Starting phenix.real_space_refine on Sun May 11 08:28:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgb_36229/05_2025/8jgb_36229_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgb_36229/05_2025/8jgb_36229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jgb_36229/05_2025/8jgb_36229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgb_36229/05_2025/8jgb_36229.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgb_36229/05_2025/8jgb_36229_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgb_36229/05_2025/8jgb_36229_neut.cif" } resolution = 2.84 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 4980 2.51 5 N 1342 2.21 5 O 1425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7796 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 421 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1612 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2488 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "R" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1529 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 4 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "S" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1710 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Time building chain proxies: 4.78, per 1000 atoms: 0.61 Number of scatterers: 7796 At special positions: 0 Unit cell: (102.6, 119.88, 122.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1425 8.00 N 1342 7.00 C 4980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 158 " - pdb=" SG CYS S 228 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.2 seconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1982 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 34.2% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'G' and resid 10 through 22 removed outlier: 3.687A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.692A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.742A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.554A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 4.128A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.752A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.902A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 281 No H-bonds generated for 'chain 'A' and resid 280 through 281' Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.392A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 4.517A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 20 removed outlier: 3.809A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'R' and resid 31 through 36 removed outlier: 3.722A pdb=" N CYS R 35 " --> pdb=" O THR R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 55 removed outlier: 3.791A pdb=" N THR R 43 " --> pdb=" O LEU R 39 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL R 48 " --> pdb=" O GLY R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 81 removed outlier: 3.732A pdb=" N ILE R 63 " --> pdb=" O ASN R 59 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE R 65 " --> pdb=" O PHE R 61 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE R 75 " --> pdb=" O ALA R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 84 No H-bonds generated for 'chain 'R' and resid 82 through 84' Processing helix chain 'R' and resid 97 through 126 removed outlier: 3.548A pdb=" N VAL R 101 " --> pdb=" O ILE R 97 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET R 102 " --> pdb=" O LEU R 98 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET R 103 " --> pdb=" O TYR R 99 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER R 105 " --> pdb=" O VAL R 101 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER R 114 " --> pdb=" O LEU R 110 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL R 116 " --> pdb=" O PHE R 112 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG R 120 " --> pdb=" O VAL R 116 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS R 121 " --> pdb=" O SER R 117 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 Processing helix chain 'R' and resid 137 through 160 removed outlier: 3.584A pdb=" N GLU R 157 " --> pdb=" O ARG R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 196 removed outlier: 3.585A pdb=" N LEU R 187 " --> pdb=" O TRP R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 201 Processing helix chain 'R' and resid 212 through 228 removed outlier: 4.089A pdb=" N VAL R 216 " --> pdb=" O THR R 212 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N THR R 217 " --> pdb=" O ARG R 213 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU R 219 " --> pdb=" O TYR R 215 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL R 222 " --> pdb=" O ILE R 218 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU R 223 " --> pdb=" O LEU R 219 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS R 228 " --> pdb=" O VAL R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 231 No H-bonds generated for 'chain 'R' and resid 229 through 231' Processing helix chain 'R' and resid 232 through 237 removed outlier: 4.208A pdb=" N PHE R 237 " --> pdb=" O GLY R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 240 No H-bonds generated for 'chain 'R' and resid 238 through 240' Processing helix chain 'R' and resid 251 through 265 removed outlier: 4.346A pdb=" N LEU R 255 " --> pdb=" O CYS R 251 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE R 259 " --> pdb=" O LEU R 255 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER R 265 " --> pdb=" O SER R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 273 Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.503A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.658A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.740A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.547A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.616A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.767A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.602A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.658A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.625A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.978A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.305A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 139 through 141 removed outlier: 4.192A pdb=" N ALA S 210 " --> pdb=" O SER S 207 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 145 through 147 removed outlier: 3.740A pdb=" N GLU S 245 " --> pdb=" O VAL S 146 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY S 224 " --> pdb=" O LEU S 244 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU S 173 " --> pdb=" O TYR S 189 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR S 189 " --> pdb=" O LEU S 173 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP S 175 " --> pdb=" O LEU S 187 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 145 through 147 removed outlier: 3.740A pdb=" N GLU S 245 " --> pdb=" O VAL S 146 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY S 224 " --> pdb=" O LEU S 244 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR S 237 " --> pdb=" O GLN S 230 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 954 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1249 1.29 - 1.42: 2138 1.42 - 1.55: 4485 1.55 - 1.68: 9 1.68 - 1.81: 68 Bond restraints: 7949 Sorted by residual: bond pdb=" CA SER A 263 " pdb=" C SER A 263 " ideal model delta sigma weight residual 1.524 1.437 0.088 1.31e-02 5.83e+03 4.48e+01 bond pdb=" C ILE B 229 " pdb=" O ILE B 229 " ideal model delta sigma weight residual 1.234 1.161 0.073 1.17e-02 7.31e+03 3.85e+01 bond pdb=" CA ALA A 11 " pdb=" CB ALA A 11 " ideal model delta sigma weight residual 1.529 1.429 0.100 1.63e-02 3.76e+03 3.79e+01 bond pdb=" C GLY B 244 " pdb=" O GLY B 244 " ideal model delta sigma weight residual 1.235 1.154 0.081 1.35e-02 5.49e+03 3.61e+01 bond pdb=" CA TRP B 211 " pdb=" C TRP B 211 " ideal model delta sigma weight residual 1.522 1.450 0.072 1.21e-02 6.83e+03 3.53e+01 ... (remaining 7944 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 10363 2.71 - 5.42: 325 5.42 - 8.12: 84 8.12 - 10.83: 22 10.83 - 13.54: 11 Bond angle restraints: 10805 Sorted by residual: angle pdb=" N ALA B 24 " pdb=" CA ALA B 24 " pdb=" C ALA B 24 " ideal model delta sigma weight residual 111.71 99.25 12.46 1.34e+00 5.57e-01 8.65e+01 angle pdb=" N CYS B 25 " pdb=" CA CYS B 25 " pdb=" C CYS B 25 " ideal model delta sigma weight residual 112.54 99.00 13.54 1.51e+00 4.39e-01 8.04e+01 angle pdb=" N ILE R 234 " pdb=" CA ILE R 234 " pdb=" C ILE R 234 " ideal model delta sigma weight residual 112.80 102.97 9.83 1.15e+00 7.56e-01 7.31e+01 angle pdb=" N HIS R 252 " pdb=" CA HIS R 252 " pdb=" C HIS R 252 " ideal model delta sigma weight residual 113.01 102.77 10.24 1.20e+00 6.94e-01 7.28e+01 angle pdb=" N SER R 38 " pdb=" CA SER R 38 " pdb=" C SER R 38 " ideal model delta sigma weight residual 113.30 101.90 11.40 1.34e+00 5.57e-01 7.24e+01 ... (remaining 10800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4107 17.65 - 35.30: 413 35.30 - 52.95: 106 52.95 - 70.60: 21 70.60 - 88.25: 4 Dihedral angle restraints: 4651 sinusoidal: 1587 harmonic: 3064 Sorted by residual: dihedral pdb=" N TYR R 99 " pdb=" C TYR R 99 " pdb=" CA TYR R 99 " pdb=" CB TYR R 99 " ideal model delta harmonic sigma weight residual 122.80 137.86 -15.06 0 2.50e+00 1.60e-01 3.63e+01 dihedral pdb=" C TYR R 99 " pdb=" N TYR R 99 " pdb=" CA TYR R 99 " pdb=" CB TYR R 99 " ideal model delta harmonic sigma weight residual -122.60 -136.57 13.97 0 2.50e+00 1.60e-01 3.12e+01 dihedral pdb=" C LEU R 203 " pdb=" N LEU R 203 " pdb=" CA LEU R 203 " pdb=" CB LEU R 203 " ideal model delta harmonic sigma weight residual -122.60 -135.82 13.22 0 2.50e+00 1.60e-01 2.79e+01 ... (remaining 4648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1209 0.146 - 0.292: 49 0.292 - 0.438: 8 0.438 - 0.584: 1 0.584 - 0.730: 1 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CA TYR R 99 " pdb=" N TYR R 99 " pdb=" C TYR R 99 " pdb=" CB TYR R 99 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CA LEU R 203 " pdb=" N LEU R 203 " pdb=" C LEU R 203 " pdb=" CB LEU R 203 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA SER S 88 " pdb=" N SER S 88 " pdb=" C SER S 88 " pdb=" CB SER S 88 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 1265 not shown) Planarity restraints: 1364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.084 5.00e-02 4.00e+02 1.24e-01 2.45e+01 pdb=" N PRO G 53 " 0.214 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 245 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLU A 245 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU A 245 " 0.020 2.00e-02 2.50e+03 pdb=" N SER A 246 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 210 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.29e+00 pdb=" C LEU B 210 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU B 210 " 0.020 2.00e-02 2.50e+03 pdb=" N TRP B 211 " 0.018 2.00e-02 2.50e+03 ... (remaining 1361 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1619 2.76 - 3.30: 6786 3.30 - 3.83: 11942 3.83 - 4.37: 14820 4.37 - 4.90: 25741 Nonbonded interactions: 60908 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.230 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.323 3.040 nonbonded pdb=" OD2 ASP G 48 " pdb=" OG SER B 281 " model vdw 2.332 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.334 3.040 ... (remaining 60903 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.880 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.010 0.100 7951 Z= 0.707 Angle : 1.224 13.540 10809 Z= 0.792 Chirality : 0.073 0.730 1268 Planarity : 0.007 0.124 1364 Dihedral : 15.632 88.252 2663 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.89 % Allowed : 24.54 % Favored : 72.57 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % 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: -2.42 (0.25), residues: 1036 helix: -2.64 (0.25), residues: 325 sheet: 0.13 (0.31), residues: 281 loop : -1.84 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 211 HIS 0.005 0.001 HIS B 183 PHE 0.034 0.003 PHE R 112 TYR 0.027 0.002 TYR A 230 ARG 0.004 0.000 ARG R 79 Details of bonding type rmsd hydrogen bonds : bond 0.27274 ( 336) hydrogen bonds : angle 9.38184 ( 954) SS BOND : bond 0.00635 ( 2) SS BOND : angle 1.43366 ( 4) covalent geometry : bond 0.01030 ( 7949) covalent geometry : angle 1.22434 (10805) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.836 Fit side-chains REVERT: A 270 LYS cc_start: 0.8733 (mptt) cc_final: 0.8510 (mmtp) REVERT: B 13 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7201 (tm-30) REVERT: B 111 TYR cc_start: 0.8656 (m-80) cc_final: 0.8312 (m-80) REVERT: B 258 ASP cc_start: 0.7804 (t0) cc_final: 0.7394 (t0) REVERT: R 63 ILE cc_start: 0.8662 (mm) cc_final: 0.8140 (mt) REVERT: R 67 ASN cc_start: 0.8152 (m-40) cc_final: 0.7701 (m110) REVERT: R 103 MET cc_start: 0.7744 (mmm) cc_final: 0.7507 (mmp) REVERT: R 186 PHE cc_start: 0.8026 (t80) cc_final: 0.7737 (t80) REVERT: R 196 LEU cc_start: 0.8101 (pp) cc_final: 0.7895 (pt) REVERT: R 263 LEU cc_start: 0.8651 (tp) cc_final: 0.8435 (tt) REVERT: S 80 PHE cc_start: 0.8622 (m-80) cc_final: 0.8359 (m-80) REVERT: S 148 VAL cc_start: 0.7820 (OUTLIER) cc_final: 0.7446 (m) REVERT: S 198 VAL cc_start: 0.8875 (m) cc_final: 0.8629 (p) outliers start: 22 outliers final: 8 residues processed: 214 average time/residue: 0.8852 time to fit residues: 203.2905 Evaluate side-chains 176 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 148 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 81 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 0.0000 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 204 GLN A 255 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 141 GLN S 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.114529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.099246 restraints weight = 11855.106| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.01 r_work: 0.3209 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7951 Z= 0.132 Angle : 0.587 5.963 10809 Z= 0.317 Chirality : 0.043 0.147 1268 Planarity : 0.005 0.070 1364 Dihedral : 4.897 50.716 1137 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.86 % Allowed : 24.93 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.26), residues: 1036 helix: -1.13 (0.28), residues: 322 sheet: 0.50 (0.32), residues: 286 loop : -1.54 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 47 HIS 0.004 0.001 HIS B 91 PHE 0.024 0.002 PHE A 274 TYR 0.015 0.001 TYR S 189 ARG 0.004 0.000 ARG R 79 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 336) hydrogen bonds : angle 5.22181 ( 954) SS BOND : bond 0.00831 ( 2) SS BOND : angle 1.09630 ( 4) covalent geometry : bond 0.00293 ( 7949) covalent geometry : angle 0.58627 (10805) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 0.835 Fit side-chains REVERT: A 270 LYS cc_start: 0.8819 (mptt) cc_final: 0.8617 (mmtp) REVERT: A 296 TYR cc_start: 0.7748 (t80) cc_final: 0.7461 (t80) REVERT: A 340 THR cc_start: 0.8356 (t) cc_final: 0.7931 (m) REVERT: A 353 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7994 (tm) REVERT: B 13 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7405 (tm130) REVERT: B 46 ARG cc_start: 0.8179 (mmt-90) cc_final: 0.7974 (mtt-85) REVERT: B 70 LEU cc_start: 0.8873 (pt) cc_final: 0.8665 (pt) REVERT: B 111 TYR cc_start: 0.8775 (m-80) cc_final: 0.8500 (m-80) REVERT: R 63 ILE cc_start: 0.8770 (mm) cc_final: 0.7942 (mt) REVERT: R 67 ASN cc_start: 0.8343 (m-40) cc_final: 0.7632 (m110) REVERT: R 145 LEU cc_start: 0.8184 (tp) cc_final: 0.7903 (tt) REVERT: R 186 PHE cc_start: 0.8251 (t80) cc_final: 0.7945 (t80) REVERT: R 226 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8406 (tp) REVERT: R 258 ILE cc_start: 0.8348 (tt) cc_final: 0.8086 (tp) REVERT: S 183 SER cc_start: 0.8680 (p) cc_final: 0.8468 (m) REVERT: S 244 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8117 (mt) outliers start: 37 outliers final: 17 residues processed: 215 average time/residue: 1.0342 time to fit residues: 237.2968 Evaluate side-chains 194 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 265 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 244 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 79 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 31 optimal weight: 0.0370 chunk 55 optimal weight: 0.3980 chunk 69 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 54 HIS ** B 259 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 = 0.3551 r_free = 0.3551 target = 0.114692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.099194 restraints weight = 11928.651| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.03 r_work: 0.3205 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7951 Z= 0.117 Angle : 0.541 6.133 10809 Z= 0.289 Chirality : 0.042 0.142 1268 Planarity : 0.004 0.060 1364 Dihedral : 4.354 48.126 1128 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.20 % Allowed : 26.51 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.27), residues: 1036 helix: -0.38 (0.30), residues: 330 sheet: 0.67 (0.32), residues: 285 loop : -1.37 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS B 91 PHE 0.022 0.001 PHE A 274 TYR 0.013 0.001 TYR S 189 ARG 0.005 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 336) hydrogen bonds : angle 4.70810 ( 954) SS BOND : bond 0.00821 ( 2) SS BOND : angle 1.16367 ( 4) covalent geometry : bond 0.00258 ( 7949) covalent geometry : angle 0.54067 (10805) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.952 Fit side-chains REVERT: A 10 LYS cc_start: 0.8058 (mtmm) cc_final: 0.7809 (mtmm) REVERT: A 296 TYR cc_start: 0.7726 (t80) cc_final: 0.7429 (t80) REVERT: A 340 THR cc_start: 0.8346 (t) cc_final: 0.7941 (m) REVERT: A 349 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7631 (mttp) REVERT: B 13 GLN cc_start: 0.7631 (tm-30) cc_final: 0.7349 (tm130) REVERT: B 46 ARG cc_start: 0.8183 (mmt-90) cc_final: 0.7963 (mtt-85) REVERT: B 52 ARG cc_start: 0.8656 (mtt90) cc_final: 0.8449 (mtt-85) REVERT: B 111 TYR cc_start: 0.8792 (m-80) cc_final: 0.8518 (m-80) REVERT: R 63 ILE cc_start: 0.8774 (mm) cc_final: 0.7947 (mt) REVERT: R 67 ASN cc_start: 0.8360 (m-40) cc_final: 0.7627 (m110) REVERT: R 226 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8409 (tp) REVERT: R 258 ILE cc_start: 0.8345 (tt) cc_final: 0.8096 (tp) REVERT: S 59 TYR cc_start: 0.8425 (m-80) cc_final: 0.8069 (m-80) REVERT: S 183 SER cc_start: 0.8578 (p) cc_final: 0.8377 (m) outliers start: 32 outliers final: 12 residues processed: 209 average time/residue: 0.9279 time to fit residues: 207.9105 Evaluate side-chains 183 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 265 SER Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 209 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 98 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.112645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.097393 restraints weight = 11781.195| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.02 r_work: 0.3175 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7951 Z= 0.174 Angle : 0.601 8.413 10809 Z= 0.315 Chirality : 0.044 0.142 1268 Planarity : 0.004 0.058 1364 Dihedral : 4.463 47.514 1127 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.72 % Allowed : 26.64 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.26), residues: 1036 helix: -0.11 (0.31), residues: 323 sheet: 0.68 (0.31), residues: 288 loop : -1.37 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 47 HIS 0.004 0.001 HIS B 91 PHE 0.021 0.002 PHE A 274 TYR 0.013 0.002 TYR A 320 ARG 0.011 0.001 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04877 ( 336) hydrogen bonds : angle 4.68389 ( 954) SS BOND : bond 0.00995 ( 2) SS BOND : angle 1.51699 ( 4) covalent geometry : bond 0.00411 ( 7949) covalent geometry : angle 0.60042 (10805) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.910 Fit side-chains REVERT: A 10 LYS cc_start: 0.8261 (mtmm) cc_final: 0.7930 (mttp) REVERT: A 252 SER cc_start: 0.8716 (OUTLIER) cc_final: 0.8294 (m) REVERT: A 296 TYR cc_start: 0.7809 (t80) cc_final: 0.7487 (t80) REVERT: A 340 THR cc_start: 0.8319 (t) cc_final: 0.8028 (m) REVERT: B 13 GLN cc_start: 0.7679 (tm-30) cc_final: 0.7297 (tm130) REVERT: B 46 ARG cc_start: 0.8181 (mmt-90) cc_final: 0.7965 (mtt-85) REVERT: B 258 ASP cc_start: 0.7965 (t0) cc_final: 0.7384 (t0) REVERT: R 63 ILE cc_start: 0.8832 (mm) cc_final: 0.7940 (mt) REVERT: R 67 ASN cc_start: 0.8336 (m-40) cc_final: 0.7589 (m110) REVERT: R 258 ILE cc_start: 0.8405 (tt) cc_final: 0.8152 (tp) REVERT: S 59 TYR cc_start: 0.8434 (m-80) cc_final: 0.8180 (m-80) outliers start: 36 outliers final: 15 residues processed: 194 average time/residue: 1.0209 time to fit residues: 211.5120 Evaluate side-chains 179 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 132 CYS Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 203 SER Chi-restraints excluded: chain S residue 209 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 chunk 97 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 0.0070 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 269 ASN B 54 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.114612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.099244 restraints weight = 11723.492| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.02 r_work: 0.3204 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7951 Z= 0.108 Angle : 0.552 7.995 10809 Z= 0.283 Chirality : 0.041 0.147 1268 Planarity : 0.004 0.053 1364 Dihedral : 4.052 40.279 1127 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.15 % Allowed : 29.40 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.27), residues: 1036 helix: 0.14 (0.31), residues: 324 sheet: 0.79 (0.31), residues: 286 loop : -1.34 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.003 0.001 HIS B 91 PHE 0.018 0.001 PHE A 274 TYR 0.012 0.001 TYR S 189 ARG 0.004 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 336) hydrogen bonds : angle 4.44664 ( 954) SS BOND : bond 0.00739 ( 2) SS BOND : angle 1.20043 ( 4) covalent geometry : bond 0.00240 ( 7949) covalent geometry : angle 0.55179 (10805) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.833 Fit side-chains REVERT: A 252 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.8301 (m) REVERT: A 296 TYR cc_start: 0.7683 (t80) cc_final: 0.7420 (t80) REVERT: A 340 THR cc_start: 0.8311 (t) cc_final: 0.8009 (m) REVERT: A 349 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7699 (mttp) REVERT: B 13 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7319 (tm130) REVERT: B 46 ARG cc_start: 0.8191 (mmt-90) cc_final: 0.7976 (mtt-85) REVERT: B 52 ARG cc_start: 0.8491 (mtt-85) cc_final: 0.8216 (mtt-85) REVERT: R 63 ILE cc_start: 0.8803 (mm) cc_final: 0.7957 (mt) REVERT: R 67 ASN cc_start: 0.8312 (m-40) cc_final: 0.7576 (m110) REVERT: R 153 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7117 (tmt-80) REVERT: R 258 ILE cc_start: 0.8288 (tt) cc_final: 0.8072 (tp) REVERT: S 59 TYR cc_start: 0.8415 (m-80) cc_final: 0.8143 (m-80) outliers start: 24 outliers final: 12 residues processed: 185 average time/residue: 1.1409 time to fit residues: 223.6738 Evaluate side-chains 180 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 153 ARG Chi-restraints excluded: chain R residue 195 SER Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 17 GLN B 44 GLN B 54 HIS B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.111888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.096619 restraints weight = 11698.163| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.02 r_work: 0.3163 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7951 Z= 0.208 Angle : 0.616 7.477 10809 Z= 0.322 Chirality : 0.045 0.143 1268 Planarity : 0.004 0.052 1364 Dihedral : 4.246 15.554 1126 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.86 % Allowed : 27.03 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.26), residues: 1036 helix: 0.16 (0.31), residues: 321 sheet: 0.72 (0.31), residues: 288 loop : -1.36 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.023 0.002 PHE R 104 TYR 0.014 0.002 TYR A 320 ARG 0.003 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.05030 ( 336) hydrogen bonds : angle 4.63022 ( 954) SS BOND : bond 0.01081 ( 2) SS BOND : angle 1.70907 ( 4) covalent geometry : bond 0.00496 ( 7949) covalent geometry : angle 0.61503 (10805) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.878 Fit side-chains REVERT: A 252 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8290 (m) REVERT: A 296 TYR cc_start: 0.7775 (t80) cc_final: 0.7409 (t80) REVERT: A 340 THR cc_start: 0.8316 (t) cc_final: 0.8082 (m) REVERT: B 13 GLN cc_start: 0.7726 (tm-30) cc_final: 0.7390 (tm-30) REVERT: B 46 ARG cc_start: 0.8204 (mmt-90) cc_final: 0.7986 (mtt-85) REVERT: B 258 ASP cc_start: 0.7920 (t0) cc_final: 0.7551 (t0) REVERT: R 63 ILE cc_start: 0.8873 (mm) cc_final: 0.8003 (mt) REVERT: R 67 ASN cc_start: 0.8318 (m-40) cc_final: 0.7580 (m110) REVERT: R 223 LEU cc_start: 0.8305 (tp) cc_final: 0.8091 (tp) REVERT: R 258 ILE cc_start: 0.8375 (tt) cc_final: 0.8110 (tp) REVERT: S 59 TYR cc_start: 0.8461 (m-80) cc_final: 0.8176 (m-80) outliers start: 37 outliers final: 23 residues processed: 186 average time/residue: 1.0122 time to fit residues: 200.6895 Evaluate side-chains 186 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 132 CYS Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 183 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 203 SER Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 218 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.114524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.098840 restraints weight = 11546.389| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.99 r_work: 0.3188 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7951 Z= 0.149 Angle : 0.575 8.361 10809 Z= 0.301 Chirality : 0.043 0.147 1268 Planarity : 0.004 0.053 1364 Dihedral : 4.057 15.466 1126 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.54 % Allowed : 28.35 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.26), residues: 1036 helix: 0.30 (0.30), residues: 324 sheet: 0.73 (0.31), residues: 288 loop : -1.33 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 47 HIS 0.004 0.001 HIS B 91 PHE 0.027 0.002 PHE R 225 TYR 0.014 0.002 TYR B 111 ARG 0.012 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 336) hydrogen bonds : angle 4.48537 ( 954) SS BOND : bond 0.00906 ( 2) SS BOND : angle 1.43950 ( 4) covalent geometry : bond 0.00352 ( 7949) covalent geometry : angle 0.57420 (10805) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.927 Fit side-chains REVERT: A 252 SER cc_start: 0.8733 (OUTLIER) cc_final: 0.8324 (m) REVERT: A 296 TYR cc_start: 0.7686 (t80) cc_final: 0.7392 (t80) REVERT: A 340 THR cc_start: 0.8319 (t) cc_final: 0.8054 (m) REVERT: B 13 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7348 (tm-30) REVERT: B 46 ARG cc_start: 0.8161 (mmt-90) cc_final: 0.7934 (mtt-85) REVERT: B 258 ASP cc_start: 0.7879 (t0) cc_final: 0.7499 (t0) REVERT: R 63 ILE cc_start: 0.8871 (mm) cc_final: 0.8017 (mt) REVERT: R 67 ASN cc_start: 0.8318 (m-40) cc_final: 0.7586 (m110) REVERT: R 81 ILE cc_start: 0.8116 (tt) cc_final: 0.7650 (pt) REVERT: R 223 LEU cc_start: 0.8324 (tp) cc_final: 0.8111 (tp) REVERT: R 258 ILE cc_start: 0.8351 (tt) cc_final: 0.8124 (tp) REVERT: S 59 TYR cc_start: 0.8411 (m-80) cc_final: 0.8133 (m-80) outliers start: 27 outliers final: 17 residues processed: 183 average time/residue: 1.0444 time to fit residues: 203.4199 Evaluate side-chains 184 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 132 CYS Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 183 SER Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 218 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 54 HIS B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.114648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098963 restraints weight = 11520.731| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.99 r_work: 0.3188 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7951 Z= 0.142 Angle : 0.584 8.583 10809 Z= 0.301 Chirality : 0.042 0.143 1268 Planarity : 0.004 0.050 1364 Dihedral : 4.018 15.480 1126 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.81 % Allowed : 28.22 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1036 helix: 0.41 (0.31), residues: 324 sheet: 0.73 (0.31), residues: 288 loop : -1.32 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 47 HIS 0.004 0.001 HIS B 91 PHE 0.019 0.002 PHE R 104 TYR 0.015 0.001 TYR B 111 ARG 0.010 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 336) hydrogen bonds : angle 4.44822 ( 954) SS BOND : bond 0.00872 ( 2) SS BOND : angle 1.50851 ( 4) covalent geometry : bond 0.00332 ( 7949) covalent geometry : angle 0.58294 (10805) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.877 Fit side-chains REVERT: A 252 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8300 (m) REVERT: A 266 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8409 (tp) REVERT: A 296 TYR cc_start: 0.7646 (t80) cc_final: 0.7328 (t80) REVERT: A 340 THR cc_start: 0.8313 (t) cc_final: 0.8059 (m) REVERT: B 13 GLN cc_start: 0.7710 (tm-30) cc_final: 0.7356 (tm-30) REVERT: B 46 ARG cc_start: 0.8155 (mmt-90) cc_final: 0.7925 (mtt-85) REVERT: B 258 ASP cc_start: 0.7861 (t0) cc_final: 0.7495 (t0) REVERT: R 63 ILE cc_start: 0.8869 (mm) cc_final: 0.8029 (mt) REVERT: R 67 ASN cc_start: 0.8316 (m-40) cc_final: 0.7599 (m110) REVERT: R 81 ILE cc_start: 0.8123 (tt) cc_final: 0.7708 (pt) REVERT: R 155 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6766 (tp) REVERT: R 223 LEU cc_start: 0.8323 (tp) cc_final: 0.8115 (tp) REVERT: R 258 ILE cc_start: 0.8350 (tt) cc_final: 0.8118 (tp) REVERT: S 59 TYR cc_start: 0.8403 (m-80) cc_final: 0.8123 (m-80) outliers start: 29 outliers final: 20 residues processed: 189 average time/residue: 1.0324 time to fit residues: 208.2343 Evaluate side-chains 191 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 132 CYS Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 183 SER Chi-restraints excluded: chain S residue 203 SER Chi-restraints excluded: chain S residue 218 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 80 optimal weight: 0.0970 chunk 41 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 54 HIS B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.113012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.097501 restraints weight = 12012.076| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.05 r_work: 0.3168 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7951 Z= 0.157 Angle : 0.593 8.665 10809 Z= 0.307 Chirality : 0.043 0.145 1268 Planarity : 0.004 0.050 1364 Dihedral : 4.052 15.608 1126 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.81 % Allowed : 28.74 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.26), residues: 1036 helix: 0.44 (0.30), residues: 324 sheet: 0.73 (0.31), residues: 288 loop : -1.30 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 47 HIS 0.004 0.001 HIS B 91 PHE 0.030 0.002 PHE R 225 TYR 0.016 0.002 TYR B 111 ARG 0.009 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 336) hydrogen bonds : angle 4.46795 ( 954) SS BOND : bond 0.00905 ( 2) SS BOND : angle 1.59241 ( 4) covalent geometry : bond 0.00370 ( 7949) covalent geometry : angle 0.59197 (10805) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.848 Fit side-chains REVERT: A 252 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8302 (m) REVERT: A 266 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8411 (tp) REVERT: A 296 TYR cc_start: 0.7627 (t80) cc_final: 0.7281 (t80) REVERT: A 340 THR cc_start: 0.8327 (t) cc_final: 0.8098 (m) REVERT: B 13 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7333 (tm-30) REVERT: B 46 ARG cc_start: 0.8159 (mmt-90) cc_final: 0.7931 (mtt-85) REVERT: B 258 ASP cc_start: 0.7889 (t0) cc_final: 0.7522 (t0) REVERT: R 63 ILE cc_start: 0.8876 (mm) cc_final: 0.8045 (mt) REVERT: R 67 ASN cc_start: 0.8328 (m-40) cc_final: 0.7608 (m110) REVERT: R 81 ILE cc_start: 0.8161 (tt) cc_final: 0.7721 (pt) REVERT: R 155 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.6790 (tp) REVERT: R 223 LEU cc_start: 0.8326 (tp) cc_final: 0.8123 (tp) REVERT: R 258 ILE cc_start: 0.8349 (tt) cc_final: 0.8095 (tp) REVERT: S 59 TYR cc_start: 0.8412 (m-80) cc_final: 0.8127 (m-80) outliers start: 29 outliers final: 21 residues processed: 187 average time/residue: 1.0076 time to fit residues: 200.7282 Evaluate side-chains 194 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 132 CYS Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 183 SER Chi-restraints excluded: chain S residue 203 SER Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 49 optimal weight: 0.0020 chunk 76 optimal weight: 0.5980 chunk 82 optimal weight: 0.0470 overall best weight: 0.3686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 54 HIS B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.114490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.099014 restraints weight = 11787.725| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.02 r_work: 0.3200 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7951 Z= 0.110 Angle : 0.561 9.164 10809 Z= 0.288 Chirality : 0.041 0.148 1268 Planarity : 0.004 0.049 1364 Dihedral : 3.830 15.342 1126 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.02 % Allowed : 30.18 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.26), residues: 1036 helix: 0.68 (0.31), residues: 321 sheet: 0.77 (0.31), residues: 293 loop : -1.18 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.030 0.001 PHE R 225 TYR 0.014 0.001 TYR B 111 ARG 0.009 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 336) hydrogen bonds : angle 4.32712 ( 954) SS BOND : bond 0.00717 ( 2) SS BOND : angle 1.34194 ( 4) covalent geometry : bond 0.00248 ( 7949) covalent geometry : angle 0.56023 (10805) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.874 Fit side-chains REVERT: A 252 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8293 (m) REVERT: A 266 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8378 (tp) REVERT: A 298 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7480 (mm-30) REVERT: A 340 THR cc_start: 0.8327 (t) cc_final: 0.8088 (m) REVERT: B 13 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7385 (tm-30) REVERT: B 46 ARG cc_start: 0.8160 (mmt-90) cc_final: 0.7936 (mtt-85) REVERT: R 63 ILE cc_start: 0.8833 (mm) cc_final: 0.7992 (mt) REVERT: R 67 ASN cc_start: 0.8321 (m-40) cc_final: 0.7593 (m110) REVERT: R 81 ILE cc_start: 0.8111 (tt) cc_final: 0.7691 (pt) REVERT: R 145 LEU cc_start: 0.8298 (tp) cc_final: 0.8003 (tt) REVERT: R 155 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6755 (tp) REVERT: R 223 LEU cc_start: 0.8332 (tp) cc_final: 0.8123 (tp) REVERT: R 258 ILE cc_start: 0.8300 (tt) cc_final: 0.8067 (tp) REVERT: S 59 TYR cc_start: 0.8381 (m-80) cc_final: 0.8026 (m-80) outliers start: 23 outliers final: 17 residues processed: 183 average time/residue: 1.0678 time to fit residues: 207.8292 Evaluate side-chains 187 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 132 CYS Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 183 SER Chi-restraints excluded: chain S residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 0.0270 chunk 74 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.113481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098054 restraints weight = 11874.649| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.03 r_work: 0.3187 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7951 Z= 0.137 Angle : 0.579 8.805 10809 Z= 0.298 Chirality : 0.042 0.144 1268 Planarity : 0.004 0.049 1364 Dihedral : 3.884 15.453 1126 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.02 % Allowed : 30.58 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.26), residues: 1036 helix: 0.69 (0.31), residues: 321 sheet: 0.76 (0.30), residues: 293 loop : -1.18 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.021 0.001 PHE R 104 TYR 0.016 0.001 TYR B 111 ARG 0.008 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 336) hydrogen bonds : angle 4.36748 ( 954) SS BOND : bond 0.00854 ( 2) SS BOND : angle 1.61598 ( 4) covalent geometry : bond 0.00320 ( 7949) covalent geometry : angle 0.57855 (10805) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6550.73 seconds wall clock time: 113 minutes 7.94 seconds (6787.94 seconds total)