Starting phenix.real_space_refine on Wed Sep 17 13:13:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iv6_60920/09_2025/9iv6_60920.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iv6_60920/09_2025/9iv6_60920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iv6_60920/09_2025/9iv6_60920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iv6_60920/09_2025/9iv6_60920.map" model { file = "/net/cci-nas-00/data/ceres_data/9iv6_60920/09_2025/9iv6_60920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iv6_60920/09_2025/9iv6_60920.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 52 5.16 5 C 5494 2.51 5 N 1485 2.21 5 O 1563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8594 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2279 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 284} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 7, 'GLN:plan1': 1, 'GLU:plan': 5, 'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "A" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1849 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 85 Chain: "B" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2447 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 7, 'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "G" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 321 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "S" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1698 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 49 Time building chain proxies: 2.47, per 1000 atoms: 0.29 Number of scatterers: 8594 At special positions: 0 Unit cell: (86.32, 123.67, 129.48, 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 52 16.00 O 1563 8.00 N 1485 7.00 C 5494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.05 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: 0.62 Conformation dependent library (CDL) restraints added in 472.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 15 sheets defined 36.2% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'R' and resid 19 through 47 removed outlier: 3.696A pdb=" N GLY R 29 " --> pdb=" O ILE R 25 " (cutoff:3.500A) Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 52 through 78 removed outlier: 3.699A pdb=" N TYR R 66 " --> pdb=" O ALA R 62 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 88 through 120 removed outlier: 3.918A pdb=" N LEU R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE R 97 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR R 98 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR R 99 " --> pdb=" O PHE R 95 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN R 100 " --> pdb=" O ILE R 96 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ILE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA R 106 " --> pdb=" O TYR R 102 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS R 109 " --> pdb=" O ILE R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 129 removed outlier: 3.557A pdb=" N ARG R 129 " --> pdb=" O ALA R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 149 Processing helix chain 'R' and resid 150 through 154 Processing helix chain 'R' and resid 177 through 188 removed outlier: 3.811A pdb=" N MET R 181 " --> pdb=" O TRP R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 211 removed outlier: 3.606A pdb=" N SER R 211 " --> pdb=" O ALA R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 254 removed outlier: 3.704A pdb=" N LEU R 229 " --> pdb=" O LEU R 225 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 258 through 275 removed outlier: 4.239A pdb=" N GLU R 262 " --> pdb=" O CYS R 258 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG R 263 " --> pdb=" O GLY R 259 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N SER R 266 " --> pdb=" O GLU R 262 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ALA R 267 " --> pdb=" O ARG R 263 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR R 275 " --> pdb=" O SER R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 287 removed outlier: 4.147A pdb=" N CYS R 279 " --> pdb=" O THR R 275 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.509A pdb=" N CYS R 287 " --> pdb=" O PRO R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 304 Processing helix chain 'A' and resid 6 through 39 removed outlier: 3.900A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.653A pdb=" N GLN A 246 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.596A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.831A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.941A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.929A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.520A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.884A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.773A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'R' and resid 158 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 217 through 218 removed outlier: 3.923A pdb=" N ASP A 233 " --> pdb=" O PHE A 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 218 removed outlier: 3.923A pdb=" N ASP A 233 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N VAL A 234 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N GLY A 47 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N ALA A 253 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARG A 42 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE A 255 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 44 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL A 257 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU A 46 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N ASP A 259 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE A 254 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N PHE A 290 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE A 256 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN A 292 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 258 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.784A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.819A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.692A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.796A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.790A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.711A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.299A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.302A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.302A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.585A pdb=" N ASN S 194 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL S 226 " --> pdb=" O GLN S 179 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1173 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: 1.38 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1369 1.30 - 1.43: 2480 1.43 - 1.56: 4877 1.56 - 1.69: 1 1.69 - 1.82: 72 Bond restraints: 8799 Sorted by residual: bond pdb=" C LEU S 4 " pdb=" O LEU S 4 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.14e-02 7.69e+03 3.98e+01 bond pdb=" C GLN A 35 " pdb=" O GLN A 35 " ideal model delta sigma weight residual 1.237 1.170 0.067 1.17e-02 7.31e+03 3.23e+01 bond pdb=" C ARG R 224 " pdb=" O ARG R 224 " ideal model delta sigma weight residual 1.236 1.165 0.071 1.26e-02 6.30e+03 3.17e+01 bond pdb=" C ARG A 356 " pdb=" O ARG A 356 " ideal model delta sigma weight residual 1.236 1.168 0.068 1.28e-02 6.10e+03 2.78e+01 bond pdb=" CA ARG R 224 " pdb=" C ARG R 224 " ideal model delta sigma weight residual 1.523 1.454 0.068 1.35e-02 5.49e+03 2.57e+01 ... (remaining 8794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11551 1.92 - 3.85: 364 3.85 - 5.77: 68 5.77 - 7.70: 11 7.70 - 9.62: 8 Bond angle restraints: 12002 Sorted by residual: angle pdb=" N GLY S 9 " pdb=" CA GLY S 9 " pdb=" C GLY S 9 " ideal model delta sigma weight residual 112.48 121.35 -8.87 1.21e+00 6.83e-01 5.38e+01 angle pdb=" CA PRO R 283 " pdb=" N PRO R 283 " pdb=" CD PRO R 283 " ideal model delta sigma weight residual 112.00 102.38 9.62 1.40e+00 5.10e-01 4.72e+01 angle pdb=" N GLN S 13 " pdb=" CA GLN S 13 " pdb=" C GLN S 13 " ideal model delta sigma weight residual 110.08 118.08 -8.00 1.38e+00 5.25e-01 3.36e+01 angle pdb=" N SER S 7 " pdb=" CA SER S 7 " pdb=" C SER S 7 " ideal model delta sigma weight residual 109.07 116.90 -7.83 1.52e+00 4.33e-01 2.66e+01 angle pdb=" N ASN R 82 " pdb=" CA ASN R 82 " pdb=" CB ASN R 82 " ideal model delta sigma weight residual 111.13 102.39 8.74 1.81e+00 3.05e-01 2.33e+01 ... (remaining 11997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 4650 17.40 - 34.80: 372 34.80 - 52.20: 66 52.20 - 69.60: 11 69.60 - 87.01: 9 Dihedral angle restraints: 5108 sinusoidal: 1764 harmonic: 3344 Sorted by residual: dihedral pdb=" CB CYS R 90 " pdb=" SG CYS R 90 " pdb=" SG CYS R 168 " pdb=" CB CYS R 168 " ideal model delta sinusoidal sigma weight residual -86.00 -154.48 68.48 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" CA GLY S 182 " pdb=" C GLY S 182 " pdb=" N GLN S 183 " pdb=" CA GLN S 183 " ideal model delta harmonic sigma weight residual 180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.34 21.66 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 5105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1068 0.066 - 0.132: 279 0.132 - 0.199: 21 0.199 - 0.265: 7 0.265 - 0.331: 3 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CA HIS R 80 " pdb=" N HIS R 80 " pdb=" C HIS R 80 " pdb=" CB HIS R 80 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA GLN A 29 " pdb=" N GLN A 29 " pdb=" C GLN A 29 " pdb=" CB GLN A 29 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA HIS R 17 " pdb=" N HIS R 17 " pdb=" C HIS R 17 " pdb=" CB HIS R 17 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1375 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 19 " -0.096 5.00e-02 4.00e+02 1.43e-01 3.27e+01 pdb=" N PRO R 20 " 0.247 5.00e-02 4.00e+02 pdb=" CA PRO R 20 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO R 20 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 282 " 0.083 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO R 283 " -0.208 5.00e-02 4.00e+02 pdb=" CA PRO R 283 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO R 283 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 70 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.68e+01 pdb=" N PRO R 71 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO R 71 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO R 71 " 0.056 5.00e-02 4.00e+02 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 101 2.64 - 3.20: 7516 3.20 - 3.77: 12234 3.77 - 4.33: 16306 4.33 - 4.90: 28537 Nonbonded interactions: 64694 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.074 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.083 3.040 nonbonded pdb=" O ARG A 283 " pdb=" OG1 THR A 284 " model vdw 2.156 3.040 nonbonded pdb=" OD1 ASN A 292 " pdb=" N LYS A 293 " model vdw 2.212 3.120 nonbonded pdb=" OD2 ASP A 331 " pdb=" NE ARG A 333 " model vdw 2.269 3.120 ... (remaining 64689 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: 2.740 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.140 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.011 0.090 8801 Z= 0.512 Angle : 0.866 9.619 12006 Z= 0.510 Chirality : 0.058 0.331 1378 Planarity : 0.008 0.143 1530 Dihedral : 13.500 87.005 2948 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.59 % Allowed : 1.65 % Favored : 97.76 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.24), residues: 1137 helix: 1.32 (0.27), residues: 378 sheet: -0.38 (0.30), residues: 274 loop : -1.89 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 191 TYR 0.045 0.003 TYR B 59 PHE 0.021 0.003 PHE B 235 TRP 0.016 0.002 TRP B 63 HIS 0.016 0.003 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.01059 ( 8799) covalent geometry : angle 0.86505 (12002) SS BOND : bond 0.01163 ( 2) SS BOND : angle 2.58471 ( 4) hydrogen bonds : bond 0.21464 ( 399) hydrogen bonds : angle 6.88484 ( 1173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 190 time to evaluate : 0.328 Fit side-chains REVERT: R 149 ASN cc_start: 0.8747 (m110) cc_final: 0.8540 (m110) REVERT: R 181 MET cc_start: 0.6620 (tpp) cc_final: 0.6379 (tpp) REVERT: A 35 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7593 (mp-120) REVERT: B 239 ASN cc_start: 0.8185 (m110) cc_final: 0.7840 (m110) REVERT: S 180 ARG cc_start: 0.8568 (mtt90) cc_final: 0.8334 (mtt90) outliers start: 5 outliers final: 1 residues processed: 191 average time/residue: 0.5413 time to fit residues: 110.2290 Evaluate side-chains 164 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain S residue 12 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.0270 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.1980 chunk 106 optimal weight: 0.2980 overall best weight: 0.2838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 17 HIS R 79 HIS A 223 GLN A 249 ASN A 292 ASN B 110 ASN B 237 ASN S 142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.120558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.106045 restraints weight = 12952.606| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.78 r_work: 0.3341 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8801 Z= 0.117 Angle : 0.555 6.616 12006 Z= 0.302 Chirality : 0.043 0.196 1378 Planarity : 0.005 0.079 1530 Dihedral : 5.181 60.312 1247 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.00 % Allowed : 10.82 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.25), residues: 1137 helix: 1.80 (0.27), residues: 387 sheet: 0.09 (0.30), residues: 286 loop : -1.71 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 347 TYR 0.013 0.001 TYR R 66 PHE 0.016 0.001 PHE A 222 TRP 0.013 0.001 TRP B 297 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8799) covalent geometry : angle 0.55494 (12002) SS BOND : bond 0.00591 ( 2) SS BOND : angle 1.27986 ( 4) hydrogen bonds : bond 0.04921 ( 399) hydrogen bonds : angle 4.48837 ( 1173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.330 Fit side-chains REVERT: R 181 MET cc_start: 0.7718 (tpp) cc_final: 0.7448 (tpp) REVERT: B 237 ASN cc_start: 0.7744 (t0) cc_final: 0.7369 (t0) REVERT: B 239 ASN cc_start: 0.8449 (m110) cc_final: 0.8067 (m110) REVERT: B 258 ASP cc_start: 0.7625 (t0) cc_final: 0.7359 (t0) outliers start: 17 outliers final: 7 residues processed: 180 average time/residue: 0.5655 time to fit residues: 108.1830 Evaluate side-chains 167 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 158 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 1.9990 chunk 112 optimal weight: 0.0570 chunk 42 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 0.0030 chunk 66 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 102 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 overall best weight: 0.4508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.119025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.104300 restraints weight = 12798.467| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.82 r_work: 0.3323 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8801 Z= 0.119 Angle : 0.530 6.373 12006 Z= 0.286 Chirality : 0.042 0.180 1378 Planarity : 0.005 0.056 1530 Dihedral : 4.804 57.914 1247 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.35 % Allowed : 13.41 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.25), residues: 1137 helix: 2.12 (0.27), residues: 391 sheet: 0.24 (0.30), residues: 282 loop : -1.49 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 124 TYR 0.012 0.001 TYR B 59 PHE 0.014 0.001 PHE A 222 TRP 0.012 0.001 TRP A 244 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8799) covalent geometry : angle 0.52962 (12002) SS BOND : bond 0.00599 ( 2) SS BOND : angle 1.06427 ( 4) hydrogen bonds : bond 0.04744 ( 399) hydrogen bonds : angle 4.09260 ( 1173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.317 Fit side-chains REVERT: R 181 MET cc_start: 0.7863 (tpp) cc_final: 0.7584 (tpp) REVERT: R 202 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7931 (ttt-90) REVERT: B 237 ASN cc_start: 0.7715 (t0) cc_final: 0.7460 (t0) REVERT: B 239 ASN cc_start: 0.8475 (m110) cc_final: 0.8240 (m110) REVERT: B 258 ASP cc_start: 0.7793 (t0) cc_final: 0.7447 (t0) REVERT: B 340 ASN cc_start: 0.7978 (t0) cc_final: 0.7736 (t0) REVERT: S 6 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: S 21 SER cc_start: 0.8392 (p) cc_final: 0.8190 (m) REVERT: S 84 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8341 (p) outliers start: 20 outliers final: 12 residues processed: 181 average time/residue: 0.5819 time to fit residues: 111.8564 Evaluate side-chains 175 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 108 optimal weight: 0.0980 chunk 17 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 48 optimal weight: 0.0370 chunk 36 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 390 GLN B 176 GLN B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.104362 restraints weight = 13000.370| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.80 r_work: 0.3317 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8801 Z= 0.120 Angle : 0.522 6.507 12006 Z= 0.281 Chirality : 0.042 0.173 1378 Planarity : 0.004 0.052 1530 Dihedral : 4.658 57.341 1246 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.41 % Allowed : 14.00 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.25), residues: 1137 helix: 2.25 (0.27), residues: 392 sheet: 0.24 (0.30), residues: 294 loop : -1.34 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 124 TYR 0.012 0.001 TYR R 268 PHE 0.014 0.001 PHE A 222 TRP 0.011 0.001 TRP A 244 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8799) covalent geometry : angle 0.52203 (12002) SS BOND : bond 0.00580 ( 2) SS BOND : angle 1.06685 ( 4) hydrogen bonds : bond 0.04659 ( 399) hydrogen bonds : angle 3.95208 ( 1173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.312 Fit side-chains REVERT: R 181 MET cc_start: 0.7908 (tpp) cc_final: 0.7676 (tpp) REVERT: R 202 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7943 (ttt-90) REVERT: B 96 ARG cc_start: 0.8084 (ptp90) cc_final: 0.7769 (mtt180) REVERT: B 237 ASN cc_start: 0.7761 (t0) cc_final: 0.7487 (t0) REVERT: B 239 ASN cc_start: 0.8478 (m110) cc_final: 0.8238 (m110) REVERT: B 258 ASP cc_start: 0.7898 (t0) cc_final: 0.7476 (t0) REVERT: S 91 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8490 (p) outliers start: 29 outliers final: 13 residues processed: 172 average time/residue: 0.5768 time to fit residues: 105.5277 Evaluate side-chains 171 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 145 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 45 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 89 optimal weight: 0.0970 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 390 GLN B 155 ASN B 176 GLN B 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.117205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102504 restraints weight = 13176.720| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.87 r_work: 0.3295 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8801 Z= 0.125 Angle : 0.522 6.110 12006 Z= 0.280 Chirality : 0.042 0.141 1378 Planarity : 0.004 0.051 1530 Dihedral : 4.606 57.250 1246 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.41 % Allowed : 14.71 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.25), residues: 1137 helix: 2.30 (0.27), residues: 395 sheet: 0.42 (0.31), residues: 280 loop : -1.29 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.012 0.001 TYR R 268 PHE 0.014 0.001 PHE A 222 TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8799) covalent geometry : angle 0.52159 (12002) SS BOND : bond 0.00615 ( 2) SS BOND : angle 1.15500 ( 4) hydrogen bonds : bond 0.04743 ( 399) hydrogen bonds : angle 3.90814 ( 1173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: R 181 MET cc_start: 0.7913 (tpp) cc_final: 0.7688 (tpp) REVERT: R 202 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7886 (ttt-90) REVERT: A 350 THR cc_start: 0.8175 (t) cc_final: 0.7781 (p) REVERT: B 96 ARG cc_start: 0.8062 (ptp90) cc_final: 0.7765 (mtt180) REVERT: B 237 ASN cc_start: 0.7804 (t0) cc_final: 0.7542 (t0) REVERT: B 239 ASN cc_start: 0.8456 (m110) cc_final: 0.8222 (m110) REVERT: B 258 ASP cc_start: 0.7928 (t0) cc_final: 0.7446 (t0) REVERT: S 6 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: S 91 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8493 (p) outliers start: 29 outliers final: 17 residues processed: 169 average time/residue: 0.6093 time to fit residues: 109.4162 Evaluate side-chains 176 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 206 ARG Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 145 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 0.0770 chunk 38 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 176 GLN B 220 GLN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.116383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101680 restraints weight = 13236.331| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.87 r_work: 0.3281 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8801 Z= 0.136 Angle : 0.533 6.156 12006 Z= 0.286 Chirality : 0.042 0.133 1378 Planarity : 0.004 0.050 1530 Dihedral : 4.645 57.347 1246 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.41 % Allowed : 15.18 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.25), residues: 1137 helix: 2.33 (0.27), residues: 395 sheet: 0.44 (0.31), residues: 274 loop : -1.22 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 124 TYR 0.014 0.001 TYR R 66 PHE 0.016 0.001 PHE B 151 TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8799) covalent geometry : angle 0.53223 (12002) SS BOND : bond 0.00648 ( 2) SS BOND : angle 1.09540 ( 4) hydrogen bonds : bond 0.05052 ( 399) hydrogen bonds : angle 3.92522 ( 1173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.324 Fit side-chains REVERT: R 181 MET cc_start: 0.7961 (tpp) cc_final: 0.7740 (tpp) REVERT: R 202 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7898 (ttt-90) REVERT: A 350 THR cc_start: 0.8214 (t) cc_final: 0.7813 (p) REVERT: B 96 ARG cc_start: 0.8093 (ptp90) cc_final: 0.7825 (mtt180) REVERT: B 237 ASN cc_start: 0.7814 (t0) cc_final: 0.7569 (t0) REVERT: B 239 ASN cc_start: 0.8481 (m110) cc_final: 0.8243 (m110) REVERT: B 258 ASP cc_start: 0.7910 (t0) cc_final: 0.7473 (t0) REVERT: B 262 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7883 (mtp) REVERT: S 91 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8502 (p) outliers start: 29 outliers final: 17 residues processed: 182 average time/residue: 0.5864 time to fit residues: 113.5383 Evaluate side-chains 184 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 145 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 106 optimal weight: 0.0570 chunk 73 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 176 GLN B 220 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.117286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.102586 restraints weight = 13315.324| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.90 r_work: 0.3295 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8801 Z= 0.119 Angle : 0.516 6.194 12006 Z= 0.275 Chirality : 0.041 0.129 1378 Planarity : 0.004 0.049 1530 Dihedral : 4.531 58.339 1246 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.18 % Allowed : 16.12 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.25), residues: 1137 helix: 2.36 (0.27), residues: 397 sheet: 0.52 (0.31), residues: 280 loop : -1.17 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.014 0.001 TYR R 163 PHE 0.015 0.001 PHE R 19 TRP 0.012 0.001 TRP A 244 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8799) covalent geometry : angle 0.51558 (12002) SS BOND : bond 0.00635 ( 2) SS BOND : angle 1.16288 ( 4) hydrogen bonds : bond 0.04539 ( 399) hydrogen bonds : angle 3.84484 ( 1173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: R 181 MET cc_start: 0.8003 (tpp) cc_final: 0.7763 (tpp) REVERT: R 202 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7936 (ttt-90) REVERT: A 325 THR cc_start: 0.8876 (p) cc_final: 0.8622 (t) REVERT: B 96 ARG cc_start: 0.8111 (ptp90) cc_final: 0.7832 (mtt180) REVERT: B 237 ASN cc_start: 0.7826 (t0) cc_final: 0.7595 (t0) REVERT: B 239 ASN cc_start: 0.8476 (m110) cc_final: 0.8219 (m110) REVERT: B 258 ASP cc_start: 0.7916 (t0) cc_final: 0.7457 (t0) REVERT: B 262 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7748 (mtp) REVERT: B 327 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8376 (t) REVERT: S 91 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8477 (p) REVERT: S 140 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.7691 (mtm) outliers start: 27 outliers final: 17 residues processed: 177 average time/residue: 0.6013 time to fit residues: 113.1760 Evaluate side-chains 182 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 206 ARG Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 145 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 176 GLN B 220 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.114412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.099848 restraints weight = 13225.807| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.85 r_work: 0.3252 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8801 Z= 0.189 Angle : 0.584 7.010 12006 Z= 0.312 Chirality : 0.044 0.135 1378 Planarity : 0.005 0.049 1530 Dihedral : 4.867 61.438 1246 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.41 % Allowed : 17.06 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.25), residues: 1137 helix: 2.28 (0.27), residues: 391 sheet: 0.53 (0.31), residues: 277 loop : -1.22 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 18 TYR 0.018 0.002 TYR R 66 PHE 0.021 0.002 PHE B 151 TRP 0.015 0.002 TRP B 82 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 8799) covalent geometry : angle 0.58371 (12002) SS BOND : bond 0.00809 ( 2) SS BOND : angle 1.17546 ( 4) hydrogen bonds : bond 0.06014 ( 399) hydrogen bonds : angle 4.10986 ( 1173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.326 Fit side-chains REVERT: R 181 MET cc_start: 0.8037 (tpp) cc_final: 0.7778 (tpp) REVERT: R 202 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7890 (ttt-90) REVERT: A 350 THR cc_start: 0.8261 (t) cc_final: 0.7938 (p) REVERT: B 59 TYR cc_start: 0.8328 (m-80) cc_final: 0.7969 (m-80) REVERT: B 96 ARG cc_start: 0.8123 (ptp90) cc_final: 0.7872 (mtt180) REVERT: B 237 ASN cc_start: 0.7829 (t0) cc_final: 0.7540 (t0) REVERT: B 239 ASN cc_start: 0.8476 (m110) cc_final: 0.8215 (m110) REVERT: B 258 ASP cc_start: 0.7964 (t0) cc_final: 0.7463 (t0) REVERT: B 327 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8424 (t) REVERT: S 140 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.7711 (mtm) outliers start: 29 outliers final: 14 residues processed: 178 average time/residue: 0.6060 time to fit residues: 114.5486 Evaluate side-chains 180 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 145 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 390 GLN B 220 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.115766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.101118 restraints weight = 13193.656| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.87 r_work: 0.3272 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8801 Z= 0.145 Angle : 0.550 6.824 12006 Z= 0.294 Chirality : 0.042 0.130 1378 Planarity : 0.004 0.051 1530 Dihedral : 4.768 63.513 1246 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.59 % Allowed : 18.00 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.25), residues: 1137 helix: 2.24 (0.27), residues: 397 sheet: 0.51 (0.31), residues: 284 loop : -1.20 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 202 TYR 0.015 0.002 TYR R 66 PHE 0.026 0.002 PHE R 19 TRP 0.013 0.001 TRP A 244 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8799) covalent geometry : angle 0.54995 (12002) SS BOND : bond 0.00700 ( 2) SS BOND : angle 1.13176 ( 4) hydrogen bonds : bond 0.05207 ( 399) hydrogen bonds : angle 3.98764 ( 1173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.369 Fit side-chains REVERT: R 181 MET cc_start: 0.8039 (tpp) cc_final: 0.7797 (tpp) REVERT: R 202 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7955 (ttt-90) REVERT: A 350 THR cc_start: 0.8237 (t) cc_final: 0.7871 (p) REVERT: B 59 TYR cc_start: 0.8348 (m-80) cc_final: 0.7992 (m-80) REVERT: B 237 ASN cc_start: 0.7831 (t0) cc_final: 0.7591 (t0) REVERT: B 239 ASN cc_start: 0.8491 (m110) cc_final: 0.8226 (m110) REVERT: B 258 ASP cc_start: 0.7909 (t0) cc_final: 0.7392 (t0) REVERT: B 262 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7728 (mtp) REVERT: B 327 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8364 (t) REVERT: S 140 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.7700 (mtm) outliers start: 22 outliers final: 14 residues processed: 170 average time/residue: 0.6354 time to fit residues: 114.4402 Evaluate side-chains 179 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 74 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 46 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 220 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.116188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.101585 restraints weight = 13186.747| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.86 r_work: 0.3283 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8801 Z= 0.132 Angle : 0.543 7.111 12006 Z= 0.289 Chirality : 0.042 0.130 1378 Planarity : 0.004 0.049 1530 Dihedral : 4.201 17.146 1243 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.47 % Allowed : 18.24 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.26), residues: 1137 helix: 2.27 (0.27), residues: 397 sheet: 0.53 (0.31), residues: 284 loop : -1.18 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 18 TYR 0.015 0.001 TYR R 163 PHE 0.031 0.002 PHE R 19 TRP 0.013 0.001 TRP A 244 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8799) covalent geometry : angle 0.54257 (12002) SS BOND : bond 0.00662 ( 2) SS BOND : angle 1.09018 ( 4) hydrogen bonds : bond 0.04966 ( 399) hydrogen bonds : angle 3.92977 ( 1173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.362 Fit side-chains REVERT: R 181 MET cc_start: 0.8008 (tpp) cc_final: 0.7761 (tpp) REVERT: R 202 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7933 (ttt-90) REVERT: A 350 THR cc_start: 0.8195 (t) cc_final: 0.7819 (p) REVERT: B 59 TYR cc_start: 0.8353 (m-80) cc_final: 0.7999 (m-80) REVERT: B 237 ASN cc_start: 0.7816 (t0) cc_final: 0.7569 (t0) REVERT: B 239 ASN cc_start: 0.8488 (m110) cc_final: 0.8212 (m110) REVERT: B 258 ASP cc_start: 0.7899 (t0) cc_final: 0.7383 (t0) REVERT: B 262 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7769 (mtp) REVERT: B 327 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8320 (t) REVERT: S 6 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7663 (pt0) REVERT: S 140 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.7667 (mtm) outliers start: 21 outliers final: 13 residues processed: 168 average time/residue: 0.6107 time to fit residues: 108.8778 Evaluate side-chains 179 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 266 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 105 optimal weight: 0.4980 chunk 112 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 0.0670 chunk 96 optimal weight: 3.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 220 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.118725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.103969 restraints weight = 13219.778| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.89 r_work: 0.3319 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8801 Z= 0.106 Angle : 0.511 7.173 12006 Z= 0.271 Chirality : 0.041 0.127 1378 Planarity : 0.004 0.051 1530 Dihedral : 3.940 16.535 1243 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.24 % Allowed : 18.59 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.26), residues: 1137 helix: 2.46 (0.27), residues: 392 sheet: 0.63 (0.31), residues: 285 loop : -1.14 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 18 TYR 0.015 0.001 TYR R 163 PHE 0.013 0.001 PHE S 68 TRP 0.014 0.001 TRP A 244 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8799) covalent geometry : angle 0.51089 (12002) SS BOND : bond 0.00517 ( 2) SS BOND : angle 1.05254 ( 4) hydrogen bonds : bond 0.04054 ( 399) hydrogen bonds : angle 3.75954 ( 1173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3993.76 seconds wall clock time: 68 minutes 34.96 seconds (4114.96 seconds total)