Starting phenix.real_space_refine on Fri Aug 22 20:00:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gcm_29935/08_2025/8gcm_29935_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gcm_29935/08_2025/8gcm_29935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gcm_29935/08_2025/8gcm_29935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gcm_29935/08_2025/8gcm_29935.map" model { file = "/net/cci-nas-00/data/ceres_data/8gcm_29935/08_2025/8gcm_29935_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gcm_29935/08_2025/8gcm_29935_neut.cif" } resolution = 3.5 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= -0.002 sd= 0.060 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: 5 Type Number sf(0) Gaussians S 53 5.16 5 C 4769 2.51 5 N 1295 2.21 5 O 1389 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7508 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1430 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'TRANS': 197} Chain breaks: 5 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE%COO:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "B" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2384 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 16, 'GLN:plan1': 4, 'ARG:plan': 10, 'GLU:plan': 6, 'ASN:plan1': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 156 Chain: "C" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 352 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "E" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1672 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 56 Chain: "R" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1640 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 10, 'TRANS': 243} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 321 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'PHE:plan': 6, 'ASN:plan1': 5, 'ARG:plan': 9, 'GLU:plan': 5, 'TYR:plan': 5, 'ASP:plan': 3, 'GLN:plan1': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 193 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'YX9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.23, per 1000 atoms: 0.30 Number of scatterers: 7508 At special positions: 0 Unit cell: (89.79, 119.355, 127.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 F 2 9.00 O 1389 8.00 N 1295 7.00 C 4769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 92 " - pdb=" SG CYS R 170 " 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: 0.68 Conformation dependent library (CDL) restraints added in 483.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 33.4% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 6 through 29 removed outlier: 4.622A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 removed outlier: 3.767A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.128A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 212' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.688A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.567A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.610A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.644A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.896A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 31 through 42 removed outlier: 4.177A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 removed outlier: 3.616A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.656A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.630A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'R' and resid 24 through 45 removed outlier: 4.066A pdb=" N PHE R 28 " --> pdb=" O PRO R 24 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE R 29 " --> pdb=" O ALA R 25 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY R 31 " --> pdb=" O MET R 27 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL R 32 " --> pdb=" O PHE R 28 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL R 33 " --> pdb=" O ILE R 29 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 50 Processing helix chain 'R' and resid 54 through 72 removed outlier: 3.601A pdb=" N LEU R 70 " --> pdb=" O LEU R 66 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL R 72 " --> pdb=" O GLY R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 77 removed outlier: 3.967A pdb=" N THR R 76 " --> pdb=" O SER R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 106 removed outlier: 3.506A pdb=" N LEU R 99 " --> pdb=" O SER R 95 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU R 100 " --> pdb=" O THR R 96 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 114 Processing helix chain 'R' and resid 115 through 120 Processing helix chain 'R' and resid 123 through 130 Processing helix chain 'R' and resid 134 through 156 removed outlier: 4.066A pdb=" N LEU R 138 " --> pdb=" O ARG R 134 " (cutoff:3.500A) Proline residue: R 154 - end of helix Processing helix chain 'R' and resid 184 through 219 removed outlier: 3.881A pdb=" N CYS R 207 " --> pdb=" O ASN R 203 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU R 211 " --> pdb=" O CYS R 207 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET R 218 " --> pdb=" O HIS R 214 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG R 219 " --> pdb=" O ARG R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 284 removed outlier: 3.639A pdb=" N VAL R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE R 272 " --> pdb=" O ILE R 268 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU R 273 " --> pdb=" O GLN R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 298 removed outlier: 4.112A pdb=" N VAL R 289 " --> pdb=" O SER R 285 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN R 295 " --> pdb=" O ARG R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 319 removed outlier: 3.564A pdb=" N SER R 319 " --> pdb=" O ILE R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 325 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.918A pdb=" N ASP A 200 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 221 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.918A pdb=" N ASP A 200 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.017A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.005A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.687A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.607A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 191 removed outlier: 3.801A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.708A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278 removed outlier: 4.050A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 6 through 7 removed outlier: 3.723A pdb=" N SER E 7 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.820A pdb=" N GLU E 46 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 49 through 50 removed outlier: 3.920A pdb=" N TYR E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 141 through 142 removed outlier: 3.660A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER E 204 " --> pdb=" O THR E 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.772A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 852 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: 1.25 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1223 1.26 - 1.40: 1952 1.40 - 1.54: 4323 1.54 - 1.68: 73 1.68 - 1.82: 76 Bond restraints: 7647 Sorted by residual: bond pdb=" C14 YX9 R 501 " pdb=" C18 YX9 R 501 " ideal model delta sigma weight residual 1.535 1.305 0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C16 YX9 R 501 " pdb=" C17 YX9 R 501 " ideal model delta sigma weight residual 1.515 1.330 0.185 2.00e-02 2.50e+03 8.52e+01 bond pdb=" C14 YX9 R 501 " pdb=" N15 YX9 R 501 " ideal model delta sigma weight residual 1.458 1.598 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C17 YX9 R 501 " pdb=" C18 YX9 R 501 " ideal model delta sigma weight residual 1.525 1.665 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" C16 YX9 R 501 " pdb=" N15 YX9 R 501 " ideal model delta sigma weight residual 1.349 1.475 -0.126 2.00e-02 2.50e+03 3.96e+01 ... (remaining 7642 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 10161 3.44 - 6.87: 239 6.87 - 10.31: 38 10.31 - 13.74: 4 13.74 - 17.18: 1 Bond angle restraints: 10443 Sorted by residual: angle pdb=" C SER R 73 " pdb=" N PRO R 74 " pdb=" CA PRO R 74 " ideal model delta sigma weight residual 119.19 136.37 -17.18 1.06e+00 8.90e-01 2.63e+02 angle pdb=" N ILE R 29 " pdb=" CA ILE R 29 " pdb=" C ILE R 29 " ideal model delta sigma weight residual 110.72 122.06 -11.34 1.01e+00 9.80e-01 1.26e+02 angle pdb=" N MET R 27 " pdb=" CA MET R 27 " pdb=" C MET R 27 " ideal model delta sigma weight residual 111.03 120.67 -9.64 1.11e+00 8.12e-01 7.54e+01 angle pdb=" C ILE R 23 " pdb=" N PRO R 24 " pdb=" CA PRO R 24 " ideal model delta sigma weight residual 119.84 130.45 -10.61 1.25e+00 6.40e-01 7.20e+01 angle pdb=" N ALA R 25 " pdb=" CA ALA R 25 " pdb=" C ALA R 25 " ideal model delta sigma weight residual 111.28 120.23 -8.95 1.09e+00 8.42e-01 6.74e+01 ... (remaining 10438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4062 18.00 - 36.00: 304 36.00 - 54.00: 63 54.00 - 71.99: 13 71.99 - 89.99: 8 Dihedral angle restraints: 4450 sinusoidal: 1332 harmonic: 3118 Sorted by residual: dihedral pdb=" CA PHE R 97 " pdb=" C PHE R 97 " pdb=" N ILE R 98 " pdb=" CA ILE R 98 " ideal model delta harmonic sigma weight residual -180.00 -151.65 -28.35 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CB CYS R 92 " pdb=" SG CYS R 92 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 44.83 48.17 1 1.00e+01 1.00e-02 3.20e+01 dihedral pdb=" C VAL R 306 " pdb=" N VAL R 306 " pdb=" CA VAL R 306 " pdb=" CB VAL R 306 " ideal model delta harmonic sigma weight residual -122.00 -135.79 13.79 0 2.50e+00 1.60e-01 3.04e+01 ... (remaining 4447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1106 0.098 - 0.197: 122 0.197 - 0.295: 21 0.295 - 0.393: 3 0.393 - 0.492: 3 Chirality restraints: 1255 Sorted by residual: chirality pdb=" CA VAL R 306 " pdb=" N VAL R 306 " pdb=" C VAL R 306 " pdb=" CB VAL R 306 " both_signs ideal model delta sigma weight residual False 2.44 1.95 0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" CA LYS B 280 " pdb=" N LYS B 280 " pdb=" C LYS B 280 " pdb=" CB LYS B 280 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA MET R 27 " pdb=" N MET R 27 " pdb=" C MET R 27 " pdb=" CB MET R 27 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 1252 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 276 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C VAL B 276 " 0.069 2.00e-02 2.50e+03 pdb=" O VAL B 276 " -0.025 2.00e-02 2.50e+03 pdb=" N SER B 277 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 150 " 0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C PHE R 150 " -0.060 2.00e-02 2.50e+03 pdb=" O PHE R 150 " 0.022 2.00e-02 2.50e+03 pdb=" N CYS R 151 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 321 " 0.047 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO R 322 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO R 322 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 322 " 0.038 5.00e-02 4.00e+02 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1272 2.76 - 3.29: 6737 3.29 - 3.83: 11485 3.83 - 4.36: 12412 4.36 - 4.90: 22557 Nonbonded interactions: 54463 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.223 3.040 nonbonded pdb=" O GLU R 93 " pdb=" OG1 THR R 96 " model vdw 2.284 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.304 3.040 nonbonded pdb=" OG SER B 245 " pdb=" N ASP B 246 " model vdw 2.313 3.120 nonbonded pdb=" O SER R 114 " pdb=" OG SER R 114 " model vdw 2.357 3.040 ... (remaining 54458 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.490 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 0.230 7649 Z= 0.581 Angle : 1.248 17.178 10447 Z= 0.784 Chirality : 0.072 0.492 1255 Planarity : 0.007 0.071 1330 Dihedral : 14.656 89.992 2424 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.77 % Allowed : 1.85 % Favored : 97.38 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % 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: -3.35 (0.24), residues: 1047 helix: -0.78 (0.29), residues: 312 sheet: -2.82 (0.28), residues: 271 loop : -2.80 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 160 TYR 0.020 0.002 TYR B 85 PHE 0.026 0.003 PHE B 235 TRP 0.037 0.003 TRP B 339 HIS 0.010 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00995 ( 7647) covalent geometry : angle 1.24750 (10443) SS BOND : bond 0.00927 ( 2) SS BOND : angle 1.71354 ( 4) hydrogen bonds : bond 0.16285 ( 300) hydrogen bonds : angle 7.53178 ( 852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.307 Fit side-chains REVERT: B 17 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8119 (tm-30) REVERT: E 246 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7051 (mm-30) REVERT: R 117 ARG cc_start: 0.7936 (mtm110) cc_final: 0.7452 (mtm110) REVERT: R 169 TRP cc_start: 0.6528 (p-90) cc_final: 0.6140 (p-90) REVERT: R 217 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.5330 (t80) outliers start: 5 outliers final: 3 residues processed: 111 average time/residue: 0.1111 time to fit residues: 16.1639 Evaluate side-chains 89 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 217 PHE Chi-restraints excluded: chain R residue 315 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0030 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN R 313 GLN R 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.136583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.104308 restraints weight = 12477.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.103779 restraints weight = 9075.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.105253 restraints weight = 7217.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.105995 restraints weight = 5366.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.106601 restraints weight = 5007.968| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7649 Z= 0.121 Angle : 0.598 6.973 10447 Z= 0.320 Chirality : 0.043 0.141 1255 Planarity : 0.004 0.058 1330 Dihedral : 8.492 81.151 1171 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.62 % Allowed : 12.00 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.67 (0.25), residues: 1047 helix: 0.11 (0.30), residues: 323 sheet: -2.57 (0.29), residues: 275 loop : -2.60 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 160 TYR 0.014 0.001 TYR R 184 PHE 0.015 0.001 PHE R 126 TRP 0.025 0.002 TRP B 82 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7647) covalent geometry : angle 0.59797 (10443) SS BOND : bond 0.00544 ( 2) SS BOND : angle 1.19486 ( 4) hydrogen bonds : bond 0.03542 ( 300) hydrogen bonds : angle 5.21744 ( 852) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: B 17 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7888 (tm-30) REVERT: B 222 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: E 246 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6950 (mm-30) REVERT: R 117 ARG cc_start: 0.7993 (mtm110) cc_final: 0.7509 (mtm110) outliers start: 4 outliers final: 1 residues processed: 92 average time/residue: 0.1163 time to fit residues: 13.8942 Evaluate side-chains 81 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain E residue 80 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 15 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.130348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.098852 restraints weight = 12748.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.098436 restraints weight = 7905.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.099304 restraints weight = 8130.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.100068 restraints weight = 5629.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.100756 restraints weight = 5071.432| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 7649 Z= 0.255 Angle : 0.684 6.972 10447 Z= 0.369 Chirality : 0.046 0.207 1255 Planarity : 0.005 0.061 1330 Dihedral : 8.136 71.060 1163 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 2.62 % Allowed : 16.77 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.56 (0.26), residues: 1047 helix: 0.35 (0.31), residues: 319 sheet: -2.53 (0.29), residues: 267 loop : -2.65 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 283 TYR 0.013 0.002 TYR E 190 PHE 0.027 0.002 PHE B 235 TRP 0.026 0.003 TRP B 339 HIS 0.009 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00605 ( 7647) covalent geometry : angle 0.68314 (10443) SS BOND : bond 0.00755 ( 2) SS BOND : angle 1.71316 ( 4) hydrogen bonds : bond 0.04251 ( 300) hydrogen bonds : angle 5.24980 ( 852) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.315 Fit side-chains REVERT: B 17 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 222 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: E 246 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6985 (mm-30) REVERT: R 117 ARG cc_start: 0.8211 (mtm110) cc_final: 0.7688 (mtm110) REVERT: R 217 PHE cc_start: 0.6480 (OUTLIER) cc_final: 0.4588 (t80) outliers start: 17 outliers final: 9 residues processed: 94 average time/residue: 0.1103 time to fit residues: 13.6807 Evaluate side-chains 92 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 217 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 13 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.133291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.100795 restraints weight = 12801.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.101448 restraints weight = 8171.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.102638 restraints weight = 7018.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.103036 restraints weight = 5320.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.103604 restraints weight = 4987.559| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7649 Z= 0.150 Angle : 0.580 6.846 10447 Z= 0.312 Chirality : 0.043 0.149 1255 Planarity : 0.004 0.052 1330 Dihedral : 6.800 59.016 1163 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.62 % Allowed : 20.46 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.27 (0.26), residues: 1047 helix: 0.68 (0.32), residues: 314 sheet: -2.38 (0.29), residues: 266 loop : -2.50 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 160 TYR 0.013 0.001 TYR R 184 PHE 0.016 0.001 PHE B 235 TRP 0.023 0.002 TRP B 82 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7647) covalent geometry : angle 0.57920 (10443) SS BOND : bond 0.00563 ( 2) SS BOND : angle 1.28148 ( 4) hydrogen bonds : bond 0.03322 ( 300) hydrogen bonds : angle 4.85111 ( 852) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.303 Fit side-chains REVERT: B 17 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7880 (tm-30) REVERT: B 222 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: E 38 ARG cc_start: 0.8488 (mtm180) cc_final: 0.8193 (mtm-85) REVERT: E 231 GLN cc_start: 0.8336 (pp30) cc_final: 0.7851 (pp30) REVERT: E 246 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6930 (mm-30) REVERT: R 117 ARG cc_start: 0.8133 (mtm110) cc_final: 0.7582 (mtm110) REVERT: R 169 TRP cc_start: 0.7800 (p90) cc_final: 0.7538 (p90) outliers start: 17 outliers final: 11 residues processed: 100 average time/residue: 0.1128 time to fit residues: 14.8210 Evaluate side-chains 94 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 197 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 0.2980 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN ** E 231 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 = 0.3833 r_free = 0.3833 target = 0.131802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.099851 restraints weight = 12685.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.098576 restraints weight = 9237.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.099702 restraints weight = 7296.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.101006 restraints weight = 5722.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.101331 restraints weight = 5064.109| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7649 Z= 0.174 Angle : 0.604 7.015 10447 Z= 0.323 Chirality : 0.043 0.171 1255 Planarity : 0.004 0.060 1330 Dihedral : 6.015 59.493 1163 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.85 % Allowed : 20.62 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.25 (0.26), residues: 1047 helix: 0.73 (0.32), residues: 314 sheet: -2.43 (0.29), residues: 271 loop : -2.46 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 160 TYR 0.012 0.001 TYR R 184 PHE 0.017 0.002 PHE B 235 TRP 0.021 0.002 TRP B 82 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 7647) covalent geometry : angle 0.60326 (10443) SS BOND : bond 0.00617 ( 2) SS BOND : angle 1.41279 ( 4) hydrogen bonds : bond 0.03429 ( 300) hydrogen bonds : angle 4.82727 ( 852) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.270 Fit side-chains REVERT: B 10 GLU cc_start: 0.6199 (OUTLIER) cc_final: 0.5842 (tp30) REVERT: B 17 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7873 (tm-30) REVERT: B 301 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7267 (mtmm) REVERT: E 38 ARG cc_start: 0.8508 (mtm180) cc_final: 0.8181 (mtm-85) REVERT: E 246 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6880 (mm-30) REVERT: R 117 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7584 (mtm110) outliers start: 25 outliers final: 15 residues processed: 105 average time/residue: 0.1056 time to fit residues: 14.5850 Evaluate side-chains 98 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 197 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.0570 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 chunk 67 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN B 259 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.137572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.106135 restraints weight = 12461.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105322 restraints weight = 8090.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.106998 restraints weight = 6879.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.107841 restraints weight = 5051.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.108514 restraints weight = 4427.847| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7649 Z= 0.092 Angle : 0.524 10.248 10447 Z= 0.276 Chirality : 0.040 0.131 1255 Planarity : 0.004 0.056 1330 Dihedral : 5.305 55.837 1163 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.85 % Allowed : 20.77 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.82 (0.26), residues: 1047 helix: 1.10 (0.32), residues: 314 sheet: -2.04 (0.30), residues: 273 loop : -2.31 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 160 TYR 0.018 0.001 TYR R 184 PHE 0.008 0.001 PHE R 101 TRP 0.022 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 7647) covalent geometry : angle 0.52352 (10443) SS BOND : bond 0.00399 ( 2) SS BOND : angle 1.08778 ( 4) hydrogen bonds : bond 0.02511 ( 300) hydrogen bonds : angle 4.39579 ( 852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.312 Fit side-chains REVERT: A 251 ASP cc_start: 0.8432 (t0) cc_final: 0.8218 (t0) REVERT: B 10 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5859 (tp30) REVERT: B 17 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7953 (tm-30) REVERT: B 300 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7948 (mm) REVERT: E 38 ARG cc_start: 0.8232 (mtm180) cc_final: 0.7971 (mtp180) REVERT: E 246 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6794 (mm-30) REVERT: R 117 ARG cc_start: 0.7950 (mtm110) cc_final: 0.7559 (mtm110) outliers start: 25 outliers final: 11 residues processed: 112 average time/residue: 0.1049 time to fit residues: 15.3326 Evaluate side-chains 98 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain R residue 197 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 57 optimal weight: 0.0000 chunk 82 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 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 = 0.3882 r_free = 0.3882 target = 0.136302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105657 restraints weight = 12615.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.103682 restraints weight = 8140.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.105718 restraints weight = 7124.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.106369 restraints weight = 4925.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.107036 restraints weight = 4598.630| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7649 Z= 0.101 Angle : 0.532 8.857 10447 Z= 0.281 Chirality : 0.041 0.133 1255 Planarity : 0.004 0.063 1330 Dihedral : 5.249 58.530 1163 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.92 % Allowed : 22.62 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.60 (0.27), residues: 1047 helix: 1.28 (0.32), residues: 314 sheet: -1.98 (0.30), residues: 268 loop : -2.14 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.016 0.001 TYR R 184 PHE 0.010 0.001 PHE B 234 TRP 0.028 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 7647) covalent geometry : angle 0.53178 (10443) SS BOND : bond 0.00443 ( 2) SS BOND : angle 1.15422 ( 4) hydrogen bonds : bond 0.02615 ( 300) hydrogen bonds : angle 4.30078 ( 852) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.285 Fit side-chains REVERT: A 251 ASP cc_start: 0.8427 (t0) cc_final: 0.8208 (t0) REVERT: B 10 GLU cc_start: 0.6129 (OUTLIER) cc_final: 0.5916 (tp30) REVERT: B 17 GLN cc_start: 0.8346 (tm-30) cc_final: 0.7993 (tm-30) REVERT: E 38 ARG cc_start: 0.8238 (mtm180) cc_final: 0.7903 (ttp-170) REVERT: E 246 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6545 (mm-30) REVERT: R 117 ARG cc_start: 0.7959 (mtm110) cc_final: 0.7529 (mtm110) outliers start: 19 outliers final: 14 residues processed: 104 average time/residue: 0.0964 time to fit residues: 13.2855 Evaluate side-chains 99 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 315 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 30 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 40 optimal weight: 0.0030 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.135533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.103808 restraints weight = 12587.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.102815 restraints weight = 8213.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.104760 restraints weight = 6838.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.105081 restraints weight = 5118.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107699 restraints weight = 4867.651| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7649 Z= 0.114 Angle : 0.545 8.720 10447 Z= 0.286 Chirality : 0.041 0.133 1255 Planarity : 0.004 0.061 1330 Dihedral : 5.182 57.491 1163 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.92 % Allowed : 23.23 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.52 (0.27), residues: 1047 helix: 1.34 (0.32), residues: 312 sheet: -1.91 (0.30), residues: 268 loop : -2.09 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 21 TYR 0.016 0.001 TYR R 184 PHE 0.011 0.001 PHE B 234 TRP 0.025 0.002 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7647) covalent geometry : angle 0.54438 (10443) SS BOND : bond 0.00480 ( 2) SS BOND : angle 1.25792 ( 4) hydrogen bonds : bond 0.02708 ( 300) hydrogen bonds : angle 4.27643 ( 852) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.313 Fit side-chains REVERT: A 21 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7703 (ttp-110) REVERT: B 17 GLN cc_start: 0.8377 (tm-30) cc_final: 0.8051 (tm-30) REVERT: E 34 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6621 (tpp) REVERT: E 38 ARG cc_start: 0.8285 (mtm180) cc_final: 0.7937 (ttp-170) REVERT: R 117 ARG cc_start: 0.7950 (mtm110) cc_final: 0.7533 (mtm110) outliers start: 19 outliers final: 12 residues processed: 103 average time/residue: 0.0971 time to fit residues: 13.4343 Evaluate side-chains 95 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain R residue 197 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 72 optimal weight: 0.9980 chunk 85 optimal weight: 0.0070 chunk 96 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.134271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.102828 restraints weight = 12572.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.101638 restraints weight = 8360.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.103090 restraints weight = 7259.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.103868 restraints weight = 5058.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.104312 restraints weight = 4731.833| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7649 Z= 0.136 Angle : 0.567 8.597 10447 Z= 0.298 Chirality : 0.042 0.139 1255 Planarity : 0.004 0.063 1330 Dihedral : 5.245 56.962 1163 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.08 % Allowed : 23.54 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.54 (0.26), residues: 1047 helix: 1.37 (0.32), residues: 313 sheet: -1.95 (0.31), residues: 261 loop : -2.13 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 21 TYR 0.016 0.001 TYR R 184 PHE 0.013 0.001 PHE B 234 TRP 0.026 0.002 TRP B 82 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7647) covalent geometry : angle 0.56625 (10443) SS BOND : bond 0.00533 ( 2) SS BOND : angle 1.37115 ( 4) hydrogen bonds : bond 0.02948 ( 300) hydrogen bonds : angle 4.33981 ( 852) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.343 Fit side-chains REVERT: A 333 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7508 (tm-30) REVERT: B 17 GLN cc_start: 0.8362 (tm-30) cc_final: 0.8009 (tm-30) REVERT: E 38 ARG cc_start: 0.8280 (mtm180) cc_final: 0.7922 (ttp-170) REVERT: R 117 ARG cc_start: 0.8015 (mtm110) cc_final: 0.7543 (mtm110) REVERT: R 217 PHE cc_start: 0.6285 (OUTLIER) cc_final: 0.4438 (t80) outliers start: 20 outliers final: 14 residues processed: 103 average time/residue: 0.1108 time to fit residues: 14.9243 Evaluate side-chains 96 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 217 PHE Chi-restraints excluded: chain R residue 315 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 80 optimal weight: 0.0170 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.103430 restraints weight = 12337.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.103612 restraints weight = 7292.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.104581 restraints weight = 6868.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.105244 restraints weight = 5024.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.107757 restraints weight = 4467.875| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7649 Z= 0.112 Angle : 0.571 10.465 10447 Z= 0.296 Chirality : 0.041 0.133 1255 Planarity : 0.004 0.065 1330 Dihedral : 5.132 56.455 1163 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.92 % Allowed : 24.00 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.39 (0.27), residues: 1047 helix: 1.47 (0.31), residues: 316 sheet: -1.82 (0.31), residues: 260 loop : -2.08 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.017 0.001 TYR R 184 PHE 0.010 0.001 PHE B 234 TRP 0.026 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7647) covalent geometry : angle 0.57057 (10443) SS BOND : bond 0.00469 ( 2) SS BOND : angle 1.18771 ( 4) hydrogen bonds : bond 0.02729 ( 300) hydrogen bonds : angle 4.27926 ( 852) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.366 Fit side-chains REVERT: A 333 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7484 (tm-30) REVERT: B 17 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8073 (tm-30) REVERT: B 301 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7215 (mtmm) REVERT: E 38 ARG cc_start: 0.8236 (mtm180) cc_final: 0.7856 (ttp-170) REVERT: R 117 ARG cc_start: 0.7942 (mtm110) cc_final: 0.7401 (mtm110) outliers start: 19 outliers final: 14 residues processed: 97 average time/residue: 0.1024 time to fit residues: 13.2043 Evaluate side-chains 95 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 315 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 102 optimal weight: 30.0000 chunk 51 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.136444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.104832 restraints weight = 12326.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.103397 restraints weight = 8078.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105235 restraints weight = 6895.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.106138 restraints weight = 4918.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106882 restraints weight = 4401.592| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7649 Z= 0.111 Angle : 0.553 9.580 10447 Z= 0.290 Chirality : 0.041 0.133 1255 Planarity : 0.004 0.065 1330 Dihedral : 5.055 56.300 1163 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.92 % Allowed : 24.31 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.27), residues: 1047 helix: 1.57 (0.31), residues: 320 sheet: -1.80 (0.31), residues: 262 loop : -2.06 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 21 TYR 0.017 0.001 TYR R 184 PHE 0.010 0.001 PHE B 234 TRP 0.025 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7647) covalent geometry : angle 0.55213 (10443) SS BOND : bond 0.00471 ( 2) SS BOND : angle 1.21677 ( 4) hydrogen bonds : bond 0.02668 ( 300) hydrogen bonds : angle 4.21089 ( 852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1414.88 seconds wall clock time: 25 minutes 5.01 seconds (1505.01 seconds total)