Starting phenix.real_space_refine on Thu Sep 18 02:51:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ism_60838/09_2025/9ism_60838.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ism_60838/09_2025/9ism_60838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ism_60838/09_2025/9ism_60838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ism_60838/09_2025/9ism_60838.map" model { file = "/net/cci-nas-00/data/ceres_data/9ism_60838/09_2025/9ism_60838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ism_60838/09_2025/9ism_60838.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 8310 2.51 5 N 2222 2.21 5 O 2488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13082 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4620 Classifications: {'peptide': 595} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 562} Chain: "B" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1921 Classifications: {'peptide': 249} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 232} Chain: "C" Number of atoms: 4620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4620 Classifications: {'peptide': 595} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 562} Chain: "D" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1921 Classifications: {'peptide': 249} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 232} Time building chain proxies: 2.69, per 1000 atoms: 0.21 Number of scatterers: 13082 At special positions: 0 Unit cell: (120.75, 97.98, 104.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2488 8.00 N 2222 7.00 C 8310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 415 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 76 " distance=2.03 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: 0.77 Conformation dependent library (CDL) restraints added in 484.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3004 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 26 sheets defined 19.8% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 removed outlier: 3.684A pdb=" N GLU A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 102 removed outlier: 4.233A pdb=" N ALA A 100 " --> pdb=" O PRO A 96 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.632A pdb=" N GLY A 221 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.746A pdb=" N THR A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.611A pdb=" N LYS A 236 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 Processing helix chain 'A' and resid 542 through 548 Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 582 through 583 No H-bonds generated for 'chain 'A' and resid 582 through 583' Processing helix chain 'A' and resid 584 through 588 removed outlier: 4.555A pdb=" N ASP A 588 " --> pdb=" O PRO A 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 51 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 65 through 71 Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 143 through 155 removed outlier: 3.549A pdb=" N ASP B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N TYR B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 179 removed outlier: 3.556A pdb=" N GLY B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 197 removed outlier: 5.148A pdb=" N ARG B 193 " --> pdb=" O PRO B 189 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TYR B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 259 removed outlier: 3.986A pdb=" N GLU B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Proline residue: B 249 - end of helix Processing helix chain 'C' and resid 2 through 10 removed outlier: 3.733A pdb=" N GLU C 6 " --> pdb=" O ASP C 2 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 10 " --> pdb=" O GLU C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 102 removed outlier: 4.095A pdb=" N ALA C 100 " --> pdb=" O PRO C 96 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 217 through 221 removed outlier: 3.630A pdb=" N GLY C 221 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 229 removed outlier: 3.512A pdb=" N GLY C 228 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 224 through 229' Processing helix chain 'C' and resid 233 through 238 removed outlier: 3.618A pdb=" N LYS C 236 " --> pdb=" O ASP C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 375 Processing helix chain 'C' and resid 542 through 548 Processing helix chain 'C' and resid 557 through 562 Processing helix chain 'C' and resid 564 through 568 Processing helix chain 'C' and resid 582 through 583 No H-bonds generated for 'chain 'C' and resid 582 through 583' Processing helix chain 'C' and resid 584 through 588 removed outlier: 4.542A pdb=" N ASP C 588 " --> pdb=" O PRO C 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 50 removed outlier: 3.566A pdb=" N VAL D 46 " --> pdb=" O ILE D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 66 Processing helix chain 'D' and resid 117 through 122 Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 143 through 155 removed outlier: 3.644A pdb=" N ASP D 147 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ALA D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N TYR D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL D 155 " --> pdb=" O LEU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 179 removed outlier: 3.516A pdb=" N MET D 172 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 173 " --> pdb=" O PRO D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 197 removed outlier: 4.831A pdb=" N ARG D 193 " --> pdb=" O PRO D 189 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP D 197 " --> pdb=" O ARG D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 247 through 259 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 3.579A pdb=" N LEU A 486 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP A 508 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP A 500 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU A 506 " --> pdb=" O ASP A 500 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 47 removed outlier: 6.908A pdb=" N VAL A 577 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR A 45 " --> pdb=" O VAL A 575 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 575 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU A 580 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLN A 529 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 61 removed outlier: 3.870A pdb=" N TRP A 88 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLY A 79 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE A 86 " --> pdb=" O GLY A 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 removed outlier: 3.907A pdb=" N TRP A 145 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN A 137 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR A 143 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 165 removed outlier: 6.541A pdb=" N LEU A 184 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG A 197 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA A 186 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.299A pdb=" N ILE A 280 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY A 293 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY A 282 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.783A pdb=" N ASP A 339 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A 345 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 358 through 361 removed outlier: 4.064A pdb=" N SER A 360 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 382 through 385 removed outlier: 5.608A pdb=" N LYS A 383 " --> pdb=" O TRP A 418 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TRP A 418 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 437 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 399 through 401 removed outlier: 3.708A pdb=" N GLY A 453 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TRP A 467 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 22 through 25 removed outlier: 6.444A pdb=" N VAL B 22 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU B 59 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA B 24 " --> pdb=" O LEU B 59 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 78 through 82 removed outlier: 4.590A pdb=" N GLY B 81 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA B 226 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR B 96 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 127 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N PHE B 187 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.848A pdb=" N TYR B 96 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 205 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 26 through 27 removed outlier: 3.911A pdb=" N LEU C 486 " --> pdb=" O THR C 482 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP C 508 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP C 500 " --> pdb=" O LEU C 506 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU C 506 " --> pdb=" O ASP C 500 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 40 through 47 removed outlier: 6.974A pdb=" N VAL C 577 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR C 45 " --> pdb=" O VAL C 575 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C 575 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU C 580 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLN C 529 " --> pdb=" O LEU C 580 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.510A pdb=" N LEU C 59 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TRP C 88 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N GLY C 79 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE C 86 " --> pdb=" O GLY C 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.913A pdb=" N TRP C 145 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN C 137 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR C 143 " --> pdb=" O ASN C 137 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 163 through 165 removed outlier: 6.579A pdb=" N LEU C 184 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG C 197 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA C 186 " --> pdb=" O VAL C 195 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 247 through 249 removed outlier: 3.966A pdb=" N PHE C 292 " --> pdb=" O GLY C 282 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP C 284 " --> pdb=" O ALA C 290 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA C 290 " --> pdb=" O ASP C 284 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 311 through 316 removed outlier: 6.559A pdb=" N ASP C 339 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 345 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 358 through 361 removed outlier: 4.001A pdb=" N SER C 360 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 382 through 385 removed outlier: 5.343A pdb=" N LYS C 383 " --> pdb=" O TRP C 418 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TRP C 418 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN C 437 " --> pdb=" O ASP C 417 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 399 through 401 removed outlier: 3.905A pdb=" N GLY C 453 " --> pdb=" O GLU C 471 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TRP C 467 " --> pdb=" O ALA C 457 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 19 through 24 removed outlier: 6.266A pdb=" N LEU D 20 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL D 57 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL D 22 " --> pdb=" O VAL D 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.796A pdb=" N GLY D 81 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA D 226 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASP D 83 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASP D 224 " --> pdb=" O ASP D 83 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR D 96 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL D 127 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N PHE D 187 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 90 through 91 removed outlier: 3.866A pdb=" N TYR D 96 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 205 " --> pdb=" O PHE D 102 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1005 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: 1.67 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4282 1.34 - 1.46: 3195 1.46 - 1.59: 5823 1.59 - 1.71: 0 1.71 - 1.83: 112 Bond restraints: 13412 Sorted by residual: bond pdb=" CB ASN A 356 " pdb=" CG ASN A 356 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.06e+00 bond pdb=" CA ASP D 85 " pdb=" CB ASP D 85 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 8.99e-01 bond pdb=" CA ASP D 107 " pdb=" CB ASP D 107 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.97e-01 bond pdb=" CB PRO A 264 " pdb=" CG PRO A 264 " ideal model delta sigma weight residual 1.506 1.472 0.034 3.90e-02 6.57e+02 7.52e-01 bond pdb=" CB PRO C 264 " pdb=" CG PRO C 264 " ideal model delta sigma weight residual 1.506 1.472 0.034 3.90e-02 6.57e+02 7.41e-01 ... (remaining 13407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 17773 1.70 - 3.40: 384 3.40 - 5.10: 37 5.10 - 6.79: 5 6.79 - 8.49: 3 Bond angle restraints: 18202 Sorted by residual: angle pdb=" CA GLN C 395 " pdb=" C GLN C 395 " pdb=" N GLY C 396 " ideal model delta sigma weight residual 116.84 122.52 -5.68 1.71e+00 3.42e-01 1.11e+01 angle pdb=" C ALA D 106 " pdb=" N ASP D 107 " pdb=" CA ASP D 107 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.71e+00 angle pdb=" N ARG A 426 " pdb=" CA ARG A 426 " pdb=" C ARG A 426 " ideal model delta sigma weight residual 111.03 114.29 -3.26 1.11e+00 8.12e-01 8.62e+00 angle pdb=" C ALA D 84 " pdb=" N ASP D 85 " pdb=" CA ASP D 85 " ideal model delta sigma weight residual 121.54 126.77 -5.23 1.91e+00 2.74e-01 7.49e+00 angle pdb=" CA GLN C 395 " pdb=" C GLN C 395 " pdb=" O GLN C 395 " ideal model delta sigma weight residual 120.51 116.70 3.81 1.43e+00 4.89e-01 7.11e+00 ... (remaining 18197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 7240 17.39 - 34.78: 559 34.78 - 52.17: 90 52.17 - 69.55: 22 69.55 - 86.94: 7 Dihedral angle restraints: 7918 sinusoidal: 3150 harmonic: 4768 Sorted by residual: dihedral pdb=" CA PHE A 281 " pdb=" C PHE A 281 " pdb=" N GLY A 282 " pdb=" CA GLY A 282 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA CYS A 415 " pdb=" C CYS A 415 " pdb=" N MET A 416 " pdb=" CA MET A 416 " ideal model delta harmonic sigma weight residual -180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA TRP C 14 " pdb=" C TRP C 14 " pdb=" N VAL C 15 " pdb=" CA VAL C 15 " ideal model delta harmonic sigma weight residual -180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 7915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1176 0.033 - 0.066: 493 0.066 - 0.099: 156 0.099 - 0.133: 89 0.133 - 0.166: 6 Chirality restraints: 1920 Sorted by residual: chirality pdb=" CB ILE C 237 " pdb=" CA ILE C 237 " pdb=" CG1 ILE C 237 " pdb=" CG2 ILE C 237 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CA ASP D 85 " pdb=" N ASP D 85 " pdb=" C ASP D 85 " pdb=" CB ASP D 85 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ASN A 356 " pdb=" N ASN A 356 " pdb=" C ASN A 356 " pdb=" CB ASN A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 1917 not shown) Planarity restraints: 2376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 551 " 0.052 5.00e-02 4.00e+02 7.89e-02 9.96e+00 pdb=" N PRO C 552 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO C 552 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 552 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 188 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO B 189 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 189 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 189 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 19 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C LYS A 19 " 0.032 2.00e-02 2.50e+03 pdb=" O LYS A 19 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN A 20 " -0.011 2.00e-02 2.50e+03 ... (remaining 2373 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 190 2.68 - 3.24: 11512 3.24 - 3.79: 18362 3.79 - 4.35: 25699 4.35 - 4.90: 44218 Nonbonded interactions: 99981 Sorted by model distance: nonbonded pdb=" OG1 THR A 191 " pdb=" OE1 GLU A 193 " model vdw 2.129 3.040 nonbonded pdb=" OG1 THR C 140 " pdb=" OE1 GLU C 142 " model vdw 2.193 3.040 nonbonded pdb=" O LYS C 19 " pdb=" ND2 ASN C 20 " model vdw 2.199 3.120 nonbonded pdb=" OD2 ASP C 303 " pdb=" NH2 ARG D 161 " model vdw 2.215 3.120 nonbonded pdb=" NH1 ARG A 109 " pdb=" OE1 GLN A 395 " model vdw 2.222 3.120 ... (remaining 99976 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.220 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 0.003 0.034 13416 Z= 0.136 Angle : 0.581 8.493 18210 Z= 0.310 Chirality : 0.045 0.166 1920 Planarity : 0.004 0.079 2376 Dihedral : 12.728 86.943 4902 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.19), residues: 1680 helix: 0.84 (0.36), residues: 228 sheet: -0.21 (0.24), residues: 446 loop : -1.17 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 109 TYR 0.014 0.001 TYR B 96 PHE 0.023 0.001 PHE A 281 TRP 0.012 0.001 TRP C 145 HIS 0.005 0.001 HIS C 397 Details of bonding type rmsd covalent geometry : bond 0.00320 (13412) covalent geometry : angle 0.58000 (18202) SS BOND : bond 0.00250 ( 4) SS BOND : angle 1.65786 ( 8) hydrogen bonds : bond 0.17526 ( 379) hydrogen bonds : angle 6.16765 ( 1005) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.474 Fit side-chains REVERT: A 438 MET cc_start: 0.7554 (mtp) cc_final: 0.7160 (mtt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.7398 time to fit residues: 103.4608 Evaluate side-chains 93 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0470 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 413 HIS C 20 ASN C 68 HIS C 380 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.069618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.043991 restraints weight = 42178.210| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 3.65 r_work: 0.2521 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13416 Z= 0.266 Angle : 0.639 6.142 18210 Z= 0.340 Chirality : 0.046 0.158 1920 Planarity : 0.005 0.057 2376 Dihedral : 4.804 18.746 1832 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.17 % Allowed : 6.96 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.19), residues: 1680 helix: 0.31 (0.33), residues: 248 sheet: -0.20 (0.24), residues: 446 loop : -1.09 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 99 TYR 0.013 0.001 TYR C 535 PHE 0.018 0.001 PHE A 281 TRP 0.014 0.001 TRP C 476 HIS 0.006 0.001 HIS C 397 Details of bonding type rmsd covalent geometry : bond 0.00627 (13412) covalent geometry : angle 0.63827 (18202) SS BOND : bond 0.00281 ( 4) SS BOND : angle 1.25657 ( 8) hydrogen bonds : bond 0.05270 ( 379) hydrogen bonds : angle 5.17978 ( 1005) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.8678 (ptp-170) cc_final: 0.8323 (ptp90) REVERT: A 378 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8268 (tmm) REVERT: B 65 TYR cc_start: 0.8706 (m-80) cc_final: 0.8481 (m-80) REVERT: B 158 ARG cc_start: 0.8169 (mpt180) cc_final: 0.7921 (mpt180) REVERT: B 227 MET cc_start: 0.9142 (mtt) cc_final: 0.8909 (mmt) REVERT: C 540 TRP cc_start: 0.8065 (OUTLIER) cc_final: 0.7598 (t60) REVERT: D 55 GLN cc_start: 0.6955 (tm-30) cc_final: 0.6601 (pp30) REVERT: D 180 LYS cc_start: 0.9189 (mppt) cc_final: 0.8966 (mppt) outliers start: 16 outliers final: 6 residues processed: 102 average time/residue: 0.6395 time to fit residues: 70.9388 Evaluate side-chains 102 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 540 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 70 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN C 54 HIS C 380 HIS C 448 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.069148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.043820 restraints weight = 42553.825| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 3.65 r_work: 0.2517 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13416 Z= 0.218 Angle : 0.583 6.124 18210 Z= 0.309 Chirality : 0.045 0.160 1920 Planarity : 0.004 0.047 2376 Dihedral : 4.719 19.710 1832 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.10 % Allowed : 8.36 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.19), residues: 1680 helix: 0.32 (0.33), residues: 250 sheet: -0.28 (0.24), residues: 454 loop : -1.07 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.018 0.001 TYR D 150 PHE 0.014 0.001 PHE A 281 TRP 0.012 0.001 TRP C 476 HIS 0.004 0.001 HIS C 397 Details of bonding type rmsd covalent geometry : bond 0.00521 (13412) covalent geometry : angle 0.58228 (18202) SS BOND : bond 0.00274 ( 4) SS BOND : angle 0.97837 ( 8) hydrogen bonds : bond 0.04844 ( 379) hydrogen bonds : angle 4.97080 ( 1005) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 378 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8598 (tmm) REVERT: A 392 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7658 (m-10) REVERT: B 65 TYR cc_start: 0.8673 (m-80) cc_final: 0.8435 (m-80) REVERT: B 158 ARG cc_start: 0.8098 (mpt180) cc_final: 0.7704 (mpt180) REVERT: C 278 MET cc_start: 0.8662 (mmm) cc_final: 0.8436 (mmm) REVERT: C 310 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8212 (mmt) REVERT: C 540 TRP cc_start: 0.8141 (OUTLIER) cc_final: 0.7591 (t60) REVERT: D 55 GLN cc_start: 0.7063 (tm-30) cc_final: 0.6718 (pp30) outliers start: 15 outliers final: 5 residues processed: 97 average time/residue: 0.6504 time to fit residues: 68.7743 Evaluate side-chains 96 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 540 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 124 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 ASN C 217 ASN C 380 HIS ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.068534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.043216 restraints weight = 42427.646| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 3.59 r_work: 0.2505 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13416 Z= 0.245 Angle : 0.598 5.769 18210 Z= 0.317 Chirality : 0.045 0.159 1920 Planarity : 0.004 0.041 2376 Dihedral : 4.768 19.234 1832 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.83 % Allowed : 9.16 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.19), residues: 1680 helix: 0.27 (0.32), residues: 250 sheet: -0.28 (0.24), residues: 454 loop : -1.09 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 158 TYR 0.017 0.001 TYR D 150 PHE 0.011 0.001 PHE A 281 TRP 0.013 0.001 TRP C 476 HIS 0.003 0.001 HIS C 397 Details of bonding type rmsd covalent geometry : bond 0.00584 (13412) covalent geometry : angle 0.59805 (18202) SS BOND : bond 0.00278 ( 4) SS BOND : angle 0.95875 ( 8) hydrogen bonds : bond 0.04935 ( 379) hydrogen bonds : angle 4.95381 ( 1005) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8279 (tmm) REVERT: B 50 MET cc_start: 0.8330 (tmm) cc_final: 0.7749 (ppp) REVERT: B 65 TYR cc_start: 0.8662 (m-80) cc_final: 0.8454 (m-80) REVERT: B 158 ARG cc_start: 0.8025 (mpt180) cc_final: 0.7651 (mpt180) REVERT: C 310 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8161 (mmt) REVERT: C 392 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7654 (m-10) REVERT: C 540 TRP cc_start: 0.8165 (OUTLIER) cc_final: 0.7579 (t60) REVERT: D 55 GLN cc_start: 0.7179 (tm-30) cc_final: 0.6795 (pp30) outliers start: 25 outliers final: 5 residues processed: 102 average time/residue: 0.5939 time to fit residues: 66.2567 Evaluate side-chains 93 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 392 TYR Chi-restraints excluded: chain C residue 540 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 148 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 16 optimal weight: 0.0870 chunk 43 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 67 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 5 optimal weight: 0.0770 overall best weight: 0.8918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN C 380 HIS ** D 27 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 = 0.3395 r_free = 0.3395 target = 0.070910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.045705 restraints weight = 42580.182| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.63 r_work: 0.2563 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13416 Z= 0.102 Angle : 0.520 6.909 18210 Z= 0.274 Chirality : 0.043 0.158 1920 Planarity : 0.004 0.038 2376 Dihedral : 4.396 18.198 1832 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.32 % Allowed : 10.63 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.20), residues: 1680 helix: 0.31 (0.32), residues: 262 sheet: -0.25 (0.24), residues: 454 loop : -0.99 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 158 TYR 0.012 0.001 TYR C 535 PHE 0.006 0.001 PHE A 281 TRP 0.012 0.001 TRP C 145 HIS 0.003 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00240 (13412) covalent geometry : angle 0.51996 (18202) SS BOND : bond 0.00188 ( 4) SS BOND : angle 0.74866 ( 8) hydrogen bonds : bond 0.03397 ( 379) hydrogen bonds : angle 4.85327 ( 1005) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 378 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8524 (tmm) REVERT: B 65 TYR cc_start: 0.8578 (m-80) cc_final: 0.8331 (m-80) REVERT: B 122 GLU cc_start: 0.9447 (mt-10) cc_final: 0.9185 (pp20) REVERT: B 158 ARG cc_start: 0.7966 (mpt180) cc_final: 0.7612 (mpt180) REVERT: C 540 TRP cc_start: 0.8091 (OUTLIER) cc_final: 0.7811 (t60) REVERT: D 55 GLN cc_start: 0.7286 (tm-30) cc_final: 0.6921 (pp30) outliers start: 18 outliers final: 5 residues processed: 96 average time/residue: 0.6719 time to fit residues: 70.2707 Evaluate side-chains 93 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 540 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 93 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS ** D 27 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 = 0.3352 r_free = 0.3352 target = 0.068492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.043169 restraints weight = 42366.520| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 3.62 r_work: 0.2506 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13416 Z= 0.244 Angle : 0.596 6.933 18210 Z= 0.314 Chirality : 0.045 0.158 1920 Planarity : 0.004 0.036 2376 Dihedral : 4.622 18.747 1832 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.69 % Allowed : 10.63 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.20), residues: 1680 helix: 0.36 (0.33), residues: 250 sheet: -0.27 (0.24), residues: 454 loop : -1.01 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 99 TYR 0.016 0.001 TYR D 150 PHE 0.011 0.001 PHE A 281 TRP 0.010 0.001 TRP C 476 HIS 0.003 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00586 (13412) covalent geometry : angle 0.59597 (18202) SS BOND : bond 0.00280 ( 4) SS BOND : angle 0.95985 ( 8) hydrogen bonds : bond 0.04757 ( 379) hydrogen bonds : angle 4.89084 ( 1005) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 310 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8457 (mtt) REVERT: A 378 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8402 (tmm) REVERT: A 392 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8049 (m-10) REVERT: B 50 MET cc_start: 0.8569 (tmm) cc_final: 0.7825 (ppp) REVERT: B 122 GLU cc_start: 0.9434 (mt-10) cc_final: 0.9169 (pp20) REVERT: B 158 ARG cc_start: 0.7947 (mpt180) cc_final: 0.7594 (mpt180) REVERT: C 269 MET cc_start: 0.9469 (OUTLIER) cc_final: 0.9193 (mmm) REVERT: C 310 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8130 (mmt) REVERT: C 392 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7669 (m-10) REVERT: C 540 TRP cc_start: 0.8104 (OUTLIER) cc_final: 0.7392 (t60) REVERT: D 55 GLN cc_start: 0.7351 (tm-30) cc_final: 0.6945 (pp30) REVERT: D 137 MET cc_start: 0.8280 (mmm) cc_final: 0.7989 (mtm) outliers start: 23 outliers final: 7 residues processed: 100 average time/residue: 0.6520 time to fit residues: 71.2069 Evaluate side-chains 100 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 392 TYR Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 540 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 147 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 159 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN C 1 ASN ** D 27 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 = 0.3377 r_free = 0.3377 target = 0.070107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.044995 restraints weight = 42791.779| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 3.59 r_work: 0.2537 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13416 Z= 0.144 Angle : 0.553 7.327 18210 Z= 0.291 Chirality : 0.043 0.157 1920 Planarity : 0.004 0.039 2376 Dihedral : 4.478 18.622 1832 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.47 % Allowed : 10.70 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.19), residues: 1680 helix: 0.45 (0.33), residues: 250 sheet: -0.29 (0.23), residues: 454 loop : -0.96 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 158 TYR 0.017 0.001 TYR B 65 PHE 0.007 0.001 PHE C 578 TRP 0.011 0.001 TRP A 145 HIS 0.003 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00347 (13412) covalent geometry : angle 0.55317 (18202) SS BOND : bond 0.00228 ( 4) SS BOND : angle 0.81606 ( 8) hydrogen bonds : bond 0.03879 ( 379) hydrogen bonds : angle 4.86354 ( 1005) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 310 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8388 (mtt) REVERT: A 378 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8540 (tmm) REVERT: B 122 GLU cc_start: 0.9422 (mt-10) cc_final: 0.9163 (pp20) REVERT: B 148 MET cc_start: 0.8400 (ttt) cc_final: 0.8189 (ttt) REVERT: B 158 ARG cc_start: 0.7937 (mpt180) cc_final: 0.7576 (mpt180) REVERT: C 269 MET cc_start: 0.9473 (OUTLIER) cc_final: 0.9201 (mmm) REVERT: C 310 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8085 (mmt) REVERT: C 392 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7578 (m-10) REVERT: C 540 TRP cc_start: 0.8096 (OUTLIER) cc_final: 0.7753 (t60) REVERT: D 27 GLN cc_start: 0.8253 (mt0) cc_final: 0.8029 (mt0) REVERT: D 55 GLN cc_start: 0.7417 (tm-30) cc_final: 0.7023 (pp30) outliers start: 20 outliers final: 6 residues processed: 102 average time/residue: 0.6766 time to fit residues: 75.2039 Evaluate side-chains 100 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 392 TYR Chi-restraints excluded: chain C residue 540 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 120 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 30 optimal weight: 0.0670 chunk 163 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** D 27 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 = 0.3369 r_free = 0.3369 target = 0.069632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.044253 restraints weight = 42494.945| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 3.60 r_work: 0.2523 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13416 Z= 0.169 Angle : 0.580 9.360 18210 Z= 0.303 Chirality : 0.043 0.156 1920 Planarity : 0.004 0.038 2376 Dihedral : 4.504 18.783 1832 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.54 % Allowed : 11.80 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.19), residues: 1680 helix: 0.45 (0.33), residues: 250 sheet: -0.30 (0.23), residues: 454 loop : -0.94 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 99 TYR 0.013 0.001 TYR D 150 PHE 0.008 0.001 PHE A 281 TRP 0.012 0.001 TRP C 540 HIS 0.003 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00407 (13412) covalent geometry : angle 0.58001 (18202) SS BOND : bond 0.00210 ( 4) SS BOND : angle 0.82087 ( 8) hydrogen bonds : bond 0.04148 ( 379) hydrogen bonds : angle 4.87185 ( 1005) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 310 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8422 (mtt) REVERT: A 378 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8482 (tmm) REVERT: A 394 ASN cc_start: 0.7252 (p0) cc_final: 0.6963 (p0) REVERT: B 50 MET cc_start: 0.8755 (tmm) cc_final: 0.7763 (ppp) REVERT: B 122 GLU cc_start: 0.9412 (mt-10) cc_final: 0.9160 (pp20) REVERT: B 158 ARG cc_start: 0.7869 (mpt180) cc_final: 0.7499 (mpt180) REVERT: C 269 MET cc_start: 0.9479 (OUTLIER) cc_final: 0.9210 (mmm) REVERT: C 310 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8091 (mmt) REVERT: C 392 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7596 (m-10) REVERT: C 540 TRP cc_start: 0.8108 (OUTLIER) cc_final: 0.7757 (t60) REVERT: D 27 GLN cc_start: 0.8263 (mt0) cc_final: 0.8055 (mt0) REVERT: D 55 GLN cc_start: 0.7436 (tm-30) cc_final: 0.7031 (pp30) outliers start: 21 outliers final: 7 residues processed: 101 average time/residue: 0.6842 time to fit residues: 75.3531 Evaluate side-chains 102 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 392 TYR Chi-restraints excluded: chain C residue 540 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 17 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 110 optimal weight: 0.4980 chunk 157 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN B 27 GLN ** D 27 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 = 0.3401 r_free = 0.3401 target = 0.070623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.045469 restraints weight = 42174.724| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 3.59 r_work: 0.2573 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13416 Z= 0.104 Angle : 0.548 8.650 18210 Z= 0.285 Chirality : 0.043 0.158 1920 Planarity : 0.004 0.038 2376 Dihedral : 4.303 17.967 1832 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.17 % Allowed : 12.39 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.20), residues: 1680 helix: 0.35 (0.32), residues: 262 sheet: -0.25 (0.23), residues: 454 loop : -0.89 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 99 TYR 0.012 0.001 TYR C 535 PHE 0.006 0.001 PHE A 421 TRP 0.012 0.001 TRP C 145 HIS 0.002 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00250 (13412) covalent geometry : angle 0.54785 (18202) SS BOND : bond 0.00153 ( 4) SS BOND : angle 0.85617 ( 8) hydrogen bonds : bond 0.03256 ( 379) hydrogen bonds : angle 4.85652 ( 1005) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 378 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8472 (tmm) REVERT: B 50 MET cc_start: 0.8698 (tmm) cc_final: 0.7809 (ppp) REVERT: B 122 GLU cc_start: 0.9393 (mt-10) cc_final: 0.9137 (pp20) REVERT: B 158 ARG cc_start: 0.7803 (mpt180) cc_final: 0.7419 (mpt180) REVERT: C 269 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.9190 (mmm) REVERT: C 310 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8051 (mmt) REVERT: D 27 GLN cc_start: 0.8298 (mt0) cc_final: 0.8060 (mt0) REVERT: D 55 GLN cc_start: 0.7534 (tm-30) cc_final: 0.7141 (pp30) outliers start: 16 outliers final: 4 residues processed: 96 average time/residue: 0.6692 time to fit residues: 70.1572 Evaluate side-chains 95 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 310 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 132 ASN ** D 27 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 = 0.3390 r_free = 0.3390 target = 0.070178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.045025 restraints weight = 42399.583| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.59 r_work: 0.2570 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13416 Z= 0.124 Angle : 0.562 8.890 18210 Z= 0.293 Chirality : 0.043 0.156 1920 Planarity : 0.004 0.039 2376 Dihedral : 4.307 17.890 1832 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.88 % Allowed : 12.83 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.20), residues: 1680 helix: 0.42 (0.32), residues: 262 sheet: -0.24 (0.23), residues: 454 loop : -0.84 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 158 TYR 0.011 0.001 TYR C 535 PHE 0.007 0.001 PHE C 578 TRP 0.014 0.001 TRP C 540 HIS 0.003 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00300 (13412) covalent geometry : angle 0.56179 (18202) SS BOND : bond 0.00168 ( 4) SS BOND : angle 0.83687 ( 8) hydrogen bonds : bond 0.03614 ( 379) hydrogen bonds : angle 4.81680 ( 1005) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 378 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8507 (tmm) REVERT: B 50 MET cc_start: 0.8725 (tmm) cc_final: 0.7816 (ppp) REVERT: B 122 GLU cc_start: 0.9407 (mt-10) cc_final: 0.9156 (pp20) REVERT: B 158 ARG cc_start: 0.7782 (mpt180) cc_final: 0.7389 (mpt180) REVERT: C 269 MET cc_start: 0.9449 (OUTLIER) cc_final: 0.9198 (mmm) REVERT: C 310 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8054 (mmt) REVERT: C 540 TRP cc_start: 0.8012 (t60) cc_final: 0.7697 (t60) REVERT: D 27 GLN cc_start: 0.8288 (mt0) cc_final: 0.8036 (mt0) REVERT: D 55 GLN cc_start: 0.7540 (tm-30) cc_final: 0.7147 (pp30) outliers start: 12 outliers final: 5 residues processed: 93 average time/residue: 0.6890 time to fit residues: 69.8301 Evaluate side-chains 95 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 57 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 148 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 47 optimal weight: 0.0870 chunk 65 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN B 27 GLN C 1 ASN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.071288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.046167 restraints weight = 41757.835| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.61 r_work: 0.2599 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13416 Z= 0.099 Angle : 0.544 10.273 18210 Z= 0.282 Chirality : 0.042 0.188 1920 Planarity : 0.004 0.040 2376 Dihedral : 4.160 17.503 1832 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.66 % Allowed : 12.98 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.20), residues: 1680 helix: 0.38 (0.32), residues: 262 sheet: -0.22 (0.23), residues: 454 loop : -0.82 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 105 TYR 0.011 0.001 TYR C 535 PHE 0.007 0.001 PHE C 421 TRP 0.011 0.001 TRP C 145 HIS 0.002 0.001 HIS A 393 Details of bonding type rmsd covalent geometry : bond 0.00237 (13412) covalent geometry : angle 0.54345 (18202) SS BOND : bond 0.00149 ( 4) SS BOND : angle 0.80500 ( 8) hydrogen bonds : bond 0.03083 ( 379) hydrogen bonds : angle 4.82432 ( 1005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4528.65 seconds wall clock time: 77 minutes 59.05 seconds (4679.05 seconds total)