Starting phenix.real_space_refine on Sun Aug 24 12:46:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v45_42965/08_2025/8v45_42965.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v45_42965/08_2025/8v45_42965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v45_42965/08_2025/8v45_42965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v45_42965/08_2025/8v45_42965.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v45_42965/08_2025/8v45_42965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v45_42965/08_2025/8v45_42965.map" } resolution = 3.63 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= 0.014 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 P 12 5.49 5 S 82 5.16 5 C 12612 2.51 5 N 3327 2.21 5 O 3780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s 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: 19813 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2985 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 10, 'TRANS': 368} Chain breaks: 6 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3050 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 372} Chain breaks: 7 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2939 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 10, 'TRANS': 364} Chain breaks: 7 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3042 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 371} Chain breaks: 7 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2967 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 10, 'TRANS': 365} Chain breaks: 6 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "F" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2962 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 10, 'TRANS': 367} Chain breaks: 7 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "O" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 872 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "P" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 872 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.11, per 1000 atoms: 0.26 Number of scatterers: 19813 At special positions: 0 Unit cell: (102.85, 166.43, 168.3, 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 82 16.00 P 12 15.00 O 3780 8.00 N 3327 7.00 C 12612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 843.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4754 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 18 sheets defined 55.8% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 38 through 50 Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.754A pdb=" N ARG A 56 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.772A pdb=" N ILE A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.529A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 189 removed outlier: 4.452A pdb=" N ALA A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 237 removed outlier: 3.848A pdb=" N SER A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 259 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 297 through 333 removed outlier: 3.613A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 319 " --> pdb=" O GLN A 315 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 378 Processing helix chain 'A' and resid 399 through 414 removed outlier: 5.034A pdb=" N LEU A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LYS A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.648A pdb=" N THR A 430 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 53 through 60 removed outlier: 3.565A pdb=" N ARG B 56 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 151 through 158 removed outlier: 3.901A pdb=" N LEU B 155 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 187 removed outlier: 4.057A pdb=" N ALA B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 233 removed outlier: 4.050A pdb=" N VAL B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 261 removed outlier: 4.115A pdb=" N ALA B 261 " --> pdb=" O GLY B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 287 removed outlier: 3.682A pdb=" N SER B 275 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 319 removed outlier: 3.706A pdb=" N LEU B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 303 " --> pdb=" O GLY B 299 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 319 " --> pdb=" O GLN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 333 removed outlier: 3.987A pdb=" N PHE B 332 " --> pdb=" O SER B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 removed outlier: 3.700A pdb=" N VAL B 365 " --> pdb=" O PRO B 362 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 366 " --> pdb=" O ILE B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 362 through 366' Processing helix chain 'B' and resid 367 through 382 removed outlier: 3.823A pdb=" N ALA B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 405 through 414 Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'C' and resid 38 through 51 removed outlier: 3.688A pdb=" N VAL C 45 " --> pdb=" O THR C 41 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 60 removed outlier: 3.633A pdb=" N ARG C 56 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 113 Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 151 through 158 Processing helix chain 'C' and resid 179 through 189 Processing helix chain 'C' and resid 199 through 237 removed outlier: 3.963A pdb=" N LEU C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 259 Processing helix chain 'C' and resid 276 through 287 Processing helix chain 'C' and resid 297 through 333 removed outlier: 4.874A pdb=" N GLU C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE C 332 " --> pdb=" O SER C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 382 removed outlier: 3.631A pdb=" N ALA C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 414 removed outlier: 4.930A pdb=" N LEU C 407 " --> pdb=" O GLN C 403 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LYS C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 430 removed outlier: 3.533A pdb=" N ILE C 428 " --> pdb=" O SER C 425 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 430 " --> pdb=" O SER C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'D' and resid 38 through 51 removed outlier: 3.748A pdb=" N ASN D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 60 removed outlier: 3.662A pdb=" N ARG D 56 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 113 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 151 through 158 removed outlier: 3.536A pdb=" N LEU D 155 " --> pdb=" O PHE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 189 removed outlier: 4.195A pdb=" N ALA D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 235 removed outlier: 3.807A pdb=" N GLU D 204 " --> pdb=" O PRO D 200 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP D 205 " --> pdb=" O MET D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 261 removed outlier: 4.050A pdb=" N ILE D 260 " --> pdb=" O GLU D 256 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 287 removed outlier: 3.678A pdb=" N SER D 275 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 333 removed outlier: 3.888A pdb=" N PHE D 319 " --> pdb=" O GLN D 315 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU D 321 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE D 332 " --> pdb=" O SER D 328 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 382 removed outlier: 3.650A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 414 removed outlier: 4.754A pdb=" N LEU D 407 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LYS D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 430 removed outlier: 3.772A pdb=" N THR D 430 " --> pdb=" O SER D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 434 No H-bonds generated for 'chain 'D' and resid 432 through 434' Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 53 through 60 removed outlier: 3.800A pdb=" N ARG E 56 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 113 removed outlier: 3.769A pdb=" N ILE E 112 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU E 113 " --> pdb=" O VAL E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 138 removed outlier: 3.530A pdb=" N ASN E 138 " --> pdb=" O PHE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 158 removed outlier: 3.594A pdb=" N LEU E 155 " --> pdb=" O PHE E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 189 removed outlier: 4.199A pdb=" N ALA E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU E 187 " --> pdb=" O PHE E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 236 Processing helix chain 'E' and resid 249 through 259 Processing helix chain 'E' and resid 276 through 287 removed outlier: 3.546A pdb=" N GLU E 280 " --> pdb=" O LYS E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 333 removed outlier: 3.826A pdb=" N LEU E 301 " --> pdb=" O VAL E 297 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU E 321 " --> pdb=" O LYS E 317 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE E 332 " --> pdb=" O SER E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 378 Processing helix chain 'E' and resid 399 through 414 removed outlier: 4.975A pdb=" N LEU E 407 " --> pdb=" O GLN E 403 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS E 408 " --> pdb=" O GLU E 404 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER E 412 " --> pdb=" O LYS E 408 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN E 413 " --> pdb=" O ARG E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 430 removed outlier: 3.712A pdb=" N THR E 430 " --> pdb=" O SER E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 434 No H-bonds generated for 'chain 'E' and resid 432 through 434' Processing helix chain 'F' and resid 38 through 51 removed outlier: 3.815A pdb=" N ASN F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 60 removed outlier: 3.534A pdb=" N ARG F 56 " --> pdb=" O ASP F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 113 Processing helix chain 'F' and resid 126 through 138 Processing helix chain 'F' and resid 151 through 158 Processing helix chain 'F' and resid 178 through 189 removed outlier: 4.078A pdb=" N ALA F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 237 removed outlier: 3.749A pdb=" N LEU F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 276 through 287 removed outlier: 3.540A pdb=" N GLU F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 333 removed outlier: 4.884A pdb=" N GLU F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE F 332 " --> pdb=" O SER F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 366 removed outlier: 3.819A pdb=" N LEU F 366 " --> pdb=" O ILE F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 382 removed outlier: 3.677A pdb=" N ALA F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 414 removed outlier: 4.949A pdb=" N LEU F 407 " --> pdb=" O GLN F 403 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LYS F 408 " --> pdb=" O GLU F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 430 removed outlier: 3.642A pdb=" N THR F 430 " --> pdb=" O SER F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 434 No H-bonds generated for 'chain 'F' and resid 432 through 434' Processing helix chain 'O' and resid 6 through 26 removed outlier: 3.538A pdb=" N VAL O 10 " --> pdb=" O THR O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 42 removed outlier: 3.524A pdb=" N LEU O 33 " --> pdb=" O ASP O 29 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP O 35 " --> pdb=" O ASP O 31 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS O 38 " --> pdb=" O HIS O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 57 removed outlier: 3.598A pdb=" N VAL O 55 " --> pdb=" O ASP O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 108 removed outlier: 3.799A pdb=" N GLU O 95 " --> pdb=" O ILE O 91 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP O 96 " --> pdb=" O ASP O 92 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU O 98 " --> pdb=" O TRP O 94 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASP O 99 " --> pdb=" O GLU O 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 26 Processing helix chain 'P' and resid 29 through 42 removed outlier: 4.147A pdb=" N ASP P 35 " --> pdb=" O ASP P 31 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N HIS P 38 " --> pdb=" O HIS P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 57 Processing helix chain 'P' and resid 76 through 108 removed outlier: 3.623A pdb=" N GLU P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP P 96 " --> pdb=" O ASP P 92 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU P 98 " --> pdb=" O TRP P 94 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASP P 99 " --> pdb=" O GLU P 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 101 removed outlier: 5.289A pdb=" N TYR A 18 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 342 removed outlier: 3.558A pdb=" N SER A 361 " --> pdb=" O LEU A 353 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 101 removed outlier: 5.440A pdb=" N TYR B 18 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 145 through 148 removed outlier: 6.416A pdb=" N VAL B 389 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N CYS B 422 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE B 391 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASN B 29 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR B 423 " --> pdb=" O ASN B 29 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE B 31 " --> pdb=" O THR B 423 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 30 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AA7, first strand: chain 'C' and resid 97 through 101 removed outlier: 5.438A pdb=" N TYR C 18 " --> pdb=" O LYS C 13 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 145 through 148 removed outlier: 6.094A pdb=" N VAL C 30 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 337 through 339 removed outlier: 3.707A pdb=" N SER C 361 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 97 through 101 removed outlier: 5.722A pdb=" N TYR D 18 " --> pdb=" O LYS D 13 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 145 through 148 removed outlier: 6.160A pdb=" N SER D 146 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ASP D 392 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE D 148 " --> pdb=" O ASP D 392 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL D 389 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS D 422 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE D 391 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL D 30 " --> pdb=" O ILE D 437 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 337 through 339 Processing sheet with id=AB4, first strand: chain 'E' and resid 97 through 101 removed outlier: 3.506A pdb=" N LYS E 8 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TYR E 18 " --> pdb=" O LYS E 13 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 147 through 148 Processing sheet with id=AB6, first strand: chain 'E' and resid 337 through 341 removed outlier: 3.554A pdb=" N SER E 361 " --> pdb=" O LEU E 353 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 97 through 101 removed outlier: 5.301A pdb=" N TYR F 18 " --> pdb=" O LYS F 13 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 145 through 148 removed outlier: 6.135A pdb=" N VAL F 30 " --> pdb=" O ILE F 437 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 337 through 341 1170 hydrogen bonds defined for protein. 3318 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: 3.83 Time building geometry restraints manager: 2.31 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: 6239 1.34 - 1.46: 3281 1.46 - 1.57: 10470 1.57 - 1.69: 16 1.69 - 1.81: 158 Bond restraints: 20164 Sorted by residual: bond pdb=" C HIS B 424 " pdb=" N SER B 425 " ideal model delta sigma weight residual 1.331 1.300 0.031 2.07e-02 2.33e+03 2.31e+00 bond pdb=" O3A ATP F 501 " pdb=" PA ATP F 501 " ideal model delta sigma weight residual 1.592 1.548 0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" CB THR A 375 " pdb=" CG2 THR A 375 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 bond pdb=" CB TRP C 360 " pdb=" CG TRP C 360 " ideal model delta sigma weight residual 1.498 1.456 0.042 3.10e-02 1.04e+03 1.80e+00 bond pdb=" CA GLU C 202 " pdb=" C GLU C 202 " ideal model delta sigma weight residual 1.521 1.503 0.017 1.36e-02 5.41e+03 1.63e+00 ... (remaining 20159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 26416 2.02 - 4.03: 686 4.03 - 6.05: 73 6.05 - 8.07: 9 8.07 - 10.08: 4 Bond angle restraints: 27188 Sorted by residual: angle pdb=" C HIS D 399 " pdb=" CA HIS D 399 " pdb=" CB HIS D 399 " ideal model delta sigma weight residual 109.68 118.94 -9.26 2.05e+00 2.38e-01 2.04e+01 angle pdb=" C HIS F 399 " pdb=" CA HIS F 399 " pdb=" CB HIS F 399 " ideal model delta sigma weight residual 109.68 118.64 -8.96 2.05e+00 2.38e-01 1.91e+01 angle pdb=" C HIS C 399 " pdb=" CA HIS C 399 " pdb=" CB HIS C 399 " ideal model delta sigma weight residual 109.68 117.92 -8.24 2.05e+00 2.38e-01 1.62e+01 angle pdb=" C SER E 93 " pdb=" N ASN E 94 " pdb=" CA ASN E 94 " ideal model delta sigma weight residual 121.54 128.78 -7.24 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C SER A 93 " pdb=" N ASN A 94 " pdb=" CA ASN A 94 " ideal model delta sigma weight residual 121.54 128.51 -6.97 1.91e+00 2.74e-01 1.33e+01 ... (remaining 27183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 11343 17.71 - 35.42: 651 35.42 - 53.13: 188 53.13 - 70.84: 47 70.84 - 88.56: 8 Dihedral angle restraints: 12237 sinusoidal: 4941 harmonic: 7296 Sorted by residual: dihedral pdb=" C HIS D 399 " pdb=" N HIS D 399 " pdb=" CA HIS D 399 " pdb=" CB HIS D 399 " ideal model delta harmonic sigma weight residual -122.60 -132.08 9.48 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" C HIS F 399 " pdb=" N HIS F 399 " pdb=" CA HIS F 399 " pdb=" CB HIS F 399 " ideal model delta harmonic sigma weight residual -122.60 -131.58 8.98 0 2.50e+00 1.60e-01 1.29e+01 dihedral pdb=" CA LEU A 377 " pdb=" C LEU A 377 " pdb=" N TYR A 378 " pdb=" CA TYR A 378 " ideal model delta harmonic sigma weight residual 180.00 162.08 17.92 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 12234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2252 0.054 - 0.107: 614 0.107 - 0.161: 139 0.161 - 0.214: 8 0.214 - 0.268: 4 Chirality restraints: 3017 Sorted by residual: chirality pdb=" CB ILE B 98 " pdb=" CA ILE B 98 " pdb=" CG1 ILE B 98 " pdb=" CG2 ILE B 98 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA HIS D 399 " pdb=" N HIS D 399 " pdb=" C HIS D 399 " pdb=" CB HIS D 399 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB VAL B 233 " pdb=" CA VAL B 233 " pdb=" CG1 VAL B 233 " pdb=" CG2 VAL B 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 3014 not shown) Planarity restraints: 3463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 201 " -0.033 2.00e-02 2.50e+03 6.57e-02 4.32e+01 pdb=" C MET F 201 " 0.114 2.00e-02 2.50e+03 pdb=" O MET F 201 " -0.043 2.00e-02 2.50e+03 pdb=" N GLU F 202 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 201 " 0.029 2.00e-02 2.50e+03 5.88e-02 3.45e+01 pdb=" C MET C 201 " -0.102 2.00e-02 2.50e+03 pdb=" O MET C 201 " 0.038 2.00e-02 2.50e+03 pdb=" N GLU C 202 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 317 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C LYS E 317 " 0.061 2.00e-02 2.50e+03 pdb=" O LYS E 317 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA E 318 " -0.021 2.00e-02 2.50e+03 ... (remaining 3460 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4589 2.79 - 3.31: 17495 3.31 - 3.84: 32619 3.84 - 4.37: 36831 4.37 - 4.90: 63354 Nonbonded interactions: 154888 Sorted by model distance: nonbonded pdb=" O SER E 328 " pdb=" OG SER E 331 " model vdw 2.257 3.040 nonbonded pdb=" O TYR C 221 " pdb=" OG1 THR C 225 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR B 41 " pdb=" O2A ATP B 501 " model vdw 2.295 3.040 nonbonded pdb=" O LEU E 411 " pdb=" OG SER E 415 " model vdw 2.298 3.040 nonbonded pdb=" O TYR B 221 " pdb=" OG1 THR B 225 " model vdw 2.299 3.040 ... (remaining 154883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 235 or resid 248 through 260 or resid 275 throug \ h 296 or resid 299 through 342 or resid 349 through 444)) selection = (chain 'B' and (resid 3 through 158 or resid 176 through 260 or (resid 275 throu \ gh 287 and (name N or name CA or name C or name O or name CB )) or resid 296 or \ resid 299 through 342 or resid 349 through 383 or resid 389 through 444)) selection = (chain 'C' and (resid 3 through 235 or resid 248 through 260 or resid 275 throug \ h 296 or resid 299 through 383 or resid 389 through 444)) selection = (chain 'D' and (resid 3 through 158 or resid 176 through 260 or (resid 275 throu \ gh 287 and (name N or name CA or name C or name O or name CB )) or resid 298 thr \ ough 342 or resid 349 through 383 or resid 389 through 444)) selection = (chain 'E' and (resid 3 through 235 or resid 248 through 296 or resid 299 throug \ h 342 or resid 349 through 444)) selection = (chain 'F' and (resid 3 through 158 or resid 176 through 235 or resid 248 throug \ h 260 or resid 275 through 296 or resid 299 through 342 or resid 349 through 383 \ or resid 389 through 444)) } ncs_group { reference = chain 'O' selection = chain 'P' } 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.970 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 0.005 0.046 20164 Z= 0.220 Angle : 0.752 10.084 27188 Z= 0.436 Chirality : 0.051 0.268 3017 Planarity : 0.006 0.066 3463 Dihedral : 12.903 88.555 7483 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.65 % Allowed : 6.71 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.11 (0.16), residues: 2389 helix: -0.51 (0.13), residues: 1233 sheet: 0.14 (0.26), residues: 413 loop : -1.37 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 185 TYR 0.018 0.002 TYR B 69 PHE 0.026 0.002 PHE F 100 TRP 0.020 0.002 TRP D 158 HIS 0.024 0.003 HIS D 399 Details of bonding type rmsd covalent geometry : bond 0.00465 (20164) covalent geometry : angle 0.75159 (27188) hydrogen bonds : bond 0.14253 ( 1170) hydrogen bonds : angle 6.65635 ( 3318) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 286 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LEU cc_start: 0.9600 (mt) cc_final: 0.9309 (pp) REVERT: A 97 TYR cc_start: 0.8419 (p90) cc_final: 0.8109 (p90) REVERT: A 186 GLU cc_start: 0.9124 (tt0) cc_final: 0.8824 (tm-30) REVERT: A 203 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8500 (mt) REVERT: A 204 GLU cc_start: 0.8046 (tt0) cc_final: 0.7786 (tp30) REVERT: A 312 GLN cc_start: 0.9145 (tt0) cc_final: 0.8585 (tp-100) REVERT: A 351 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8264 (p) REVERT: A 376 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7854 (mmm) REVERT: B 87 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8340 (t80) REVERT: B 234 PHE cc_start: 0.7822 (t80) cc_final: 0.7462 (t80) REVERT: B 280 GLU cc_start: 0.8889 (tp30) cc_final: 0.8575 (tp30) REVERT: B 315 GLN cc_start: 0.8485 (tt0) cc_final: 0.8163 (tt0) REVERT: C 106 MET cc_start: 0.9275 (mtt) cc_final: 0.8935 (tmm) REVERT: C 372 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: C 382 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8322 (mmtm) REVERT: D 39 LYS cc_start: 0.5366 (OUTLIER) cc_final: 0.2514 (ptpp) REVERT: D 154 MET cc_start: 0.8960 (mtt) cc_final: 0.8015 (mtp) REVERT: D 201 MET cc_start: 0.8598 (tpt) cc_final: 0.8314 (mmp) REVERT: D 326 MET cc_start: 0.9329 (mmt) cc_final: 0.8681 (mmm) REVERT: D 372 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8229 (mm110) REVERT: D 436 MET cc_start: 0.8183 (mtp) cc_final: 0.7891 (tpp) REVERT: E 39 LYS cc_start: 0.4740 (OUTLIER) cc_final: 0.2113 (mmtp) REVERT: E 153 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7756 (m) REVERT: E 190 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8351 (tp-100) REVERT: E 326 MET cc_start: 0.9146 (mmt) cc_final: 0.8873 (mmt) REVERT: E 372 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8288 (mm-40) REVERT: E 437 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8379 (pt) REVERT: F 176 TYR cc_start: 0.6297 (OUTLIER) cc_final: 0.5766 (p90) REVERT: F 326 MET cc_start: 0.9063 (mmt) cc_final: 0.8732 (mmm) REVERT: F 400 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8893 (tp) REVERT: O 48 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.8255 (m-80) REVERT: P 78 ILE cc_start: 0.4885 (tp) cc_final: 0.3992 (tp) REVERT: P 81 LEU cc_start: 0.8371 (mt) cc_final: 0.7898 (mt) REVERT: P 90 THR cc_start: 0.8615 (p) cc_final: 0.8380 (p) outliers start: 117 outliers final: 21 residues processed: 374 average time/residue: 0.1730 time to fit residues: 95.5183 Evaluate side-chains 178 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 158 TRP Chi-restraints excluded: chain C residue 176 TYR Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 360 TRP Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 360 TRP Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 61 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.0030 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 40.0000 overall best weight: 4.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 32 HIS A 94 ASN ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN A 413 GLN B 32 HIS B 196 ASN B 413 GLN C 85 GLN C 141 GLN C 215 GLN ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 ASN D 32 HIS D 35 ASN D 85 GLN E 32 HIS E 85 GLN E 399 HIS F 26 ASN F 32 HIS ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 438 ASN O 82 GLN P 13 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.079886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.052168 restraints weight = 93124.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.053955 restraints weight = 41455.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.055183 restraints weight = 26250.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.055945 restraints weight = 20046.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056305 restraints weight = 17175.155| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20164 Z= 0.282 Angle : 0.681 11.147 27188 Z= 0.359 Chirality : 0.045 0.169 3017 Planarity : 0.005 0.059 3463 Dihedral : 8.859 80.658 2893 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.14 % Allowed : 11.93 % Favored : 84.93 % 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: 0.53 (0.17), residues: 2389 helix: 1.24 (0.14), residues: 1240 sheet: -0.16 (0.26), residues: 435 loop : -0.75 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 110 TYR 0.021 0.002 TYR A 348 PHE 0.016 0.002 PHE C 332 TRP 0.024 0.002 TRP D 158 HIS 0.010 0.002 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00614 (20164) covalent geometry : angle 0.68071 (27188) hydrogen bonds : bond 0.04595 ( 1170) hydrogen bonds : angle 5.32932 ( 3318) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 143 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LEU cc_start: 0.9595 (mt) cc_final: 0.9258 (pp) REVERT: A 97 TYR cc_start: 0.8446 (p90) cc_final: 0.8124 (p90) REVERT: A 312 GLN cc_start: 0.9150 (tt0) cc_final: 0.8640 (tp-100) REVERT: B 87 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8603 (t80) REVERT: B 280 GLU cc_start: 0.8921 (tp30) cc_final: 0.8694 (tp30) REVERT: B 315 GLN cc_start: 0.9069 (tt0) cc_final: 0.8772 (tt0) REVERT: B 360 TRP cc_start: 0.8513 (OUTLIER) cc_final: 0.6849 (t60) REVERT: C 106 MET cc_start: 0.9535 (mtt) cc_final: 0.8924 (tmm) REVERT: C 126 MET cc_start: 0.8857 (mmp) cc_final: 0.8420 (mmp) REVERT: C 372 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7051 (mp10) REVERT: C 382 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8646 (mmtm) REVERT: D 39 LYS cc_start: 0.5264 (OUTLIER) cc_final: 0.3060 (ptpp) REVERT: D 106 MET cc_start: 0.8757 (tpt) cc_final: 0.8475 (mmp) REVERT: D 312 GLN cc_start: 0.9798 (tt0) cc_final: 0.9536 (tm-30) REVERT: D 326 MET cc_start: 0.9381 (mmt) cc_final: 0.8852 (mmm) REVERT: D 372 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8050 (mm110) REVERT: D 436 MET cc_start: 0.8422 (mtp) cc_final: 0.8085 (tpp) REVERT: E 39 LYS cc_start: 0.4468 (OUTLIER) cc_final: 0.2461 (mtmm) REVERT: E 154 MET cc_start: 0.9293 (ptp) cc_final: 0.8931 (ptp) REVERT: E 190 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8259 (tp-100) REVERT: E 210 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8928 (tt0) REVERT: E 372 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8889 (mm110) REVERT: F 129 MET cc_start: 0.9318 (mtt) cc_final: 0.9040 (mpp) REVERT: F 176 TYR cc_start: 0.6031 (OUTLIER) cc_final: 0.4936 (p90) REVERT: F 202 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8260 (tp30) REVERT: F 309 ARG cc_start: 0.9024 (mtt-85) cc_final: 0.8773 (mtt-85) REVERT: F 436 MET cc_start: 0.8883 (mtp) cc_final: 0.8426 (mtt) REVERT: P 5 MET cc_start: 0.8026 (tpp) cc_final: 0.7474 (tmm) REVERT: P 78 ILE cc_start: 0.3764 (tp) cc_final: 0.3148 (tp) outliers start: 65 outliers final: 30 residues processed: 197 average time/residue: 0.1479 time to fit residues: 46.0401 Evaluate side-chains 166 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 360 TRP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain P residue 32 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 12 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 142 optimal weight: 20.0000 chunk 51 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 224 optimal weight: 7.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS B 85 GLN C 32 HIS C 312 GLN ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 HIS ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN P 88 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.079142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.051541 restraints weight = 95395.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.053366 restraints weight = 42894.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.054581 restraints weight = 27191.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.055352 restraints weight = 20877.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.055666 restraints weight = 17894.023| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20164 Z= 0.270 Angle : 0.645 12.963 27188 Z= 0.338 Chirality : 0.044 0.170 3017 Planarity : 0.004 0.047 3463 Dihedral : 8.384 76.523 2864 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.67 % Allowed : 12.31 % Favored : 84.02 % 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: 1.03 (0.18), residues: 2389 helix: 1.70 (0.15), residues: 1236 sheet: -0.23 (0.25), residues: 444 loop : -0.40 (0.26), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 23 TYR 0.016 0.002 TYR C 69 PHE 0.017 0.002 PHE C 332 TRP 0.020 0.002 TRP D 158 HIS 0.007 0.001 HIS D 399 Details of bonding type rmsd covalent geometry : bond 0.00588 (20164) covalent geometry : angle 0.64466 (27188) hydrogen bonds : bond 0.04362 ( 1170) hydrogen bonds : angle 5.16269 ( 3318) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 136 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LEU cc_start: 0.9577 (mt) cc_final: 0.9203 (pp) REVERT: A 97 TYR cc_start: 0.8499 (p90) cc_final: 0.8204 (p90) REVERT: A 312 GLN cc_start: 0.9143 (tt0) cc_final: 0.8621 (tp-100) REVERT: B 87 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8599 (t80) REVERT: B 315 GLN cc_start: 0.9110 (tt0) cc_final: 0.8697 (tt0) REVERT: B 360 TRP cc_start: 0.8602 (OUTLIER) cc_final: 0.6784 (t60) REVERT: C 106 MET cc_start: 0.9550 (mtt) cc_final: 0.8915 (tmm) REVERT: C 144 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8053 (ttp80) REVERT: D 39 LYS cc_start: 0.5458 (OUTLIER) cc_final: 0.3023 (ptpp) REVERT: D 106 MET cc_start: 0.8774 (tpt) cc_final: 0.8560 (mmp) REVERT: D 312 GLN cc_start: 0.9788 (tt0) cc_final: 0.9546 (tm-30) REVERT: D 326 MET cc_start: 0.9410 (mmt) cc_final: 0.8888 (mmp) REVERT: D 338 MET cc_start: 0.9245 (tpt) cc_final: 0.8513 (tpt) REVERT: D 372 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8028 (mm110) REVERT: D 436 MET cc_start: 0.8483 (mtp) cc_final: 0.8171 (tpp) REVERT: E 39 LYS cc_start: 0.4532 (OUTLIER) cc_final: 0.2239 (mtmm) REVERT: E 154 MET cc_start: 0.9299 (ptp) cc_final: 0.9010 (ptp) REVERT: E 372 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8988 (mm110) REVERT: E 437 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8409 (pt) REVERT: F 129 MET cc_start: 0.9301 (mtt) cc_final: 0.9039 (mpp) REVERT: F 176 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.4843 (p90) REVERT: F 309 ARG cc_start: 0.9086 (mtt-85) cc_final: 0.8816 (mtt-85) REVERT: F 326 MET cc_start: 0.8993 (mmm) cc_final: 0.8759 (mmm) REVERT: F 392 ASP cc_start: 0.8566 (t0) cc_final: 0.8319 (t0) REVERT: F 436 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8346 (mtt) REVERT: P 82 GLN cc_start: 0.8459 (mt0) cc_final: 0.8248 (mp10) outliers start: 76 outliers final: 41 residues processed: 196 average time/residue: 0.1428 time to fit residues: 44.8496 Evaluate side-chains 169 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 360 TRP Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 61 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 3 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 238 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 122 optimal weight: 30.0000 chunk 200 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 185 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 ASN ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.079042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.051598 restraints weight = 94747.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.053332 restraints weight = 44991.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.054446 restraints weight = 29192.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.055246 restraints weight = 22822.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.055623 restraints weight = 19606.141| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 20164 Z= 0.260 Angle : 0.631 12.358 27188 Z= 0.329 Chirality : 0.044 0.214 3017 Planarity : 0.004 0.047 3463 Dihedral : 8.345 77.669 2862 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.86 % Allowed : 13.52 % Favored : 82.62 % 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: 1.06 (0.18), residues: 2389 helix: 1.71 (0.15), residues: 1241 sheet: -0.27 (0.25), residues: 434 loop : -0.34 (0.26), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 23 TYR 0.016 0.002 TYR C 314 PHE 0.022 0.001 PHE F 230 TRP 0.031 0.002 TRP D 402 HIS 0.012 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00569 (20164) covalent geometry : angle 0.63054 (27188) hydrogen bonds : bond 0.04229 ( 1170) hydrogen bonds : angle 5.10521 ( 3318) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 128 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LEU cc_start: 0.9465 (mt) cc_final: 0.9194 (pp) REVERT: A 312 GLN cc_start: 0.8895 (tt0) cc_final: 0.8565 (tp-100) REVERT: B 315 GLN cc_start: 0.8874 (tt0) cc_final: 0.8598 (tt0) REVERT: B 360 TRP cc_start: 0.8698 (OUTLIER) cc_final: 0.6801 (t60) REVERT: C 106 MET cc_start: 0.9410 (mtt) cc_final: 0.8873 (tmm) REVERT: C 413 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: D 39 LYS cc_start: 0.5582 (OUTLIER) cc_final: 0.1944 (mtmm) REVERT: D 312 GLN cc_start: 0.9750 (tt0) cc_final: 0.9500 (tm-30) REVERT: D 338 MET cc_start: 0.9152 (tpt) cc_final: 0.8505 (ttt) REVERT: D 372 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8191 (mm110) REVERT: D 436 MET cc_start: 0.8349 (mtp) cc_final: 0.8101 (tpp) REVERT: E 39 LYS cc_start: 0.4660 (OUTLIER) cc_final: 0.2062 (mtmm) REVERT: E 154 MET cc_start: 0.9250 (ptp) cc_final: 0.8991 (ptp) REVERT: E 190 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8204 (tp-100) REVERT: E 201 MET cc_start: 0.7581 (mmm) cc_final: 0.7318 (mmp) REVERT: E 308 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8530 (tt) REVERT: E 372 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8952 (mm110) REVERT: E 437 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8324 (pt) REVERT: F 309 ARG cc_start: 0.9067 (mtt-85) cc_final: 0.8759 (mtt-85) REVERT: F 338 MET cc_start: 0.9091 (ttp) cc_final: 0.8677 (ttp) REVERT: P 82 GLN cc_start: 0.8528 (mt0) cc_final: 0.8257 (mt0) outliers start: 80 outliers final: 53 residues processed: 192 average time/residue: 0.1397 time to fit residues: 43.2788 Evaluate side-chains 175 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 115 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 360 TRP Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain P residue 99 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 52 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 190 optimal weight: 0.0670 chunk 234 optimal weight: 40.0000 chunk 14 optimal weight: 0.6980 chunk 235 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 24 optimal weight: 8.9990 chunk 213 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 ASN C 413 GLN C 424 HIS D 85 GLN ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.081392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.054429 restraints weight = 93675.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.056305 restraints weight = 43888.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.057571 restraints weight = 28093.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.058211 restraints weight = 21582.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.058760 restraints weight = 18762.250| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20164 Z= 0.102 Angle : 0.508 8.061 27188 Z= 0.268 Chirality : 0.042 0.198 3017 Planarity : 0.003 0.042 3463 Dihedral : 7.800 77.958 2860 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.32 % Allowed : 14.73 % Favored : 82.96 % 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: 1.53 (0.18), residues: 2389 helix: 2.10 (0.15), residues: 1236 sheet: 0.02 (0.26), residues: 410 loop : -0.17 (0.25), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 305 TYR 0.013 0.001 TYR P 49 PHE 0.011 0.001 PHE B 87 TRP 0.024 0.001 TRP D 402 HIS 0.006 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00210 (20164) covalent geometry : angle 0.50817 (27188) hydrogen bonds : bond 0.03508 ( 1170) hydrogen bonds : angle 4.52098 ( 3318) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.9135 (m) cc_final: 0.8863 (t) REVERT: A 312 GLN cc_start: 0.8805 (tt0) cc_final: 0.8477 (tp-100) REVERT: A 376 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8288 (mmm) REVERT: B 280 GLU cc_start: 0.8619 (tp30) cc_final: 0.8298 (tp30) REVERT: C 106 MET cc_start: 0.9361 (mtt) cc_final: 0.8924 (tmm) REVERT: C 413 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8228 (tm-30) REVERT: C 436 MET cc_start: 0.8921 (mmm) cc_final: 0.8648 (mmm) REVERT: D 39 LYS cc_start: 0.5290 (OUTLIER) cc_final: 0.1513 (mtmm) REVERT: D 312 GLN cc_start: 0.9763 (tt0) cc_final: 0.9497 (tm-30) REVERT: D 338 MET cc_start: 0.9233 (tpt) cc_final: 0.8560 (ttt) REVERT: D 372 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8150 (mm110) REVERT: D 436 MET cc_start: 0.8345 (mtp) cc_final: 0.8084 (tpp) REVERT: E 39 LYS cc_start: 0.4485 (OUTLIER) cc_final: 0.1944 (mtmm) REVERT: E 152 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8484 (ptt-90) REVERT: E 154 MET cc_start: 0.9138 (ptp) cc_final: 0.8903 (ptp) REVERT: E 190 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8224 (tp-100) REVERT: E 201 MET cc_start: 0.7714 (mmm) cc_final: 0.7443 (mmm) REVERT: E 437 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8366 (pt) REVERT: F 309 ARG cc_start: 0.9027 (mtt-85) cc_final: 0.8684 (mtt-85) REVERT: F 326 MET cc_start: 0.8817 (mmm) cc_final: 0.8598 (mmm) REVERT: P 82 GLN cc_start: 0.8406 (mt0) cc_final: 0.8201 (mt0) outliers start: 48 outliers final: 28 residues processed: 184 average time/residue: 0.1423 time to fit residues: 42.1051 Evaluate side-chains 157 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 49 TYR Chi-restraints excluded: chain P residue 99 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 93 optimal weight: 0.6980 chunk 196 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 chunk 239 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 ASN P 13 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.082462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.056645 restraints weight = 95299.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.058404 restraints weight = 46166.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.059580 restraints weight = 30005.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.060150 restraints weight = 23278.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.060658 restraints weight = 20402.719| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20164 Z= 0.125 Angle : 0.522 9.284 27188 Z= 0.273 Chirality : 0.042 0.194 3017 Planarity : 0.003 0.039 3463 Dihedral : 7.404 78.052 2853 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.32 % Allowed : 15.21 % Favored : 82.47 % 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: 1.64 (0.18), residues: 2389 helix: 2.20 (0.15), residues: 1229 sheet: 0.07 (0.26), residues: 419 loop : -0.11 (0.25), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 305 TYR 0.013 0.001 TYR P 49 PHE 0.011 0.001 PHE P 11 TRP 0.029 0.001 TRP D 402 HIS 0.011 0.001 HIS D 399 Details of bonding type rmsd covalent geometry : bond 0.00270 (20164) covalent geometry : angle 0.52250 (27188) hydrogen bonds : bond 0.03522 ( 1170) hydrogen bonds : angle 4.50898 ( 3318) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 312 GLN cc_start: 0.8783 (tt0) cc_final: 0.8487 (tp-100) REVERT: A 376 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8289 (mmm) REVERT: B 87 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.8208 (t80) REVERT: B 280 GLU cc_start: 0.8578 (tp30) cc_final: 0.8359 (tp30) REVERT: C 106 MET cc_start: 0.9316 (mtt) cc_final: 0.8910 (tmm) REVERT: C 152 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7997 (ptt-90) REVERT: C 382 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8662 (mmtm) REVERT: C 413 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8370 (tm-30) REVERT: D 39 LYS cc_start: 0.5418 (OUTLIER) cc_final: 0.1664 (mtmm) REVERT: D 312 GLN cc_start: 0.9769 (tt0) cc_final: 0.9463 (tm-30) REVERT: D 338 MET cc_start: 0.9216 (tpt) cc_final: 0.8517 (ttt) REVERT: D 372 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8139 (mm110) REVERT: D 436 MET cc_start: 0.8268 (mtp) cc_final: 0.8024 (tpp) REVERT: E 39 LYS cc_start: 0.4531 (OUTLIER) cc_final: 0.1761 (mtmm) REVERT: E 152 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8532 (ptt-90) REVERT: E 154 MET cc_start: 0.9146 (ptp) cc_final: 0.8931 (ptp) REVERT: E 190 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8253 (tp-100) REVERT: E 201 MET cc_start: 0.7725 (mmm) cc_final: 0.7380 (mmp) REVERT: E 210 GLU cc_start: 0.9277 (mt-10) cc_final: 0.9063 (tt0) REVERT: E 383 MET cc_start: 0.8421 (tmm) cc_final: 0.8052 (tmm) REVERT: F 186 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8376 (tm-30) REVERT: F 309 ARG cc_start: 0.9039 (mtt-85) cc_final: 0.8679 (mtt-85) REVERT: P 82 GLN cc_start: 0.8428 (mt0) cc_final: 0.8203 (mt0) outliers start: 48 outliers final: 32 residues processed: 159 average time/residue: 0.1433 time to fit residues: 36.5377 Evaluate side-chains 155 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 49 TYR Chi-restraints excluded: chain P residue 99 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 142 optimal weight: 0.0370 chunk 174 optimal weight: 7.9990 chunk 222 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 156 optimal weight: 30.0000 chunk 39 optimal weight: 0.0270 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 GLN 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 = 0.083215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.057756 restraints weight = 93885.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.059516 restraints weight = 44805.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.060705 restraints weight = 28873.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.061367 restraints weight = 22259.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.061827 restraints weight = 19287.564| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20164 Z= 0.101 Angle : 0.518 11.681 27188 Z= 0.267 Chirality : 0.041 0.174 3017 Planarity : 0.003 0.035 3463 Dihedral : 7.199 77.952 2853 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.12 % Allowed : 15.31 % Favored : 82.57 % 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: 1.79 (0.18), residues: 2389 helix: 2.28 (0.15), residues: 1231 sheet: 0.25 (0.26), residues: 415 loop : -0.05 (0.25), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 305 TYR 0.012 0.001 TYR P 49 PHE 0.016 0.001 PHE D 151 TRP 0.031 0.001 TRP D 402 HIS 0.006 0.001 HIS D 399 Details of bonding type rmsd covalent geometry : bond 0.00211 (20164) covalent geometry : angle 0.51826 (27188) hydrogen bonds : bond 0.03340 ( 1170) hydrogen bonds : angle 4.34401 ( 3318) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7767 (ptt-90) REVERT: A 154 MET cc_start: 0.8430 (mtp) cc_final: 0.7826 (mtp) REVERT: A 312 GLN cc_start: 0.8740 (tt0) cc_final: 0.8463 (tp-100) REVERT: B 87 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7832 (t80) REVERT: C 382 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8592 (mmtm) REVERT: C 436 MET cc_start: 0.8758 (mmm) cc_final: 0.8545 (mmm) REVERT: D 39 LYS cc_start: 0.5326 (OUTLIER) cc_final: 0.1670 (mtmm) REVERT: D 312 GLN cc_start: 0.9774 (tt0) cc_final: 0.9444 (tm-30) REVERT: D 338 MET cc_start: 0.9186 (tpt) cc_final: 0.8535 (ttt) REVERT: D 372 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8167 (mm110) REVERT: D 436 MET cc_start: 0.8221 (mtp) cc_final: 0.8001 (tpp) REVERT: E 39 LYS cc_start: 0.4479 (OUTLIER) cc_final: 0.1685 (mtmm) REVERT: E 154 MET cc_start: 0.9161 (ptp) cc_final: 0.8951 (ptp) REVERT: E 190 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8227 (tp-100) REVERT: E 201 MET cc_start: 0.7789 (mmm) cc_final: 0.7416 (mmp) REVERT: E 383 MET cc_start: 0.8409 (tmm) cc_final: 0.8108 (tmm) REVERT: F 186 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8439 (tm-30) REVERT: F 309 ARG cc_start: 0.9020 (mtt-85) cc_final: 0.8645 (mtt-85) REVERT: F 326 MET cc_start: 0.9115 (tpp) cc_final: 0.8627 (mmm) outliers start: 44 outliers final: 26 residues processed: 162 average time/residue: 0.1276 time to fit residues: 33.3393 Evaluate side-chains 150 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 99 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 3.9990 chunk 198 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 216 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 202 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 HIS P 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.082388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.056729 restraints weight = 92983.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.058495 restraints weight = 44323.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.059683 restraints weight = 28566.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.060346 restraints weight = 22012.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.060604 restraints weight = 19060.040| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20164 Z= 0.136 Angle : 0.549 10.720 27188 Z= 0.280 Chirality : 0.042 0.174 3017 Planarity : 0.003 0.035 3463 Dihedral : 7.098 78.093 2849 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.27 % Allowed : 15.64 % Favored : 82.09 % 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 (0.18), residues: 2389 helix: 2.28 (0.15), residues: 1232 sheet: 0.30 (0.26), residues: 422 loop : -0.02 (0.26), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 305 TYR 0.012 0.001 TYR P 49 PHE 0.014 0.001 PHE A 435 TRP 0.027 0.001 TRP D 402 HIS 0.006 0.001 HIS D 399 Details of bonding type rmsd covalent geometry : bond 0.00296 (20164) covalent geometry : angle 0.54881 (27188) hydrogen bonds : bond 0.03451 ( 1170) hydrogen bonds : angle 4.44229 ( 3318) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7766 (t80) REVERT: C 436 MET cc_start: 0.8692 (mmm) cc_final: 0.8468 (mmm) REVERT: D 39 LYS cc_start: 0.5513 (OUTLIER) cc_final: 0.1981 (mtmm) REVERT: D 312 GLN cc_start: 0.9750 (tt0) cc_final: 0.9428 (tm-30) REVERT: D 338 MET cc_start: 0.9126 (tpt) cc_final: 0.8492 (ttt) REVERT: D 372 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8183 (mm110) REVERT: D 436 MET cc_start: 0.8129 (mtp) cc_final: 0.7899 (tpp) REVERT: E 39 LYS cc_start: 0.4672 (OUTLIER) cc_final: 0.1832 (mtmm) REVERT: E 152 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8469 (ptt-90) REVERT: E 154 MET cc_start: 0.9203 (ptp) cc_final: 0.8940 (ptp) REVERT: E 190 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8228 (tp-100) REVERT: E 201 MET cc_start: 0.7824 (mmm) cc_final: 0.7455 (mmp) REVERT: E 383 MET cc_start: 0.8487 (tmm) cc_final: 0.8224 (tmm) REVERT: E 437 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8370 (pt) REVERT: F 309 ARG cc_start: 0.9010 (mtt-85) cc_final: 0.8621 (mtt-85) REVERT: F 326 MET cc_start: 0.9140 (tpp) cc_final: 0.8530 (mmm) outliers start: 47 outliers final: 33 residues processed: 161 average time/residue: 0.1314 time to fit residues: 33.7278 Evaluate side-chains 154 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 25 PHE Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 82 GLN Chi-restraints excluded: chain P residue 99 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 191 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.082456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.057002 restraints weight = 93477.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.058674 restraints weight = 46140.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.059805 restraints weight = 30407.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.060388 restraints weight = 23666.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.060894 restraints weight = 20722.951| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20164 Z= 0.118 Angle : 0.560 14.279 27188 Z= 0.282 Chirality : 0.042 0.185 3017 Planarity : 0.003 0.034 3463 Dihedral : 6.927 78.312 2843 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.27 % Allowed : 15.84 % Favored : 81.89 % 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 (0.18), residues: 2389 helix: 2.25 (0.15), residues: 1239 sheet: 0.34 (0.26), residues: 426 loop : -0.02 (0.26), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 305 TYR 0.013 0.001 TYR P 49 PHE 0.016 0.001 PHE A 435 TRP 0.026 0.001 TRP D 402 HIS 0.006 0.001 HIS D 399 Details of bonding type rmsd covalent geometry : bond 0.00254 (20164) covalent geometry : angle 0.56037 (27188) hydrogen bonds : bond 0.03414 ( 1170) hydrogen bonds : angle 4.41271 ( 3318) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7867 (ptt-90) REVERT: A 376 MET cc_start: 0.8839 (mmm) cc_final: 0.8494 (tpp) REVERT: B 87 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7858 (t80) REVERT: C 152 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8021 (ptt-90) REVERT: C 311 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8324 (ttp-170) REVERT: C 376 MET cc_start: 0.8311 (mmm) cc_final: 0.7974 (mmt) REVERT: C 436 MET cc_start: 0.8752 (mmm) cc_final: 0.8508 (mmm) REVERT: D 39 LYS cc_start: 0.5458 (OUTLIER) cc_final: 0.2033 (mtmm) REVERT: D 312 GLN cc_start: 0.9768 (tt0) cc_final: 0.9447 (tm-30) REVERT: D 338 MET cc_start: 0.9191 (tpt) cc_final: 0.8520 (ttt) REVERT: D 372 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8139 (mm110) REVERT: D 436 MET cc_start: 0.8211 (mtp) cc_final: 0.7954 (tpp) REVERT: E 39 LYS cc_start: 0.4599 (OUTLIER) cc_final: 0.1681 (mtmm) REVERT: E 154 MET cc_start: 0.9211 (ptp) cc_final: 0.8992 (ptp) REVERT: E 190 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8217 (tp-100) REVERT: E 201 MET cc_start: 0.7663 (mmm) cc_final: 0.7436 (mmm) REVERT: E 383 MET cc_start: 0.8529 (tmm) cc_final: 0.8285 (tmm) REVERT: E 437 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8350 (pt) REVERT: F 309 ARG cc_start: 0.9035 (mtt-85) cc_final: 0.8651 (mtt-85) REVERT: F 326 MET cc_start: 0.9178 (tpp) cc_final: 0.8532 (mmm) outliers start: 47 outliers final: 36 residues processed: 159 average time/residue: 0.1331 time to fit residues: 33.4473 Evaluate side-chains 160 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 25 PHE Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 82 GLN Chi-restraints excluded: chain P residue 99 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 99 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 168 optimal weight: 20.0000 chunk 187 optimal weight: 0.0980 chunk 100 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN C 438 ASN ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 HIS P 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.079882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.053646 restraints weight = 94676.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.055275 restraints weight = 47413.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.056178 restraints weight = 31587.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.057015 restraints weight = 25070.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.057283 restraints weight = 21799.199| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 20164 Z= 0.311 Angle : 0.715 12.143 27188 Z= 0.364 Chirality : 0.046 0.194 3017 Planarity : 0.004 0.036 3463 Dihedral : 7.595 80.724 2843 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.41 % Allowed : 15.93 % Favored : 81.65 % 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: 1.31 (0.18), residues: 2389 helix: 1.84 (0.15), residues: 1238 sheet: 0.09 (0.26), residues: 436 loop : -0.24 (0.26), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 305 TYR 0.015 0.002 TYR C 378 PHE 0.018 0.002 PHE A 435 TRP 0.026 0.002 TRP D 402 HIS 0.007 0.002 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00682 (20164) covalent geometry : angle 0.71540 (27188) hydrogen bonds : bond 0.04254 ( 1170) hydrogen bonds : angle 5.05586 ( 3318) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 112 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8136 (ptt-90) REVERT: A 376 MET cc_start: 0.9055 (mmm) cc_final: 0.8798 (tpp) REVERT: B 87 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.8061 (t80) REVERT: C 152 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8128 (ptt-90) REVERT: C 376 MET cc_start: 0.8608 (mmm) cc_final: 0.8129 (mmt) REVERT: D 39 LYS cc_start: 0.5769 (OUTLIER) cc_final: 0.2160 (mtmm) REVERT: D 312 GLN cc_start: 0.9765 (tt0) cc_final: 0.9479 (tm-30) REVERT: D 338 MET cc_start: 0.9132 (tpt) cc_final: 0.8804 (tpt) REVERT: D 372 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8155 (mm110) REVERT: D 436 MET cc_start: 0.8301 (mtp) cc_final: 0.7960 (tpp) REVERT: E 39 LYS cc_start: 0.4793 (OUTLIER) cc_final: 0.1946 (mtmm) REVERT: E 152 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8170 (ptt-90) REVERT: E 190 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8186 (tp-100) REVERT: E 383 MET cc_start: 0.8714 (tmm) cc_final: 0.8415 (tmm) REVERT: E 437 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8310 (pt) REVERT: F 309 ARG cc_start: 0.9086 (mtt-85) cc_final: 0.8819 (mtt-85) outliers start: 50 outliers final: 32 residues processed: 151 average time/residue: 0.1421 time to fit residues: 33.9999 Evaluate side-chains 146 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 25 PHE Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 82 GLN Chi-restraints excluded: chain P residue 99 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 139 optimal weight: 9.9990 chunk 160 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 222 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 235 optimal weight: 30.0000 chunk 136 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 164 optimal weight: 0.0870 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** F 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.081844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.056448 restraints weight = 92407.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.058068 restraints weight = 45429.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.059162 restraints weight = 29944.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.059735 restraints weight = 23350.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.060271 restraints weight = 20481.564| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20164 Z= 0.131 Angle : 0.589 12.168 27188 Z= 0.297 Chirality : 0.042 0.166 3017 Planarity : 0.003 0.037 3463 Dihedral : 7.245 80.446 2843 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.98 % Allowed : 16.66 % Favored : 81.36 % 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: 1.70 (0.18), residues: 2389 helix: 2.16 (0.15), residues: 1231 sheet: 0.15 (0.26), residues: 437 loop : 0.04 (0.26), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 305 TYR 0.013 0.001 TYR C 378 PHE 0.013 0.001 PHE A 435 TRP 0.032 0.001 TRP D 402 HIS 0.006 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00285 (20164) covalent geometry : angle 0.58881 (27188) hydrogen bonds : bond 0.03625 ( 1170) hydrogen bonds : angle 4.66603 ( 3318) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4111.51 seconds wall clock time: 71 minutes 37.26 seconds (4297.26 seconds total)