2A ADP D1101 " pdb=" O3A ADP D1101 " pdb=" PA ADP D1101 " pdb=" PB ADP D1101 " ideal model delta sinusoidal sigma weight residual -60.00 65.40 -125.40 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O1B ADP D1101 " pdb=" O3A ADP D1101 " pdb=" PB ADP D1101 " pdb=" PA ADP D1101 " ideal model delta sinusoidal sigma weight residual -60.00 57.79 -117.80 1 2.00e+01 2.50e-03 3.52e+01 ... (remaining 8073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1885 0.058 - 0.115: 277 0.115 - 0.173: 24 0.173 - 0.231: 3 0.231 - 0.288: 4 Chirality restraints: 2193 Sorted by residual: chirality pdb=" CA TYR A 237 " pdb=" N TYR A 237 " pdb=" C TYR A 237 " pdb=" CB TYR A 237 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C3' ADP C1101 " pdb=" C2' ADP C1101 " pdb=" C4' ADP C1101 " pdb=" O3' ADP C1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C3' ADP D1101 " pdb=" C2' ADP D1101 " pdb=" C4' ADP D1101 " pdb=" O3' ADP D1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2190 not shown) Planarity restraints: 2183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 58 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO D 59 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 47 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C GLY A 47 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY A 47 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP A 48 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 41 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C ALA D 41 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA D 41 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY D 42 " 0.008 2.00e-02 2.50e+03 ... (remaining 2180 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 12 2.18 - 2.86: 4464 2.86 - 3.54: 18886 3.54 - 4.22: 31260 4.22 - 4.90: 53778 Nonbonded interactions: 108400 Sorted by model distance: nonbonded pdb=" OD2 ASP A 48 " pdb="MN MN A 501 " model vdw 1.498 2.320 nonbonded pdb=" OD2 ASP A 48 " pdb="MN MN A 502 " model vdw 1.600 2.320 nonbonded pdb=" ND2 ASN A 83 " pdb=" OP2 DC F 55 " model vdw 1.761 3.120 nonbonded pdb=" OD1 ASN B 83 " pdb="MN MN B 502 " model vdw 1.806 2.320 nonbonded pdb=" O3B ADP C1101 " pdb="MG MG C1102 " model vdw 1.816 2.170 ... (remaining 108395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 137 or resid 153 through 343 or resid 356 throug \ h 395 or resid 501 through 502)) selection = (chain 'B' and (resid 1 through 189 or resid 204 through 395 or resid 501 throug \ h 502)) } ncs_group { reference = (chain 'C' and (resid 1 through 200 or resid 875 through 1047 or resid 1101 thro \ ugh 1102)) selection = (chain 'D' and (resid 1 through 200 or resid 875 through 1047 or resid 1101 thro \ ugh 1102)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 39.270 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 13796 Z= 0.241 Angle : 0.699 13.436 19049 Z= 0.396 Chirality : 0.042 0.288 2193 Planarity : 0.003 0.048 2183 Dihedral : 18.983 172.318 5264 Min Nonbonded Distance : 1.498 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.08 % Allowed : 0.31 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP A 9 HIS 0.009 0.001 HIS A 392 PHE 0.014 0.001 PHE C 895 TYR 0.014 0.001 TYR C 882 ARG 0.009 0.000 ARG D 976 Details of bonding type rmsd hydrogen bonds : bond 0.14864 ( 621) hydrogen bonds : angle 5.72061 ( 1674) covalent geometry : bond 0.00417 (13796) covalent geometry : angle 0.69945 (19049) *********************** 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 : 1.394 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: C 189 VAL cc_start: 0.8396 (t) cc_final: 0.8010 (t) REVERT: C 1033 ILE cc_start: 0.6499 (mm) cc_final: 0.6245 (mp) REVERT: D 52 LEU cc_start: 0.7449 (tp) cc_final: 0.7076 (tp) REVERT: A 93 SER cc_start: 0.7256 (m) cc_final: 0.6498 (p) REVERT: B 246 PHE cc_start: 0.6214 (m-80) cc_final: 0.5736 (m-10) outliers start: 1 outliers final: 1 residues processed: 598 average time/residue: 0.2751 time to fit residues: 228.6140 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 : 1.347 ------------------------------------------------------------------------------- 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 130 optimal weight: 0.0670 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN ** 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 = 0.3628 r_free = 0.3628 target = 0.087615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.059846 restraints weight = 43495.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.062226 restraints weight = 24997.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.063899 restraints weight = 17149.375| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13796 Z= 0.173 Angle : 0.844 15.893 19049 Z= 0.404 Chirality : 0.047 0.229 2193 Planarity : 0.005 0.084 2183 Dihedral : 21.167 175.055 2467 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.59 % Allowed : 18.37 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1479 helix: 1.16 (0.22), residues: 541 sheet: 0.10 (0.32), residues: 264 loop : -0.39 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 880 HIS 0.007 0.001 HIS B 24 PHE 0.043 0.003 PHE C 895 TYR 0.025 0.003 TYR D 55 ARG 0.006 0.001 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.04752 ( 621) hydrogen bonds : angle 4.96485 ( 1674) covalent geometry : bond 0.00371 (13796) covalent geometry : angle 0.84358 (19049) *********************** 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 492 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 459 time to evaluate : 1.345 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: 0.9367 (m-40) cc_final: 0.9076 (t0) REVERT: C 22 PHE cc_start: 0.8788 (m-80) cc_final: 0.8363 (m-80) REVERT: C 54 LEU cc_start: 0.9773 (mt) cc_final: 0.9558 (mt) REVERT: C 74 ARG cc_start: 0.8854 (mmp80) cc_final: 0.8204 (mmp-170) REVERT: C 85 PHE cc_start: 0.9529 (p90) cc_final: 0.9201 (p90) REVERT: C 95 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8394 (t80) REVERT: C 123 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8537 (pptt) REVERT: C 139 LEU cc_start: 0.9649 (tt) cc_final: 0.9433 (pp) REVERT: C 171 GLU cc_start: 0.9127 (pt0) cc_final: 0.8921 (pp20) REVERT: C 172 LEU cc_start: 0.9315 (mt) cc_final: 0.9026 (pp) REVERT: C 182 TYR cc_start: 0.8843 (m-80) cc_final: 0.8149 (m-80) REVERT: C 189 VAL cc_start: 0.9519 (t) cc_final: 0.8827 (t) REVERT: C 197 ARG cc_start: 0.9169 (ptp-170) cc_final: 0.8797 (ptt180) REVERT: C 880 TRP cc_start: 0.9123 (m100) cc_final: 0.8550 (m100) REVERT: C 882 TYR cc_start: 0.8314 (m-80) cc_final: 0.8080 (m-80) REVERT: C 883 LEU cc_start: 0.9626 (mt) cc_final: 0.9248 (mt) REVERT: C 895 PHE cc_start: 0.9025 (t80) cc_final: 0.8159 (t80) REVERT: C 902 LEU cc_start: 0.9172 (mm) cc_final: 0.8359 (tp) REVERT: C 906 ASN cc_start: 0.9112 (m110) cc_final: 0.8558 (m110) REVERT: C 922 TYR cc_start: 0.8835 (m-80) cc_final: 0.8387 (m-10) REVERT: C 955 GLU cc_start: 0.9184 (mp0) cc_final: 0.8972 (mp0) REVERT: C 973 HIS cc_start: 0.9214 (p90) cc_final: 0.8905 (p90) REVERT: C 1016 HIS cc_start: 0.7716 (m170) cc_final: 0.7504 (m170) REVERT: C 1020 MET cc_start: 0.8683 (mmt) cc_final: 0.8355 (mmm) REVERT: D 1 MET cc_start: 0.7906 (tmm) cc_final: 0.7696 (tmm) REVERT: D 12 ASN cc_start: 0.9286 (m-40) cc_final: 0.8829 (t0) REVERT: D 55 TYR cc_start: 0.8559 (m-10) cc_final: 0.8038 (m-10) REVERT: D 72 MET cc_start: 0.7652 (ttm) cc_final: 0.7015 (ttt) REVERT: D 74 ARG cc_start: 0.8639 (mmp80) cc_final: 0.8092 (mmp-170) REVERT: D 84 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8650 (mm-30) REVERT: D 92 TYR cc_start: 0.8544 (m-80) cc_final: 0.7730 (m-10) REVERT: D 162 LEU cc_start: 0.9537 (mt) cc_final: 0.9230 (mp) REVERT: D 165 LYS cc_start: 0.9504 (mmmt) cc_final: 0.9259 (mtpt) REVERT: D 184 GLN cc_start: 0.9291 (mp10) cc_final: 0.8963 (mp10) REVERT: D 188 MET cc_start: 0.9068 (ptp) cc_final: 0.8786 (ttm) REVERT: D 190 PHE cc_start: 0.9149 (t80) cc_final: 0.8814 (t80) REVERT: D 197 ARG cc_start: 0.9451 (tpt90) cc_final: 0.9064 (tpt90) REVERT: D 884 ASN cc_start: 0.8806 (t0) cc_final: 0.8572 (t0) REVERT: D 894 LYS cc_start: 0.9205 (ttpt) cc_final: 0.8957 (ttmt) REVERT: D 914 GLN cc_start: 0.9460 (tp40) cc_final: 0.9012 (tp-100) REVERT: D 919 HIS cc_start: 0.8140 (t-170) cc_final: 0.7767 (t70) REVERT: D 941 GLN cc_start: 0.9179 (mt0) cc_final: 0.8763 (pt0) REVERT: D 989 LEU cc_start: 0.9707 (mt) cc_final: 0.9291 (tp) REVERT: D 1011 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.8787 (mm) REVERT: D 1016 HIS cc_start: 0.7925 (m-70) cc_final: 0.7708 (m170) REVERT: D 1017 VAL cc_start: 0.9590 (m) cc_final: 0.9358 (p) REVERT: D 1045 PHE cc_start: 0.8490 (m-80) cc_final: 0.8262 (m-80) REVERT: A 10 HIS cc_start: 0.9196 (m-70) cc_final: 0.8806 (m-70) REVERT: A 18 LYS cc_start: 0.9260 (mmmt) cc_final: 0.8896 (mmtm) REVERT: A 65 ARG cc_start: 0.9141 (tpm170) cc_final: 0.8845 (tpm170) REVERT: A 93 SER cc_start: 0.9529 (m) cc_final: 0.8869 (p) REVERT: A 149 LYS cc_start: 0.9633 (mttm) cc_final: 0.9171 (mttt) REVERT: A 212 PHE cc_start: 0.8283 (m-80) cc_final: 0.7962 (m-80) REVERT: A 232 MET cc_start: 0.9178 (mmm) cc_final: 0.8915 (mpp) REVERT: A 242 ILE cc_start: 0.9328 (tp) cc_final: 0.9087 (tp) REVERT: A 244 LEU cc_start: 0.9232 (mt) cc_final: 0.8684 (mt) REVERT: A 246 PHE cc_start: 0.8956 (m-80) cc_final: 0.7976 (m-80) REVERT: A 253 LYS cc_start: 0.8277 (mmmm) cc_final: 0.7768 (mmmm) REVERT: A 306 TRP cc_start: 0.8889 (m-10) cc_final: 0.8340 (m-10) REVERT: A 318 HIS cc_start: 0.8598 (m170) cc_final: 0.8316 (m90) REVERT: A 357 LEU cc_start: 0.9291 (mp) cc_final: 0.8968 (mt) REVERT: A 366 PHE cc_start: 0.9069 (t80) cc_final: 0.8616 (t80) REVERT: B 15 PHE cc_start: 0.8936 (t80) cc_final: 0.7222 (t80) REVERT: B 16 TYR cc_start: 0.8371 (m-80) cc_final: 0.8010 (m-10) REVERT: B 18 LYS cc_start: 0.9058 (mmtm) cc_final: 0.8694 (mtmm) REVERT: B 154 LEU cc_start: 0.8672 (pt) cc_final: 0.8265 (mp) REVERT: B 207 PHE cc_start: 0.8340 (t80) cc_final: 0.7069 (t80) REVERT: B 271 LEU cc_start: 0.9083 (mm) cc_final: 0.8756 (mm) REVERT: B 306 TRP cc_start: 0.7221 (m-10) cc_final: 0.6829 (m-10) REVERT: B 317 LEU cc_start: 0.9368 (tp) cc_final: 0.8947 (tp) REVERT: B 321 GLN cc_start: 0.9037 (mt0) cc_final: 0.8654 (mt0) REVERT: B 336 LEU cc_start: 0.8307 (mt) cc_final: 0.7646 (mp) REVERT: B 366 PHE cc_start: 0.9218 (t80) cc_final: 0.8876 (t80) REVERT: B 386 LEU cc_start: 0.9506 (mt) cc_final: 0.9083 (pp) outliers start: 33 outliers final: 17 residues processed: 470 average time/residue: 0.2377 time to fit residues: 162.5543 Evaluate side-chains 417 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 397 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 975 THR 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 B residue 79 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 169 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 18 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 119 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 79 optimal weight: 0.0970 chunk 117 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** 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 = 0.3605 r_free = 0.3605 target = 0.084641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.057169 restraints weight = 44245.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.059487 restraints weight = 25068.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.061072 restraints weight = 17081.677| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13796 Z= 0.160 Angle : 0.811 13.913 19049 Z= 0.386 Chirality : 0.046 0.343 2193 Planarity : 0.004 0.042 2183 Dihedral : 21.150 177.697 2467 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.61 % Allowed : 21.51 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1479 helix: 1.03 (0.23), residues: 534 sheet: 0.19 (0.33), residues: 251 loop : -0.38 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 296 HIS 0.019 0.001 HIS A 385 PHE 0.028 0.003 PHE D 33 TYR 0.025 0.003 TYR A 237 ARG 0.005 0.001 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 621) hydrogen bonds : angle 4.78424 ( 1674) covalent geometry : bond 0.00350 (13796) covalent geometry : angle 0.81117 (19049) *********************** 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 453 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 407 time to evaluate : 1.992 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: 0.9403 (m-40) cc_final: 0.9026 (m-40) REVERT: C 22 PHE cc_start: 0.8813 (m-80) cc_final: 0.8479 (m-80) REVERT: C 45 THR cc_start: 0.9779 (m) cc_final: 0.9562 (p) REVERT: C 54 LEU cc_start: 0.9769 (mt) cc_final: 0.9542 (mt) REVERT: C 72 MET cc_start: 0.8213 (ppp) cc_final: 0.7444 (ppp) REVERT: C 74 ARG cc_start: 0.8846 (mmp80) cc_final: 0.8482 (mmp80) REVERT: C 95 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8424 (t80) REVERT: C 123 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8497 (pptt) REVERT: C 171 GLU cc_start: 0.9194 (pt0) cc_final: 0.8845 (pp20) REVERT: C 172 LEU cc_start: 0.9315 (mt) cc_final: 0.8860 (mt) REVERT: C 182 TYR cc_start: 0.8889 (m-80) cc_final: 0.8394 (m-80) REVERT: C 189 VAL cc_start: 0.9436 (t) cc_final: 0.9071 (t) REVERT: C 880 TRP cc_start: 0.9107 (m100) cc_final: 0.8690 (m100) REVERT: C 882 TYR cc_start: 0.8388 (m-80) cc_final: 0.8177 (m-80) REVERT: C 893 ASP cc_start: 0.8782 (m-30) cc_final: 0.8232 (m-30) REVERT: C 895 PHE cc_start: 0.9031 (t80) cc_final: 0.8370 (t80) REVERT: C 897 LYS cc_start: 0.9334 (mtmt) cc_final: 0.8869 (mmtp) REVERT: C 902 LEU cc_start: 0.9126 (mm) cc_final: 0.8342 (tp) REVERT: C 906 ASN cc_start: 0.9143 (m110) cc_final: 0.8594 (m110) REVERT: C 955 GLU cc_start: 0.9213 (mp0) cc_final: 0.9013 (mp0) REVERT: C 973 HIS cc_start: 0.9216 (p90) cc_final: 0.8924 (p90) REVERT: C 984 GLU cc_start: 0.8316 (tp30) cc_final: 0.7825 (tp30) REVERT: C 1045 PHE cc_start: 0.8955 (m-10) cc_final: 0.8720 (m-80) REVERT: D 1 MET cc_start: 0.7891 (tmm) cc_final: 0.7684 (tmm) REVERT: D 12 ASN cc_start: 0.9415 (m-40) cc_final: 0.8858 (t0) REVERT: D 55 TYR cc_start: 0.8808 (m-10) cc_final: 0.8489 (m-10) REVERT: D 84 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8400 (mm-30) REVERT: D 92 TYR cc_start: 0.8555 (m-80) cc_final: 0.8028 (m-10) REVERT: D 155 GLN cc_start: 0.8760 (pm20) cc_final: 0.8250 (pm20) REVERT: D 162 LEU cc_start: 0.9514 (mt) cc_final: 0.9267 (mp) REVERT: D 165 LYS cc_start: 0.9497 (mmmt) cc_final: 0.9141 (mmmm) REVERT: D 184 GLN cc_start: 0.9309 (mp10) cc_final: 0.8844 (mp10) REVERT: D 188 MET cc_start: 0.9082 (ptp) cc_final: 0.8802 (ttm) REVERT: D 190 PHE cc_start: 0.9128 (t80) cc_final: 0.8726 (t80) REVERT: D 194 LYS cc_start: 0.9435 (pptt) cc_final: 0.9201 (pttm) REVERT: D 896 ARG cc_start: 0.8500 (ttm110) cc_final: 0.8033 (ttp-110) REVERT: D 914 GLN cc_start: 0.9450 (tp40) cc_final: 0.9080 (tp-100) REVERT: D 919 HIS cc_start: 0.8125 (t-170) cc_final: 0.7806 (t70) REVERT: D 983 ASP cc_start: 0.8114 (t70) cc_final: 0.7051 (t0) REVERT: D 989 LEU cc_start: 0.9683 (mt) cc_final: 0.9241 (tp) REVERT: D 1016 HIS cc_start: 0.7868 (m-70) cc_final: 0.7596 (m170) REVERT: D 1033 ILE cc_start: 0.9569 (mp) cc_final: 0.9241 (pt) REVERT: D 1036 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8689 (pp) REVERT: D 1045 PHE cc_start: 0.8684 (m-80) cc_final: 0.8367 (m-80) REVERT: A 18 LYS cc_start: 0.9348 (mmmt) cc_final: 0.9027 (mmtm) REVERT: A 58 TYR cc_start: 0.9147 (p90) cc_final: 0.8760 (p90) REVERT: A 65 ARG cc_start: 0.9108 (tpm170) cc_final: 0.8797 (tpp-160) REVERT: A 93 SER cc_start: 0.9502 (m) cc_final: 0.8964 (p) REVERT: A 149 LYS cc_start: 0.9689 (mttm) cc_final: 0.9173 (mttm) REVERT: A 212 PHE cc_start: 0.8220 (m-80) cc_final: 0.7947 (m-80) REVERT: A 229 ILE cc_start: 0.9016 (mm) cc_final: 0.8258 (mm) REVERT: A 232 MET cc_start: 0.9287 (mmm) cc_final: 0.9024 (mpp) REVERT: A 242 ILE cc_start: 0.9361 (tp) cc_final: 0.9131 (tp) REVERT: A 244 LEU cc_start: 0.9259 (mt) cc_final: 0.8988 (mt) REVERT: A 246 PHE cc_start: 0.8716 (m-80) cc_final: 0.7527 (m-80) REVERT: A 306 TRP cc_start: 0.8794 (m-10) cc_final: 0.7887 (m-10) REVERT: A 366 PHE cc_start: 0.9150 (t80) cc_final: 0.8539 (t80) REVERT: B 15 PHE cc_start: 0.9013 (t80) cc_final: 0.7918 (t80) REVERT: B 16 TYR cc_start: 0.8302 (m-80) cc_final: 0.7969 (m-80) REVERT: B 18 LYS cc_start: 0.9172 (mmtm) cc_final: 0.8934 (mmtm) REVERT: B 33 GLU cc_start: 0.9456 (tt0) cc_final: 0.9127 (pt0) REVERT: B 65 ARG cc_start: 0.9337 (mtp85) cc_final: 0.9126 (ptp-110) REVERT: B 169 CYS cc_start: 0.9603 (OUTLIER) cc_final: 0.9388 (p) REVERT: B 207 PHE cc_start: 0.9085 (t80) cc_final: 0.8280 (t80) REVERT: B 253 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7794 (mmtm) REVERT: B 282 LEU cc_start: 0.8840 (mt) cc_final: 0.8459 (mp) REVERT: B 317 LEU cc_start: 0.9393 (tp) cc_final: 0.8877 (tp) REVERT: B 321 GLN cc_start: 0.9074 (mt0) cc_final: 0.8603 (mt0) REVERT: B 366 PHE cc_start: 0.9334 (t80) cc_final: 0.8920 (t80) REVERT: B 373 GLU cc_start: 0.8887 (tp30) cc_final: 0.8335 (tm-30) outliers start: 46 outliers final: 32 residues processed: 418 average time/residue: 0.2423 time to fit residues: 148.1990 Evaluate side-chains 418 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 382 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 986 PHE Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 1036 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 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 102 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 307 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 7 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 906 ASN D1016 HIS B 224 HIS ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.081811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.054774 restraints weight = 46018.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.056960 restraints weight = 27015.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.058464 restraints weight = 18738.192| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13796 Z= 0.237 Angle : 0.778 12.835 19049 Z= 0.384 Chirality : 0.047 0.493 2193 Planarity : 0.004 0.045 2183 Dihedral : 21.174 178.952 2467 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.40 % Allowed : 22.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1479 helix: 0.99 (0.22), residues: 544 sheet: 0.15 (0.32), residues: 253 loop : -0.36 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 296 HIS 0.017 0.002 HIS A 385 PHE 0.032 0.003 PHE D 957 TYR 0.028 0.002 TYR B 165 ARG 0.005 0.001 ARG D 949 Details of bonding type rmsd hydrogen bonds : bond 0.04540 ( 621) hydrogen bonds : angle 4.96151 ( 1674) covalent geometry : bond 0.00481 (13796) covalent geometry : angle 0.77808 (19049) *********************** 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 440 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 384 time to evaluate : 1.490 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: 0.9410 (m-40) cc_final: 0.8969 (m-40) REVERT: C 22 PHE cc_start: 0.8904 (m-80) cc_final: 0.8528 (m-80) REVERT: C 45 THR cc_start: 0.9709 (m) cc_final: 0.9506 (p) REVERT: C 54 LEU cc_start: 0.9758 (mt) cc_final: 0.9497 (mt) REVERT: C 82 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7704 (tm-30) REVERT: C 171 GLU cc_start: 0.9264 (pt0) cc_final: 0.8906 (pp20) REVERT: C 172 LEU cc_start: 0.9361 (mt) cc_final: 0.8896 (mt) REVERT: C 182 TYR cc_start: 0.8975 (m-80) cc_final: 0.8434 (m-80) REVERT: C 189 VAL cc_start: 0.9490 (t) cc_final: 0.9020 (t) REVERT: C 880 TRP cc_start: 0.9032 (m100) cc_final: 0.8466 (m100) REVERT: C 882 TYR cc_start: 0.8410 (m-80) cc_final: 0.8147 (m-80) REVERT: C 893 ASP cc_start: 0.8849 (m-30) cc_final: 0.8439 (m-30) REVERT: C 895 PHE cc_start: 0.9139 (t80) cc_final: 0.8366 (t80) REVERT: C 897 LYS cc_start: 0.9362 (mtmt) cc_final: 0.8964 (mmtp) REVERT: C 902 LEU cc_start: 0.9134 (mm) cc_final: 0.8342 (tp) REVERT: C 906 ASN cc_start: 0.9217 (m110) cc_final: 0.8686 (m110) REVERT: C 921 ARG cc_start: 0.8729 (ttt180) cc_final: 0.8490 (ttt-90) REVERT: C 955 GLU cc_start: 0.9271 (mp0) cc_final: 0.9010 (mp0) REVERT: C 973 HIS cc_start: 0.9237 (p90) cc_final: 0.8820 (p90) REVERT: C 984 GLU cc_start: 0.8314 (tp30) cc_final: 0.7752 (tp30) REVERT: C 1029 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8847 (mppt) REVERT: C 1045 PHE cc_start: 0.9135 (m-10) cc_final: 0.8892 (m-80) REVERT: D 12 ASN cc_start: 0.9465 (t0) cc_final: 0.8873 (t0) REVERT: D 72 MET cc_start: 0.7637 (ttm) cc_final: 0.7238 (ttt) REVERT: D 92 TYR cc_start: 0.8676 (m-80) cc_final: 0.7871 (m-10) REVERT: D 142 LEU cc_start: 0.9347 (pp) cc_final: 0.9134 (pp) REVERT: D 155 GLN cc_start: 0.8811 (pm20) cc_final: 0.8215 (pm20) REVERT: D 158 PHE cc_start: 0.9224 (p90) cc_final: 0.8841 (p90) REVERT: D 165 LYS cc_start: 0.9499 (mmmt) cc_final: 0.9163 (mmmm) REVERT: D 184 GLN cc_start: 0.9327 (mp10) cc_final: 0.9118 (mt0) REVERT: D 188 MET cc_start: 0.9050 (ptp) cc_final: 0.8825 (ttm) REVERT: D 194 LYS cc_start: 0.9443 (pptt) cc_final: 0.9209 (ptpp) REVERT: D 884 ASN cc_start: 0.8965 (t0) cc_final: 0.8757 (t0) REVERT: D 896 ARG cc_start: 0.8635 (ttm110) cc_final: 0.8353 (ttp-110) REVERT: D 914 GLN cc_start: 0.9440 (tp40) cc_final: 0.9231 (tm-30) REVERT: D 919 HIS cc_start: 0.8299 (t-170) cc_final: 0.7590 (t70) REVERT: D 975 THR cc_start: 0.9122 (m) cc_final: 0.8763 (p) REVERT: D 983 ASP cc_start: 0.8225 (t70) cc_final: 0.6916 (t0) REVERT: D 989 LEU cc_start: 0.9729 (mt) cc_final: 0.9288 (tp) REVERT: D 1033 ILE cc_start: 0.9591 (mp) cc_final: 0.9233 (pt) REVERT: D 1036 LEU cc_start: 0.9360 (pp) cc_final: 0.8664 (pp) REVERT: A 18 LYS cc_start: 0.9401 (mmmt) cc_final: 0.8966 (mmtm) REVERT: A 58 TYR cc_start: 0.9277 (p90) cc_final: 0.8922 (p90) REVERT: A 65 ARG cc_start: 0.9132 (tpm170) cc_final: 0.8844 (tpm170) REVERT: A 93 SER cc_start: 0.9535 (m) cc_final: 0.9077 (p) REVERT: A 131 PHE cc_start: 0.9087 (t80) cc_final: 0.8830 (t80) REVERT: A 149 LYS cc_start: 0.9707 (mttm) cc_final: 0.9273 (mttm) REVERT: A 212 PHE cc_start: 0.8246 (m-80) cc_final: 0.7983 (m-80) REVERT: A 244 LEU cc_start: 0.9301 (mt) cc_final: 0.9016 (mt) REVERT: A 253 LYS cc_start: 0.8248 (mmmm) cc_final: 0.7802 (mmmm) REVERT: A 296 TRP cc_start: 0.9393 (m100) cc_final: 0.9097 (m100) REVERT: A 366 PHE cc_start: 0.9133 (t80) cc_final: 0.8454 (t80) REVERT: B 15 PHE cc_start: 0.9061 (t80) cc_final: 0.8008 (t80) REVERT: B 18 LYS cc_start: 0.9221 (mmtm) cc_final: 0.8970 (mmtm) REVERT: B 33 GLU cc_start: 0.9457 (tt0) cc_final: 0.8869 (tm-30) REVERT: B 75 CYS cc_start: 0.8382 (m) cc_final: 0.8098 (m) REVERT: B 207 PHE cc_start: 0.9286 (t80) cc_final: 0.8934 (t80) REVERT: B 271 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8872 (mm) REVERT: B 306 TRP cc_start: 0.7241 (m-10) cc_final: 0.6545 (m-10) REVERT: B 321 GLN cc_start: 0.9073 (mt0) cc_final: 0.8567 (tm-30) REVERT: B 325 GLN cc_start: 0.9414 (mt0) cc_final: 0.8896 (tm-30) REVERT: B 357 LEU cc_start: 0.9507 (tp) cc_final: 0.8880 (pp) REVERT: B 366 PHE cc_start: 0.9289 (t80) cc_final: 0.8523 (t80) REVERT: B 373 GLU cc_start: 0.8949 (tp30) cc_final: 0.8591 (tp30) REVERT: B 387 PHE cc_start: 0.9471 (t80) cc_final: 0.9235 (t80) outliers start: 56 outliers final: 42 residues processed: 404 average time/residue: 0.2421 time to fit residues: 143.1379 Evaluate side-chains 403 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 359 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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 965 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1029 LYS Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 982 LEU 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 D residue 1017 VAL Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 182 THR 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 275 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 307 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 67 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS B 234 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 = 0.3591 r_free = 0.3591 target = 0.083114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.056706 restraints weight = 44410.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.058977 restraints weight = 25587.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.060576 restraints weight = 17459.989| |-----------------------------------------------------------------------------| 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: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13796 Z= 0.146 Angle : 0.784 13.025 19049 Z= 0.369 Chirality : 0.045 0.379 2193 Planarity : 0.004 0.046 2183 Dihedral : 21.119 178.982 2467 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.16 % Allowed : 24.80 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.22), residues: 1479 helix: 1.04 (0.23), residues: 538 sheet: 0.25 (0.32), residues: 248 loop : -0.28 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 296 HIS 0.013 0.001 HIS A 385 PHE 0.034 0.002 PHE A 15 TYR 0.024 0.002 TYR B 217 ARG 0.005 0.000 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 621) hydrogen bonds : angle 4.76847 ( 1674) covalent geometry : bond 0.00323 (13796) covalent geometry : angle 0.78396 (19049) *********************** 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 435 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 382 time to evaluate : 1.334 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 9 LYS cc_start: 0.9205 (tppt) cc_final: 0.8896 (tppt) REVERT: C 12 ASN cc_start: 0.9429 (m-40) cc_final: 0.8988 (m-40) REVERT: C 22 PHE cc_start: 0.8903 (m-80) cc_final: 0.8535 (m-80) REVERT: C 54 LEU cc_start: 0.9741 (mt) cc_final: 0.9468 (mt) REVERT: C 76 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8476 (p) REVERT: C 82 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7791 (tm-30) REVERT: C 133 LEU cc_start: 0.9699 (mt) cc_final: 0.9491 (pp) REVERT: C 142 LEU cc_start: 0.9109 (pp) cc_final: 0.8692 (tt) REVERT: C 171 GLU cc_start: 0.9251 (pt0) cc_final: 0.8897 (pp20) REVERT: C 172 LEU cc_start: 0.9330 (mt) cc_final: 0.8886 (mt) REVERT: C 182 TYR cc_start: 0.8922 (m-80) cc_final: 0.8313 (m-80) REVERT: C 189 VAL cc_start: 0.9506 (t) cc_final: 0.9055 (t) REVERT: C 880 TRP cc_start: 0.9013 (m100) cc_final: 0.8566 (m100) REVERT: C 882 TYR cc_start: 0.8385 (m-80) cc_final: 0.8080 (m-80) REVERT: C 893 ASP cc_start: 0.8863 (m-30) cc_final: 0.8495 (m-30) REVERT: C 895 PHE cc_start: 0.9152 (t80) cc_final: 0.8444 (t80) REVERT: C 897 LYS cc_start: 0.9319 (mtmt) cc_final: 0.8942 (mmtp) REVERT: C 902 LEU cc_start: 0.9097 (mm) cc_final: 0.8322 (tp) REVERT: C 906 ASN cc_start: 0.9156 (m110) cc_final: 0.8627 (m110) REVERT: C 955 GLU cc_start: 0.9244 (mp0) cc_final: 0.8944 (mp0) REVERT: C 973 HIS cc_start: 0.9136 (p90) cc_final: 0.8718 (p90) REVERT: C 984 GLU cc_start: 0.8148 (tp30) cc_final: 0.7536 (tp30) REVERT: C 1029 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8833 (mmtm) REVERT: C 1045 PHE cc_start: 0.9143 (m-10) cc_final: 0.8913 (m-80) REVERT: D 12 ASN cc_start: 0.9432 (m-40) cc_final: 0.8823 (t0) REVERT: D 72 MET cc_start: 0.7194 (ttm) cc_final: 0.6376 (ttt) REVERT: D 74 ARG cc_start: 0.8415 (mmp80) cc_final: 0.7907 (mmp-170) REVERT: D 139 LEU cc_start: 0.9465 (mm) cc_final: 0.9237 (mm) REVERT: D 155 GLN cc_start: 0.8864 (pm20) cc_final: 0.8379 (pm20) REVERT: D 162 LEU cc_start: 0.9555 (mt) cc_final: 0.9288 (mp) REVERT: D 165 LYS cc_start: 0.9493 (mmmt) cc_final: 0.9142 (mmmm) REVERT: D 184 GLN cc_start: 0.9316 (mp10) cc_final: 0.9013 (mp10) REVERT: D 188 MET cc_start: 0.8991 (ptp) cc_final: 0.8742 (ttm) REVERT: D 194 LYS cc_start: 0.9442 (pptt) cc_final: 0.9207 (ptpp) REVERT: D 884 ASN cc_start: 0.8952 (t0) cc_final: 0.8705 (t0) REVERT: D 894 LYS cc_start: 0.9291 (ttpt) cc_final: 0.9038 (ptmt) REVERT: D 896 ARG cc_start: 0.8479 (ttm110) cc_final: 0.8078 (ttp-110) REVERT: D 910 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9315 (mp) REVERT: D 919 HIS cc_start: 0.8098 (t-170) cc_final: 0.7387 (t70) REVERT: D 975 THR cc_start: 0.9131 (m) cc_final: 0.8784 (p) REVERT: D 983 ASP cc_start: 0.8288 (t70) cc_final: 0.6930 (t0) REVERT: D 989 LEU cc_start: 0.9713 (mt) cc_final: 0.9207 (tp) REVERT: D 1020 MET cc_start: 0.9264 (pmm) cc_final: 0.9028 (pmm) REVERT: D 1033 ILE cc_start: 0.9567 (mp) cc_final: 0.9228 (pt) REVERT: D 1036 LEU cc_start: 0.9385 (pp) cc_final: 0.8656 (pp) REVERT: A 18 LYS cc_start: 0.9436 (mmmt) cc_final: 0.9164 (mmtm) REVERT: A 58 TYR cc_start: 0.9241 (p90) cc_final: 0.8917 (p90) REVERT: A 65 ARG cc_start: 0.9129 (tpm170) cc_final: 0.8842 (tpm170) REVERT: A 93 SER cc_start: 0.9526 (m) cc_final: 0.9110 (p) REVERT: A 131 PHE cc_start: 0.9051 (t80) cc_final: 0.8818 (t80) REVERT: A 149 LYS cc_start: 0.9674 (mttm) cc_final: 0.9220 (mttm) REVERT: A 212 PHE cc_start: 0.8303 (m-80) cc_final: 0.8022 (m-80) REVERT: A 229 ILE cc_start: 0.9238 (mm) cc_final: 0.8539 (mm) REVERT: A 232 MET cc_start: 0.9212 (mmm) cc_final: 0.8955 (mpp) REVERT: A 253 LYS cc_start: 0.8253 (mmmm) cc_final: 0.7797 (mmmm) REVERT: A 279 MET cc_start: 0.8642 (mmm) cc_final: 0.7741 (tpt) REVERT: A 296 TRP cc_start: 0.9363 (m100) cc_final: 0.9066 (m100) REVERT: A 366 PHE cc_start: 0.9102 (t80) cc_final: 0.8384 (t80) REVERT: B 15 PHE cc_start: 0.9037 (t80) cc_final: 0.8053 (t80) REVERT: B 18 LYS cc_start: 0.9254 (mmtm) cc_final: 0.8990 (mmtm) REVERT: B 33 GLU cc_start: 0.9436 (tt0) cc_final: 0.8836 (tm-30) REVERT: B 65 ARG cc_start: 0.9036 (ptp-170) cc_final: 0.8809 (ptp-110) REVERT: B 75 CYS cc_start: 0.8441 (m) cc_final: 0.6976 (t) REVERT: B 165 TYR cc_start: 0.9449 (t80) cc_final: 0.9201 (t80) REVERT: B 207 PHE cc_start: 0.9218 (t80) cc_final: 0.8812 (t80) REVERT: B 271 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8868 (mm) REVERT: B 321 GLN cc_start: 0.8987 (mt0) cc_final: 0.8443 (mt0) REVERT: B 325 GLN cc_start: 0.9360 (mt0) cc_final: 0.8939 (tm-30) REVERT: B 357 LEU cc_start: 0.9477 (tp) cc_final: 0.8846 (pp) REVERT: B 366 PHE cc_start: 0.9288 (t80) cc_final: 0.8507 (t80) REVERT: B 387 PHE cc_start: 0.9440 (t80) cc_final: 0.9195 (t80) outliers start: 53 outliers final: 34 residues processed: 403 average time/residue: 0.2584 time to fit residues: 152.7275 Evaluate side-chains 407 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 369 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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 200 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1029 LYS Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 1014 ILE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 HIS 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 B residue 43 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 307 LEU 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 54 optimal weight: 0.2980 chunk 129 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 GLN B 39 GLN B 164 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 = 0.3563 r_free = 0.3563 target = 0.081338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.055112 restraints weight = 45841.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.057335 restraints weight = 26643.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.058918 restraints weight = 18369.425| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13796 Z= 0.208 Angle : 0.766 14.451 19049 Z= 0.370 Chirality : 0.044 0.180 2193 Planarity : 0.004 0.047 2183 Dihedral : 21.106 178.378 2467 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.40 % Allowed : 26.14 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1479 helix: 0.87 (0.22), residues: 551 sheet: 0.11 (0.31), residues: 276 loop : -0.28 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 296 HIS 0.010 0.001 HIS A 385 PHE 0.031 0.003 PHE B 27 TYR 0.043 0.003 TYR D 55 ARG 0.005 0.001 ARG C 74 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 621) hydrogen bonds : angle 4.85512 ( 1674) covalent geometry : bond 0.00425 (13796) covalent geometry : angle 0.76605 (19049) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 378 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LYS cc_start: 0.9190 (tppt) cc_final: 0.8869 (tppt) REVERT: C 22 PHE cc_start: 0.8962 (m-80) cc_final: 0.8592 (m-80) REVERT: C 54 LEU cc_start: 0.9757 (mt) cc_final: 0.9492 (mt) REVERT: C 72 MET cc_start: 0.8686 (ppp) cc_final: 0.8329 (ppp) REVERT: C 182 TYR cc_start: 0.8973 (m-80) cc_final: 0.8366 (m-80) REVERT: C 189 VAL cc_start: 0.9501 (t) cc_final: 0.9089 (t) REVERT: C 880 TRP cc_start: 0.9067 (m100) cc_final: 0.8649 (m100) REVERT: C 882 TYR cc_start: 0.8456 (m-10) cc_final: 0.8100 (m-80) REVERT: C 893 ASP cc_start: 0.8969 (m-30) cc_final: 0.8521 (m-30) REVERT: C 895 PHE cc_start: 0.9181 (t80) cc_final: 0.8407 (t80) REVERT: C 897 LYS cc_start: 0.9364 (mtmt) cc_final: 0.8918 (mmtp) REVERT: C 902 LEU cc_start: 0.9077 (mm) cc_final: 0.8239 (tp) REVERT: C 906 ASN cc_start: 0.9210 (m110) cc_final: 0.8668 (m110) REVERT: C 919 HIS cc_start: 0.8318 (t70) cc_final: 0.7934 (t70) REVERT: C 955 GLU cc_start: 0.9260 (mp0) cc_final: 0.8974 (mp0) REVERT: C 984 GLU cc_start: 0.8107 (tp30) cc_final: 0.7523 (tp30) REVERT: C 1029 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8796 (mppt) REVERT: C 1045 PHE cc_start: 0.9260 (m-80) cc_final: 0.9046 (m-80) REVERT: D 12 ASN cc_start: 0.9446 (m-40) cc_final: 0.8855 (t0) REVERT: D 155 GLN cc_start: 0.8979 (pm20) cc_final: 0.8501 (pm20) REVERT: D 162 LEU cc_start: 0.9578 (mt) cc_final: 0.9280 (mp) REVERT: D 184 GLN cc_start: 0.9309 (mp10) cc_final: 0.9071 (mp10) REVERT: D 188 MET cc_start: 0.8980 (ptp) cc_final: 0.8729 (ttm) REVERT: D 194 LYS cc_start: 0.9435 (pptt) cc_final: 0.9216 (ptpp) REVERT: D 890 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8322 (ttpt) REVERT: D 894 LYS cc_start: 0.9240 (ttpt) cc_final: 0.8958 (ptmt) REVERT: D 896 ARG cc_start: 0.8555 (ttm110) cc_final: 0.8220 (ttp-110) REVERT: D 919 HIS cc_start: 0.8316 (t-170) cc_final: 0.7601 (t-90) REVERT: D 975 THR cc_start: 0.9268 (m) cc_final: 0.8923 (p) REVERT: D 983 ASP cc_start: 0.8360 (t70) cc_final: 0.6974 (t0) REVERT: D 989 LEU cc_start: 0.9711 (mt) cc_final: 0.9275 (tp) REVERT: D 1020 MET cc_start: 0.9221 (pmm) cc_final: 0.8908 (pmm) REVERT: A 16 TYR cc_start: 0.6942 (m-10) cc_final: 0.6671 (m-10) REVERT: A 58 TYR cc_start: 0.9243 (p90) cc_final: 0.8946 (p90) REVERT: A 65 ARG cc_start: 0.9146 (tpm170) cc_final: 0.8861 (tpm170) REVERT: A 93 SER cc_start: 0.9554 (m) cc_final: 0.9210 (p) REVERT: A 149 LYS cc_start: 0.9689 (mttm) cc_final: 0.9216 (mttm) REVERT: A 212 PHE cc_start: 0.8371 (m-80) cc_final: 0.8131 (m-80) REVERT: A 253 LYS cc_start: 0.8298 (mmmm) cc_final: 0.7588 (mtpp) REVERT: A 296 TRP cc_start: 0.9396 (m100) cc_final: 0.9048 (m100) REVERT: A 366 PHE cc_start: 0.9088 (t80) cc_final: 0.8212 (t80) REVERT: A 387 PHE cc_start: 0.9455 (t80) cc_final: 0.9163 (t80) REVERT: B 15 PHE cc_start: 0.9089 (t80) cc_final: 0.8164 (t80) REVERT: B 18 LYS cc_start: 0.9277 (mmtm) cc_final: 0.9013 (mmtm) REVERT: B 33 GLU cc_start: 0.9428 (tt0) cc_final: 0.9180 (pt0) REVERT: B 65 ARG cc_start: 0.9018 (ptp-170) cc_final: 0.8677 (ptp-110) REVERT: B 75 CYS cc_start: 0.8558 (m) cc_final: 0.7090 (t) REVERT: B 110 HIS cc_start: 0.8769 (t70) cc_final: 0.8297 (t-90) REVERT: B 207 PHE cc_start: 0.9274 (t80) cc_final: 0.8856 (t80) REVERT: B 271 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8944 (mm) REVERT: B 306 TRP cc_start: 0.7328 (m-10) cc_final: 0.6852 (m-10) REVERT: B 317 LEU cc_start: 0.9464 (tp) cc_final: 0.9040 (tt) REVERT: B 357 LEU cc_start: 0.9512 (tp) cc_final: 0.8963 (pp) REVERT: B 366 PHE cc_start: 0.9290 (t80) cc_final: 0.8535 (t80) REVERT: B 387 PHE cc_start: 0.9437 (t80) cc_final: 0.9164 (t80) outliers start: 56 outliers final: 40 residues processed: 399 average time/residue: 0.2825 time to fit residues: 164.7795 Evaluate side-chains 393 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 350 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 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 967 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1029 LYS Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 890 LYS Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 1011 ILE Chi-restraints excluded: chain D residue 1014 ILE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 164 HIS 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 307 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 115 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 0.0670 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN B 164 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 = 0.3579 r_free = 0.3579 target = 0.083103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.055479 restraints weight = 45212.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.057798 restraints weight = 26215.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.059419 restraints weight = 18021.437| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13796 Z= 0.158 Angle : 0.779 14.672 19049 Z= 0.368 Chirality : 0.045 0.259 2193 Planarity : 0.004 0.046 2183 Dihedral : 21.089 178.308 2467 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.00 % Allowed : 27.86 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.23), residues: 1479 helix: 0.91 (0.23), residues: 545 sheet: 0.33 (0.32), residues: 256 loop : -0.16 (0.26), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 96 HIS 0.009 0.001 HIS A 385 PHE 0.019 0.002 PHE B 27 TYR 0.021 0.002 TYR D 55 ARG 0.007 0.000 ARG D 197 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 621) hydrogen bonds : angle 4.80101 ( 1674) covalent geometry : bond 0.00349 (13796) covalent geometry : angle 0.77851 (19049) *********************** 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 421 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 370 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LYS cc_start: 0.9242 (tppt) cc_final: 0.8868 (tppt) REVERT: C 22 PHE cc_start: 0.8906 (m-80) cc_final: 0.8489 (m-80) REVERT: C 54 LEU cc_start: 0.9716 (mt) cc_final: 0.9465 (mt) REVERT: C 72 MET cc_start: 0.8590 (ppp) cc_final: 0.8263 (ppp) REVERT: C 127 ASP cc_start: 0.8762 (p0) cc_final: 0.8263 (m-30) REVERT: C 144 TYR cc_start: 0.9147 (t80) cc_final: 0.8803 (t80) REVERT: C 171 GLU cc_start: 0.9268 (pt0) cc_final: 0.9002 (pp20) REVERT: C 172 LEU cc_start: 0.9367 (mt) cc_final: 0.9138 (pp) REVERT: C 182 TYR cc_start: 0.8974 (m-80) cc_final: 0.8363 (m-80) REVERT: C 189 VAL cc_start: 0.9499 (t) cc_final: 0.9073 (t) REVERT: C 880 TRP cc_start: 0.9064 (m100) cc_final: 0.8625 (m100) REVERT: C 882 TYR cc_start: 0.8490 (m-10) cc_final: 0.8117 (m-80) REVERT: C 893 ASP cc_start: 0.8891 (m-30) cc_final: 0.8443 (m-30) REVERT: C 895 PHE cc_start: 0.9201 (t80) cc_final: 0.8508 (t80) REVERT: C 897 LYS cc_start: 0.9339 (mtmt) cc_final: 0.8936 (mmtp) REVERT: C 902 LEU cc_start: 0.9048 (mm) cc_final: 0.8216 (tp) REVERT: C 906 ASN cc_start: 0.9146 (m110) cc_final: 0.8564 (m110) REVERT: C 919 HIS cc_start: 0.8270 (t70) cc_final: 0.7895 (t70) REVERT: C 955 GLU cc_start: 0.9251 (mp0) cc_final: 0.8963 (mp0) REVERT: C 1029 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8749 (mppt) REVERT: D 12 ASN cc_start: 0.9416 (m-40) cc_final: 0.8820 (t0) REVERT: D 72 MET cc_start: 0.7439 (ttt) cc_final: 0.7222 (ttt) REVERT: D 155 GLN cc_start: 0.8993 (pm20) cc_final: 0.8495 (pm20) REVERT: D 162 LEU cc_start: 0.9583 (mt) cc_final: 0.9303 (mp) REVERT: D 184 GLN cc_start: 0.9314 (mp10) cc_final: 0.9076 (mp10) REVERT: D 188 MET cc_start: 0.8956 (ptp) cc_final: 0.8733 (ttm) REVERT: D 194 LYS cc_start: 0.9401 (pptt) cc_final: 0.9190 (ptpp) REVERT: D 890 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8356 (ttpt) REVERT: D 894 LYS cc_start: 0.9275 (ttpt) cc_final: 0.8997 (ptmt) REVERT: D 896 ARG cc_start: 0.8492 (ttm110) cc_final: 0.8122 (ttp-110) REVERT: D 919 HIS cc_start: 0.8345 (t-170) cc_final: 0.7616 (t-90) REVERT: D 975 THR cc_start: 0.9302 (m) cc_final: 0.8967 (p) REVERT: D 983 ASP cc_start: 0.8395 (t70) cc_final: 0.6947 (t0) REVERT: D 989 LEU cc_start: 0.9701 (mt) cc_final: 0.9250 (tp) REVERT: D 1020 MET cc_start: 0.9235 (pmm) cc_final: 0.8952 (pmm) REVERT: A 16 TYR cc_start: 0.6968 (m-10) cc_final: 0.6683 (m-10) REVERT: A 58 TYR cc_start: 0.9206 (p90) cc_final: 0.8905 (p90) REVERT: A 65 ARG cc_start: 0.9147 (tpm170) cc_final: 0.8859 (tpm170) REVERT: A 85 ASP cc_start: 0.5995 (p0) cc_final: 0.5757 (p0) REVERT: A 93 SER cc_start: 0.9509 (m) cc_final: 0.9227 (p) REVERT: A 212 PHE cc_start: 0.8422 (m-80) cc_final: 0.8216 (m-80) REVERT: A 253 LYS cc_start: 0.8303 (mmmm) cc_final: 0.7462 (mtpp) REVERT: A 279 MET cc_start: 0.8550 (mmm) cc_final: 0.7765 (tpt) REVERT: A 296 TRP cc_start: 0.9425 (m100) cc_final: 0.9160 (m100) REVERT: A 366 PHE cc_start: 0.9118 (t80) cc_final: 0.8234 (t80) REVERT: A 387 PHE cc_start: 0.9449 (t80) cc_final: 0.9139 (t80) REVERT: B 15 PHE cc_start: 0.9093 (t80) cc_final: 0.8162 (t80) REVERT: B 18 LYS cc_start: 0.9282 (mmtm) cc_final: 0.9013 (mmtm) REVERT: B 33 GLU cc_start: 0.9426 (tt0) cc_final: 0.8884 (tm-30) REVERT: B 65 ARG cc_start: 0.9014 (ptp-170) cc_final: 0.8735 (ptp-110) REVERT: B 75 CYS cc_start: 0.8521 (m) cc_final: 0.7247 (t) REVERT: B 110 HIS cc_start: 0.8760 (t70) cc_final: 0.8240 (t-90) REVERT: B 113 GLN cc_start: 0.8850 (tp-100) cc_final: 0.8623 (tm-30) REVERT: B 165 TYR cc_start: 0.9475 (t80) cc_final: 0.9265 (t80) REVERT: B 207 PHE cc_start: 0.9257 (t80) cc_final: 0.8827 (t80) REVERT: B 271 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8967 (mm) REVERT: B 306 TRP cc_start: 0.7268 (m-10) cc_final: 0.6741 (m-10) REVERT: B 357 LEU cc_start: 0.9475 (tp) cc_final: 0.8966 (pp) REVERT: B 366 PHE cc_start: 0.9276 (t80) cc_final: 0.8501 (t80) REVERT: B 387 PHE cc_start: 0.9434 (t80) cc_final: 0.9063 (t80) outliers start: 51 outliers final: 43 residues processed: 391 average time/residue: 0.2374 time to fit residues: 135.5012 Evaluate side-chains 398 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 352 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1029 LYS Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 890 LYS Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 993 THR 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 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 161 TYR Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 HIS 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 307 LEU Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 71 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.083185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.054918 restraints weight = 47023.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.057226 restraints weight = 27310.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.058816 restraints weight = 18883.224| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5674 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= 0.170 Angle : 0.800 14.194 19049 Z= 0.375 Chirality : 0.047 0.359 2193 Planarity : 0.004 0.047 2183 Dihedral : 21.081 178.575 2467 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.24 % Allowed : 28.34 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1479 helix: 0.83 (0.22), residues: 551 sheet: 0.33 (0.33), residues: 251 loop : -0.18 (0.26), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 96 HIS 0.020 0.001 HIS B 164 PHE 0.024 0.002 PHE B 27 TYR 0.021 0.002 TYR B 217 ARG 0.006 0.000 ARG D 197 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 621) hydrogen bonds : angle 4.81685 ( 1674) covalent geometry : bond 0.00368 (13796) covalent geometry : angle 0.80040 (19049) *********************** 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 424 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 370 time to evaluate : 1.358 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 9 LYS cc_start: 0.9256 (tppt) cc_final: 0.8892 (tppt) REVERT: C 22 PHE cc_start: 0.8931 (m-80) cc_final: 0.8530 (m-80) REVERT: C 72 MET cc_start: 0.8505 (ppp) cc_final: 0.8205 (ppp) REVERT: C 144 TYR cc_start: 0.9139 (t80) cc_final: 0.8855 (t80) REVERT: C 171 GLU cc_start: 0.9276 (pt0) cc_final: 0.8979 (pp20) REVERT: C 172 LEU cc_start: 0.9364 (mt) cc_final: 0.9147 (pp) REVERT: C 182 TYR cc_start: 0.8990 (m-80) cc_final: 0.8356 (m-80) REVERT: C 189 VAL cc_start: 0.9478 (t) cc_final: 0.9048 (t) REVERT: C 190 PHE cc_start: 0.8569 (t80) cc_final: 0.8297 (t80) REVERT: C 880 TRP cc_start: 0.9068 (m100) cc_final: 0.8660 (m100) REVERT: C 882 TYR cc_start: 0.8496 (m-10) cc_final: 0.8152 (m-80) REVERT: C 893 ASP cc_start: 0.8847 (m-30) cc_final: 0.8445 (m-30) REVERT: C 895 PHE cc_start: 0.9180 (t80) cc_final: 0.8461 (t80) REVERT: C 897 LYS cc_start: 0.9362 (mtmt) cc_final: 0.8944 (mmtp) REVERT: C 902 LEU cc_start: 0.9038 (mm) cc_final: 0.8215 (tp) REVERT: C 906 ASN cc_start: 0.9150 (m110) cc_final: 0.8605 (m110) REVERT: C 919 HIS cc_start: 0.8262 (t70) cc_final: 0.7892 (t70) REVERT: C 955 GLU cc_start: 0.9263 (mp0) cc_final: 0.8973 (mp0) REVERT: C 1029 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8795 (mppt) REVERT: C 1045 PHE cc_start: 0.9180 (m-80) cc_final: 0.8898 (m-80) REVERT: D 4 LEU cc_start: 0.9029 (pt) cc_final: 0.8732 (mp) REVERT: D 12 ASN cc_start: 0.9414 (m-40) cc_final: 0.8824 (t0) REVERT: D 142 LEU cc_start: 0.8989 (pt) cc_final: 0.8686 (pp) REVERT: D 155 GLN cc_start: 0.9007 (pm20) cc_final: 0.8505 (pm20) REVERT: D 162 LEU cc_start: 0.9583 (mt) cc_final: 0.9313 (mp) REVERT: D 194 LYS cc_start: 0.9394 (pptt) cc_final: 0.9180 (ptpp) REVERT: D 890 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8362 (ttpt) REVERT: D 896 ARG cc_start: 0.8501 (ttm110) cc_final: 0.8141 (ttp-110) REVERT: D 919 HIS cc_start: 0.8438 (t-170) cc_final: 0.7670 (t-90) REVERT: D 923 LEU cc_start: 0.9628 (mm) cc_final: 0.9383 (tp) REVERT: D 975 THR cc_start: 0.9327 (m) cc_final: 0.8989 (p) REVERT: D 983 ASP cc_start: 0.8302 (t70) cc_final: 0.6870 (t0) REVERT: D 989 LEU cc_start: 0.9696 (mt) cc_final: 0.9261 (tp) REVERT: D 993 THR cc_start: 0.9642 (OUTLIER) cc_final: 0.9402 (p) REVERT: D 1020 MET cc_start: 0.9240 (pmm) cc_final: 0.8953 (pmm) REVERT: A 16 TYR cc_start: 0.7132 (m-10) cc_final: 0.6896 (m-10) REVERT: A 58 TYR cc_start: 0.9210 (p90) cc_final: 0.8912 (p90) REVERT: A 65 ARG cc_start: 0.9150 (tpm170) cc_final: 0.8867 (tpm170) REVERT: A 85 ASP cc_start: 0.6088 (p0) cc_final: 0.5861 (p0) REVERT: A 93 SER cc_start: 0.9510 (m) cc_final: 0.9278 (p) REVERT: A 212 PHE cc_start: 0.8496 (m-80) cc_final: 0.8255 (m-80) REVERT: A 253 LYS cc_start: 0.8280 (mmmm) cc_final: 0.7434 (mtpp) REVERT: A 279 MET cc_start: 0.8581 (mmm) cc_final: 0.7802 (tpt) REVERT: A 296 TRP cc_start: 0.9440 (m100) cc_final: 0.9178 (m100) REVERT: A 366 PHE cc_start: 0.9116 (t80) cc_final: 0.8233 (t80) REVERT: A 387 PHE cc_start: 0.9438 (t80) cc_final: 0.9110 (t80) REVERT: B 15 PHE cc_start: 0.9081 (t80) cc_final: 0.8164 (t80) REVERT: B 18 LYS cc_start: 0.9288 (mmtm) cc_final: 0.9016 (mmtm) REVERT: B 27 PHE cc_start: 0.9612 (t80) cc_final: 0.9374 (t80) REVERT: B 33 GLU cc_start: 0.9424 (tt0) cc_final: 0.8875 (tm-30) REVERT: B 65 ARG cc_start: 0.9017 (ptp-170) cc_final: 0.8734 (ptp-110) REVERT: B 75 CYS cc_start: 0.8558 (m) cc_final: 0.7331 (t) REVERT: B 94 ARG cc_start: 0.9405 (ttp-110) cc_final: 0.9199 (ptm160) REVERT: B 110 HIS cc_start: 0.8752 (t70) cc_final: 0.8252 (t-90) REVERT: B 113 GLN cc_start: 0.8848 (tp-100) cc_final: 0.8632 (tm-30) REVERT: B 207 PHE cc_start: 0.9271 (t80) cc_final: 0.8739 (t80) REVERT: B 271 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8961 (mm) REVERT: B 306 TRP cc_start: 0.7269 (m-10) cc_final: 0.6658 (m-10) REVERT: B 357 LEU cc_start: 0.9471 (tp) cc_final: 0.8985 (pp) REVERT: B 366 PHE cc_start: 0.9289 (t80) cc_final: 0.8523 (t80) REVERT: B 387 PHE cc_start: 0.9378 (t80) cc_final: 0.9037 (t80) outliers start: 54 outliers final: 43 residues processed: 396 average time/residue: 0.2377 time to fit residues: 136.6789 Evaluate side-chains 409 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 362 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 123 LYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1029 LYS Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 890 LYS Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 993 THR 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 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 132 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 HIS 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 307 LEU Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** 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 = 0.3566 r_free = 0.3566 target = 0.080885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.054524 restraints weight = 47652.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.056690 restraints weight = 28127.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.058204 restraints weight = 19609.129| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 13796 Z= 0.297 Angle : 0.848 12.723 19049 Z= 0.415 Chirality : 0.048 0.313 2193 Planarity : 0.005 0.060 2183 Dihedral : 21.153 179.593 2467 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.47 % Allowed : 28.18 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.22), residues: 1479 helix: 0.71 (0.22), residues: 543 sheet: -0.10 (0.30), residues: 289 loop : -0.24 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 96 HIS 0.026 0.002 HIS B 164 PHE 0.027 0.003 PHE C 27 TYR 0.023 0.002 TYR C 55 ARG 0.010 0.001 ARG D 197 Details of bonding type rmsd hydrogen bonds : bond 0.04548 ( 621) hydrogen bonds : angle 5.08384 ( 1674) covalent geometry : bond 0.00597 (13796) covalent geometry : angle 0.84804 (19049) *********************** 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 402 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 345 time to evaluate : 1.345 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 9 LYS cc_start: 0.9252 (tppt) cc_final: 0.8883 (tppt) REVERT: C 22 PHE cc_start: 0.8937 (m-80) cc_final: 0.8518 (m-80) REVERT: C 72 MET cc_start: 0.8489 (ppp) cc_final: 0.8195 (ppp) REVERT: C 113 ARG cc_start: 0.8094 (mtp180) cc_final: 0.7729 (mtp180) REVERT: C 144 TYR cc_start: 0.9214 (t80) cc_final: 0.8983 (t80) REVERT: C 182 TYR cc_start: 0.9020 (m-80) cc_final: 0.8408 (m-80) REVERT: C 189 VAL cc_start: 0.9517 (t) cc_final: 0.9132 (t) REVERT: C 190 PHE cc_start: 0.8513 (t80) cc_final: 0.8207 (t80) REVERT: C 193 HIS cc_start: 0.9061 (t-90) cc_final: 0.8773 (t-90) REVERT: C 197 ARG cc_start: 0.9056 (ptp-170) cc_final: 0.8326 (ptt180) REVERT: C 880 TRP cc_start: 0.9111 (m100) cc_final: 0.8695 (m100) REVERT: C 882 TYR cc_start: 0.8517 (m-10) cc_final: 0.8118 (m-80) REVERT: C 893 ASP cc_start: 0.8823 (m-30) cc_final: 0.8419 (m-30) REVERT: C 895 PHE cc_start: 0.9188 (t80) cc_final: 0.8404 (t80) REVERT: C 897 LYS cc_start: 0.9398 (mtmt) cc_final: 0.8937 (mmtm) REVERT: C 906 ASN cc_start: 0.9245 (m110) cc_final: 0.8950 (m110) REVERT: C 919 HIS cc_start: 0.8381 (t70) cc_final: 0.8031 (t70) REVERT: C 955 GLU cc_start: 0.9272 (mp0) cc_final: 0.8964 (mp0) REVERT: C 1029 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8849 (mppt) REVERT: C 1045 PHE cc_start: 0.9275 (m-80) cc_final: 0.8874 (m-80) REVERT: D 12 ASN cc_start: 0.9435 (m-40) cc_final: 0.8879 (t0) REVERT: D 142 LEU cc_start: 0.9048 (pt) cc_final: 0.8842 (pp) REVERT: D 155 GLN cc_start: 0.9007 (pm20) cc_final: 0.8627 (pm20) REVERT: D 194 LYS cc_start: 0.9391 (pptt) cc_final: 0.9181 (ptpp) REVERT: D 890 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8381 (ttmt) REVERT: D 894 LYS cc_start: 0.9217 (ptmt) cc_final: 0.8919 (ptmt) REVERT: D 896 ARG cc_start: 0.8541 (ttm110) cc_final: 0.8178 (ttp-110) REVERT: D 919 HIS cc_start: 0.8530 (t-170) cc_final: 0.8084 (t70) REVERT: D 983 ASP cc_start: 0.8275 (t70) cc_final: 0.7542 (t70) REVERT: D 1016 HIS cc_start: 0.7539 (m170) cc_final: 0.7296 (m170) REVERT: D 1020 MET cc_start: 0.9285 (pmm) cc_final: 0.9016 (pmm) REVERT: A 16 TYR cc_start: 0.7102 (m-10) cc_final: 0.6883 (m-10) REVERT: A 58 TYR cc_start: 0.9249 (p90) cc_final: 0.8970 (p90) REVERT: A 65 ARG cc_start: 0.9170 (tpm170) cc_final: 0.8819 (tpp-160) REVERT: A 85 ASP cc_start: 0.6262 (p0) cc_final: 0.6019 (p0) REVERT: A 149 LYS cc_start: 0.9654 (mttm) cc_final: 0.9267 (mttm) REVERT: A 232 MET cc_start: 0.9323 (mmm) cc_final: 0.8869 (mpp) REVERT: A 279 MET cc_start: 0.8543 (mmm) cc_final: 0.7790 (tpt) REVERT: A 296 TRP cc_start: 0.9457 (m100) cc_final: 0.9132 (m100) REVERT: A 366 PHE cc_start: 0.9126 (t80) cc_final: 0.8291 (t80) REVERT: A 385 HIS cc_start: 0.9316 (m-70) cc_final: 0.8941 (m-70) REVERT: A 387 PHE cc_start: 0.9393 (t80) cc_final: 0.9070 (t80) REVERT: B 15 PHE cc_start: 0.9107 (t80) cc_final: 0.8240 (t80) REVERT: B 18 LYS cc_start: 0.9290 (mmtm) cc_final: 0.9030 (mmtm) REVERT: B 27 PHE cc_start: 0.9654 (t80) cc_final: 0.9409 (t80) REVERT: B 33 GLU cc_start: 0.9426 (tt0) cc_final: 0.8918 (tm-30) REVERT: B 65 ARG cc_start: 0.9029 (ptp-170) cc_final: 0.8778 (ptp-110) REVERT: B 75 CYS cc_start: 0.8435 (m) cc_final: 0.8069 (m) REVERT: B 99 PHE cc_start: 0.8936 (m-80) cc_final: 0.8710 (m-80) REVERT: B 110 HIS cc_start: 0.8762 (t70) cc_final: 0.8290 (t-90) REVERT: B 113 GLN cc_start: 0.8945 (tp40) cc_final: 0.8338 (tm-30) REVERT: B 271 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8984 (mm) REVERT: B 366 PHE cc_start: 0.9276 (t80) cc_final: 0.8567 (t80) REVERT: B 387 PHE cc_start: 0.9372 (t80) cc_final: 0.9042 (t80) outliers start: 57 outliers final: 46 residues processed: 375 average time/residue: 0.2491 time to fit residues: 135.3634 Evaluate side-chains 382 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 333 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ILE 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 123 LYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1029 LYS Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1033 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 890 LYS Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1011 ILE Chi-restraints excluded: chain D residue 1014 ILE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain 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 164 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 126 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 145 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 0.0970 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** 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 = 0.3584 r_free = 0.3584 target = 0.082447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.055968 restraints weight = 45567.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.058233 restraints weight = 26668.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.059830 restraints weight = 18326.341| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13796 Z= 0.146 Angle : 0.878 14.624 19049 Z= 0.401 Chirality : 0.047 0.330 2193 Planarity : 0.004 0.064 2183 Dihedral : 21.121 178.949 2467 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.53 % Allowed : 29.91 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.23), residues: 1479 helix: 0.98 (0.23), residues: 533 sheet: 0.06 (0.32), residues: 251 loop : -0.11 (0.26), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 96 HIS 0.007 0.001 HIS A 385 PHE 0.024 0.002 PHE C 27 TYR 0.021 0.002 TYR B 217 ARG 0.015 0.001 ARG A 2 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 621) hydrogen bonds : angle 4.79139 ( 1674) covalent geometry : bond 0.00331 (13796) covalent geometry : angle 0.87757 (19049) ********************** 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 409 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 364 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 LYS cc_start: 0.9233 (tppt) cc_final: 0.8872 (tppt) REVERT: C 22 PHE cc_start: 0.8860 (m-80) cc_final: 0.8424 (m-80) REVERT: C 72 MET cc_start: 0.8362 (ppp) cc_final: 0.8129 (ppp) REVERT: C 113 ARG cc_start: 0.8105 (mtp180) cc_final: 0.7774 (mtp180) REVERT: C 144 TYR cc_start: 0.9149 (t80) cc_final: 0.8904 (t80) REVERT: C 171 GLU cc_start: 0.9254 (pt0) cc_final: 0.8981 (pp20) REVERT: C 172 LEU cc_start: 0.9364 (mt) cc_final: 0.9142 (pp) REVERT: C 182 TYR cc_start: 0.8989 (m-80) cc_final: 0.8281 (m-80) REVERT: C 189 VAL cc_start: 0.9491 (t) cc_final: 0.9035 (t) REVERT: C 190 PHE cc_start: 0.8426 (t80) cc_final: 0.8221 (t80) REVERT: C 880 TRP cc_start: 0.9082 (m100) cc_final: 0.8629 (m100) REVERT: C 882 TYR cc_start: 0.8515 (m-10) cc_final: 0.8108 (m-80) REVERT: C 893 ASP cc_start: 0.8867 (m-30) cc_final: 0.8382 (m-30) REVERT: C 895 PHE cc_start: 0.9158 (t80) cc_final: 0.8362 (t80) REVERT: C 897 LYS cc_start: 0.9362 (mtmt) cc_final: 0.8948 (mmtp) REVERT: C 906 ASN cc_start: 0.9225 (m110) cc_final: 0.8938 (m110) REVERT: C 919 HIS cc_start: 0.8310 (t70) cc_final: 0.7971 (t70) REVERT: C 955 GLU cc_start: 0.9312 (mp0) cc_final: 0.8996 (mp0) REVERT: C 1029 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8796 (mppt) REVERT: C 1045 PHE cc_start: 0.9217 (m-80) cc_final: 0.8828 (m-80) REVERT: D 12 ASN cc_start: 0.9414 (m-40) cc_final: 0.8792 (t0) REVERT: D 74 ARG cc_start: 0.8574 (mmp80) cc_final: 0.7946 (mmp-170) REVERT: D 155 GLN cc_start: 0.8961 (pm20) cc_final: 0.8616 (pm20) REVERT: D 162 LEU cc_start: 0.9541 (mt) cc_final: 0.9244 (mp) REVERT: D 188 MET cc_start: 0.8884 (ppp) cc_final: 0.8675 (pmm) REVERT: D 194 LYS cc_start: 0.9367 (pptt) cc_final: 0.9154 (ptpp) REVERT: D 890 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8474 (ttmt) REVERT: D 894 LYS cc_start: 0.9287 (ptmt) cc_final: 0.8955 (ptmt) REVERT: D 896 ARG cc_start: 0.8348 (ttm110) cc_final: 0.7998 (ttp-110) REVERT: D 919 HIS cc_start: 0.8282 (t-170) cc_final: 0.7839 (t70) REVERT: D 1016 HIS cc_start: 0.7369 (m170) cc_final: 0.7131 (m170) REVERT: D 1020 MET cc_start: 0.9268 (pmm) cc_final: 0.8933 (pmm) REVERT: A 1 MET cc_start: 0.8222 (tmm) cc_final: 0.7765 (tpt) REVERT: A 2 ARG cc_start: 0.9010 (mtt-85) cc_final: 0.8609 (mtm180) REVERT: A 16 TYR cc_start: 0.7073 (m-10) cc_final: 0.6820 (m-10) REVERT: A 58 TYR cc_start: 0.9186 (p90) cc_final: 0.8899 (p90) REVERT: A 65 ARG cc_start: 0.9146 (tpm170) cc_final: 0.8880 (tpm170) REVERT: A 85 ASP cc_start: 0.6260 (p0) cc_final: 0.6055 (p0) REVERT: A 149 LYS cc_start: 0.9636 (mttm) cc_final: 0.9277 (mttm) REVERT: A 212 PHE cc_start: 0.8483 (m-80) cc_final: 0.8241 (m-80) REVERT: A 220 LEU cc_start: 0.9377 (mm) cc_final: 0.9013 (mm) REVERT: A 232 MET cc_start: 0.9343 (mmm) cc_final: 0.8877 (mpp) REVERT: A 279 MET cc_start: 0.8569 (mmm) cc_final: 0.7790 (tpt) REVERT: A 296 TRP cc_start: 0.9441 (m100) cc_final: 0.9204 (m100) REVERT: A 366 PHE cc_start: 0.9089 (t80) cc_final: 0.8209 (t80) REVERT: A 385 HIS cc_start: 0.9300 (m-70) cc_final: 0.8923 (m-70) REVERT: A 387 PHE cc_start: 0.9351 (t80) cc_final: 0.9005 (t80) REVERT: B 1 MET cc_start: 0.7960 (tpp) cc_final: 0.7718 (tpt) REVERT: B 15 PHE cc_start: 0.9091 (t80) cc_final: 0.8202 (t80) REVERT: B 18 LYS cc_start: 0.9290 (mmtm) cc_final: 0.9019 (mmtm) REVERT: B 33 GLU cc_start: 0.9416 (tt0) cc_final: 0.8895 (tm-30) REVERT: B 65 ARG cc_start: 0.9031 (ptp-170) cc_final: 0.8657 (ptp-110) REVERT: B 75 CYS cc_start: 0.8577 (m) cc_final: 0.8284 (m) REVERT: B 99 PHE cc_start: 0.8917 (m-80) cc_final: 0.8666 (m-80) REVERT: B 110 HIS cc_start: 0.8675 (t70) cc_final: 0.8239 (t-90) REVERT: B 113 GLN cc_start: 0.8900 (tp40) cc_final: 0.8509 (tm-30) REVERT: B 207 PHE cc_start: 0.9189 (t80) cc_final: 0.8742 (t80) REVERT: B 253 LYS cc_start: 0.8174 (mmmt) cc_final: 0.7667 (mmtp) REVERT: B 260 PHE cc_start: 0.8966 (m-80) cc_final: 0.8119 (m-10) REVERT: B 271 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9012 (mm) REVERT: B 279 MET cc_start: 0.8683 (mmt) cc_final: 0.8000 (tpt) REVERT: B 366 PHE cc_start: 0.9225 (t80) cc_final: 0.8477 (t80) REVERT: B 387 PHE cc_start: 0.9362 (t80) cc_final: 0.9005 (t80) outliers start: 45 outliers final: 40 residues processed: 385 average time/residue: 0.2808 time to fit residues: 156.8835 Evaluate side-chains 389 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 346 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1029 LYS Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 890 LYS Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1014 ILE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1024 ILE Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 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 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 104 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 GLN ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.082105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.055788 restraints weight = 46014.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.058018 restraints weight = 26819.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.059605 restraints weight = 18476.756| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13796 Z= 0.156 Angle : 0.868 14.131 19049 Z= 0.396 Chirality : 0.047 0.360 2193 Planarity : 0.004 0.064 2183 Dihedral : 21.113 179.703 2467 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.53 % Allowed : 29.98 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.23), residues: 1479 helix: 1.00 (0.23), residues: 535 sheet: 0.03 (0.31), residues: 273 loop : -0.12 (0.27), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 30 HIS 0.006 0.001 HIS A 385 PHE 0.023 0.002 PHE B 27 TYR 0.020 0.002 TYR B 217 ARG 0.008 0.000 ARG D 197 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 621) hydrogen bonds : angle 4.79609 ( 1674) covalent geometry : bond 0.00352 (13796) covalent geometry : angle 0.86760 (19049) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6083.19 seconds wall clock time: 108 minutes 30.39 seconds (6510.39 seconds total)