Starting phenix.real_space_refine on Wed Nov 19 05:28:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c1h_7331/11_2025/6c1h_7331.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c1h_7331/11_2025/6c1h_7331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6c1h_7331/11_2025/6c1h_7331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c1h_7331/11_2025/6c1h_7331.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6c1h_7331/11_2025/6c1h_7331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c1h_7331/11_2025/6c1h_7331.map" } resolution = 3.9 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= -0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 126 5.16 5 C 13105 2.51 5 N 3625 2.21 5 O 4095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20966 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "B" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "C" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "E" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "P" Number of atoms: 5570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5570 Classifications: {'peptide': 729} Incomplete info: {'backbone_only': 71, 'n_c_alpha_c_only': 1} Link IDs: {'CIS': 8, 'PCIS': 3, 'PTRANS': 20, 'TRANS': 697} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 367 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'TYR:plan': 4, 'GLU:plan': 8, 'ARG:plan': 6, 'GLN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 185 Chain: "R" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 591 Classifications: {'peptide': 148} Incomplete info: {'backbone_only': 136, 'n_c_alpha_c_only': 1} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 143} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 587 Unresolved non-hydrogen angles: 842 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 173 Planarities with less than four sites: {'ASP:plan': 17, 'GLN:plan1': 6, 'GLU:plan': 21, 'PHE:plan': 8, 'ARG:plan': 6, 'ASN:plan1': 6, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 308 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.75, per 1000 atoms: 0.23 Number of scatterers: 20966 At special positions: 0 Unit cell: (202.8, 109.2, 193.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 126 16.00 P 10 15.00 Mg 5 11.99 O 4095 8.00 N 3625 7.00 C 13105 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: 1.45 Conformation dependent library (CDL) restraints added in 906.9 milliseconds 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4714 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 32 sheets defined 51.9% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.624A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.696A pdb=" N LEU A 65 " --> pdb=" O ARG A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.651A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.911A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.740A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.590A pdb=" N GLU A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.720A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 349 through 355 removed outlier: 3.880A pdb=" N PHE A 352 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.724A pdb=" N ALA A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.625A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.696A pdb=" N LEU B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.652A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.911A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.739A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 197 Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 251 through 254 Processing helix chain 'B' and resid 255 through 263 removed outlier: 3.590A pdb=" N GLU B 259 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.720A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 349 through 355 removed outlier: 3.880A pdb=" N PHE B 352 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 366 removed outlier: 3.724A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.624A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.695A pdb=" N LEU C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.651A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.911A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.739A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 197 Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 251 through 254 Processing helix chain 'C' and resid 255 through 263 removed outlier: 3.590A pdb=" N GLU C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.719A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 355 removed outlier: 3.880A pdb=" N PHE C 352 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 366 removed outlier: 3.724A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.624A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.695A pdb=" N LEU D 65 " --> pdb=" O ARG D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.652A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.911A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.740A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 197 Processing helix chain 'D' and resid 202 through 216 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 251 through 254 Processing helix chain 'D' and resid 255 through 263 removed outlier: 3.590A pdb=" N GLU D 259 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.720A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 349 through 355 removed outlier: 3.880A pdb=" N PHE D 352 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.724A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 removed outlier: 3.625A pdb=" N GLN E 59 " --> pdb=" O GLY E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.696A pdb=" N LEU E 65 " --> pdb=" O ARG E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.651A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.911A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.739A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 197 Processing helix chain 'E' and resid 202 through 216 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 251 through 254 Processing helix chain 'E' and resid 255 through 263 removed outlier: 3.590A pdb=" N GLU E 259 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU E 261 " --> pdb=" O CYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.720A pdb=" N ALA E 319 " --> pdb=" O LYS E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 349 through 355 removed outlier: 3.880A pdb=" N PHE E 352 " --> pdb=" O LEU E 349 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 366 removed outlier: 3.724A pdb=" N ALA E 365 " --> pdb=" O GLU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'P' and resid 19 through 23 Processing helix chain 'P' and resid 27 through 41 removed outlier: 3.640A pdb=" N PHE P 31 " --> pdb=" O ASN P 27 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP P 33 " --> pdb=" O GLU P 29 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS P 41 " --> pdb=" O LYS P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 64 removed outlier: 3.872A pdb=" N TYR P 64 " --> pdb=" O LEU P 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 61 through 64' Processing helix chain 'P' and resid 65 through 73 removed outlier: 3.713A pdb=" N GLU P 70 " --> pdb=" O PRO P 66 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP P 71 " --> pdb=" O GLU P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 97 removed outlier: 3.759A pdb=" N ARG P 93 " --> pdb=" O ASP P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 113 through 129 Processing helix chain 'P' and resid 131 through 153 removed outlier: 3.848A pdb=" N VAL P 135 " --> pdb=" O LYS P 131 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN P 141 " --> pdb=" O GLN P 137 " (cutoff:3.500A) Proline residue: P 147 - end of helix removed outlier: 3.631A pdb=" N PHE P 152 " --> pdb=" O VAL P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 197 removed outlier: 4.182A pdb=" N VAL P 196 " --> pdb=" O LYS P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 205 through 215 removed outlier: 4.220A pdb=" N TYR P 209 " --> pdb=" O PHE P 205 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA P 215 " --> pdb=" O LEU P 211 " (cutoff:3.500A) Processing helix chain 'P' and resid 216 through 223 Processing helix chain 'P' and resid 228 through 232 removed outlier: 3.554A pdb=" N ARG P 231 " --> pdb=" O ASP P 228 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR P 232 " --> pdb=" O PHE P 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 228 through 232' Processing helix chain 'P' and resid 246 through 262 removed outlier: 3.645A pdb=" N ARG P 252 " --> pdb=" O ALA P 248 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 281 Processing helix chain 'P' and resid 282 through 284 No H-bonds generated for 'chain 'P' and resid 282 through 284' Processing helix chain 'P' and resid 303 through 314 Processing helix chain 'P' and resid 316 through 325 removed outlier: 3.920A pdb=" N LEU P 320 " --> pdb=" O ASP P 316 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER P 325 " --> pdb=" O GLU P 321 " (cutoff:3.500A) Processing helix chain 'P' and resid 341 through 373 removed outlier: 3.803A pdb=" N GLU P 370 " --> pdb=" O ASN P 366 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER P 371 " --> pdb=" O ARG P 367 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE P 372 " --> pdb=" O ILE P 368 " (cutoff:3.500A) Processing helix chain 'P' and resid 398 through 430 Processing helix chain 'P' and resid 442 through 451 removed outlier: 3.546A pdb=" N ASN P 451 " --> pdb=" O ASP P 447 " (cutoff:3.500A) Processing helix chain 'P' and resid 455 through 466 removed outlier: 3.553A pdb=" N MET P 459 " --> pdb=" O GLY P 455 " (cutoff:3.500A) Processing helix chain 'P' and resid 471 through 483 Processing helix chain 'P' and resid 525 through 531 removed outlier: 3.694A pdb=" N ASN P 531 " --> pdb=" O VAL P 527 " (cutoff:3.500A) Processing helix chain 'P' and resid 535 through 545 removed outlier: 3.635A pdb=" N SER P 539 " --> pdb=" O TYR P 535 " (cutoff:3.500A) Processing helix chain 'P' and resid 547 through 554 Processing helix chain 'P' and resid 555 through 558 removed outlier: 3.963A pdb=" N ASN P 558 " --> pdb=" O PRO P 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 555 through 558' Processing helix chain 'P' and resid 569 through 587 Processing helix chain 'P' and resid 608 through 620 Processing helix chain 'P' and resid 620 through 629 removed outlier: 3.580A pdb=" N ASN P 624 " --> pdb=" O GLY P 620 " (cutoff:3.500A) Processing helix chain 'P' and resid 638 through 645 Processing helix chain 'P' and resid 646 through 649 removed outlier: 3.603A pdb=" N CYS P 649 " --> pdb=" O LYS P 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 646 through 649' Processing helix chain 'P' and resid 659 through 671 Processing helix chain 'P' and resid 674 through 676 No H-bonds generated for 'chain 'P' and resid 674 through 676' Processing helix chain 'P' and resid 689 through 731 removed outlier: 4.104A pdb=" N LEU P 693 " --> pdb=" O ASN P 689 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU P 705 " --> pdb=" O LYS P 701 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP P 706 " --> pdb=" O GLN P 702 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 19 removed outlier: 4.047A pdb=" N GLU R 11 " --> pdb=" O GLU R 7 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE R 19 " --> pdb=" O ALA R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 39 removed outlier: 3.715A pdb=" N MET R 36 " --> pdb=" O LEU R 32 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU R 39 " --> pdb=" O VAL R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 56 removed outlier: 3.961A pdb=" N VAL R 55 " --> pdb=" O MET R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 76 Processing helix chain 'R' and resid 77 through 79 No H-bonds generated for 'chain 'R' and resid 77 through 79' Processing helix chain 'R' and resid 81 through 93 removed outlier: 3.939A pdb=" N ILE R 85 " --> pdb=" O SER R 81 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 112 Processing helix chain 'R' and resid 117 through 129 Processing helix chain 'R' and resid 140 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.919A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.341A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.918A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.341A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.919A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.341A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.918A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.341A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.918A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AC5, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.341A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC8, first strand: chain 'P' and resid 45 through 48 removed outlier: 6.462A pdb=" N VAL P 52 " --> pdb=" O ARG P 594 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE P 596 " --> pdb=" O VAL P 52 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER P 54 " --> pdb=" O ILE P 596 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY P 108 " --> pdb=" O ILE P 388 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASP P 175 " --> pdb=" O PRO P 180 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 154 through 155 Processing sheet with id=AD1, first strand: chain 'P' and resid 286 through 289 removed outlier: 4.691A pdb=" N GLU P 297 " --> pdb=" O GLU P 289 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 326 through 330 Processing sheet with id=AD3, first strand: chain 'P' and resid 489 through 490 Processing sheet with id=AD4, first strand: chain 'P' and resid 634 through 637 Processing sheet with id=AD5, first strand: chain 'R' and resid 99 through 101 989 hydrogen bonds defined for protein. 2778 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: 4.87 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5555 1.33 - 1.45: 3841 1.45 - 1.57: 11755 1.57 - 1.69: 15 1.69 - 1.81: 216 Bond restraints: 21382 Sorted by residual: bond pdb=" CA PRO P 568 " pdb=" C PRO P 568 " ideal model delta sigma weight residual 1.520 1.556 -0.036 1.42e-02 4.96e+03 6.44e+00 bond pdb=" C SER P 81 " pdb=" N PRO P 82 " ideal model delta sigma weight residual 1.331 1.359 -0.028 1.20e-02 6.94e+03 5.43e+00 bond pdb=" N LYS P 495 " pdb=" CA LYS P 495 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.31e+00 bond pdb=" C PRO P 568 " pdb=" N THR P 569 " ideal model delta sigma weight residual 1.329 1.359 -0.030 1.40e-02 5.10e+03 4.64e+00 bond pdb=" CA ARG D 95 " pdb=" CB ARG D 95 " ideal model delta sigma weight residual 1.533 1.506 0.028 1.37e-02 5.33e+03 4.10e+00 ... (remaining 21377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 28118 2.46 - 4.91: 642 4.91 - 7.37: 102 7.37 - 9.82: 10 9.82 - 12.28: 3 Bond angle restraints: 28875 Sorted by residual: angle pdb=" C SER P 494 " pdb=" N LYS P 495 " pdb=" CA LYS P 495 " ideal model delta sigma weight residual 121.70 133.98 -12.28 1.80e+00 3.09e-01 4.65e+01 angle pdb=" N ILE B 289 " pdb=" CA ILE B 289 " pdb=" C ILE B 289 " ideal model delta sigma weight residual 113.53 107.52 6.01 9.80e-01 1.04e+00 3.77e+01 angle pdb=" N ILE D 289 " pdb=" CA ILE D 289 " pdb=" C ILE D 289 " ideal model delta sigma weight residual 113.53 107.54 5.99 9.80e-01 1.04e+00 3.74e+01 angle pdb=" N ILE C 289 " pdb=" CA ILE C 289 " pdb=" C ILE C 289 " ideal model delta sigma weight residual 113.53 107.54 5.99 9.80e-01 1.04e+00 3.73e+01 angle pdb=" N ILE E 289 " pdb=" CA ILE E 289 " pdb=" C ILE E 289 " ideal model delta sigma weight residual 113.53 107.55 5.98 9.80e-01 1.04e+00 3.73e+01 ... (remaining 28870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.67: 12381 25.67 - 51.33: 207 51.33 - 77.00: 13 77.00 - 102.66: 1 102.66 - 128.33: 5 Dihedral angle restraints: 12607 sinusoidal: 5042 harmonic: 7565 Sorted by residual: dihedral pdb=" CA ASN P 563 " pdb=" C ASN P 563 " pdb=" N LEU P 564 " pdb=" CA LEU P 564 " ideal model delta harmonic sigma weight residual 180.00 133.51 46.49 0 5.00e+00 4.00e-02 8.65e+01 dihedral pdb=" CA ARG P 629 " pdb=" C ARG P 629 " pdb=" N ALA P 630 " pdb=" CA ALA P 630 " ideal model delta harmonic sigma weight residual -180.00 -137.41 -42.59 0 5.00e+00 4.00e-02 7.25e+01 dihedral pdb=" CA LEU P 564 " pdb=" C LEU P 564 " pdb=" N LYS P 565 " pdb=" CA LYS P 565 " ideal model delta harmonic sigma weight residual 180.00 143.63 36.37 0 5.00e+00 4.00e-02 5.29e+01 ... (remaining 12604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2099 0.051 - 0.101: 740 0.101 - 0.152: 173 0.152 - 0.203: 50 0.203 - 0.253: 11 Chirality restraints: 3073 Sorted by residual: chirality pdb=" CB ILE P 404 " pdb=" CA ILE P 404 " pdb=" CG1 ILE P 404 " pdb=" CG2 ILE P 404 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE C 71 " pdb=" CA ILE C 71 " pdb=" CG1 ILE C 71 " pdb=" CG2 ILE C 71 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE A 71 " pdb=" CA ILE A 71 " pdb=" CG1 ILE A 71 " pdb=" CG2 ILE A 71 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 3070 not shown) Planarity restraints: 3802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG P 466 " 0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO P 467 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO P 467 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO P 467 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG P 629 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.95e+00 pdb=" C ARG P 629 " -0.055 2.00e-02 2.50e+03 pdb=" O ARG P 629 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA P 630 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN P 689 " 0.051 5.00e-02 4.00e+02 7.70e-02 9.49e+00 pdb=" N PRO P 690 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO P 690 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO P 690 " 0.042 5.00e-02 4.00e+02 ... (remaining 3799 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 7 2.27 - 2.93: 8315 2.93 - 3.58: 29433 3.58 - 4.24: 49244 4.24 - 4.90: 81208 Nonbonded interactions: 168207 Sorted by model distance: nonbonded pdb=" CD2 LEU P 142 " pdb=" CE MET P 170 " model vdw 1.611 3.880 nonbonded pdb=" O1A ADP A 401 " pdb="MG MG A 402 " model vdw 2.164 2.170 nonbonded pdb=" O1A ADP C 401 " pdb="MG MG C 402 " model vdw 2.167 2.170 nonbonded pdb=" O1A ADP E 401 " pdb="MG MG E 402 " model vdw 2.185 2.170 nonbonded pdb=" O1A ADP D 401 " pdb="MG MG D 402 " model vdw 2.194 2.170 ... (remaining 168202 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 6.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.790 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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 0.064 21382 Z= 0.234 Angle : 0.925 12.278 28875 Z= 0.535 Chirality : 0.057 0.253 3073 Planarity : 0.007 0.080 3802 Dihedral : 10.022 128.330 7893 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.77 % Favored : 94.19 % Rotamer: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: -4.15 (0.12), residues: 2738 helix: -2.87 (0.10), residues: 1185 sheet: -2.19 (0.24), residues: 360 loop : -2.66 (0.14), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 466 TYR 0.027 0.002 TYR P 47 PHE 0.020 0.002 PHE P 324 TRP 0.034 0.004 TRP A 340 HIS 0.009 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00479 (21382) covalent geometry : angle 0.92492 (28875) hydrogen bonds : bond 0.13680 ( 989) hydrogen bonds : angle 9.70489 ( 2778) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 0.811 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: symmetry clash REVERT: E 190 MET cc_start: 0.8011 (ttp) cc_final: 0.7805 (tmm) REVERT: E 212 ILE cc_start: 0.8868 (mt) cc_final: 0.8640 (tp) REVERT: P 171 ASP cc_start: 0.7756 (m-30) cc_final: 0.7058 (m-30) REVERT: P 211 LEU cc_start: 0.9238 (tp) cc_final: 0.8922 (pp) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.1738 time to fit residues: 65.1111 Evaluate side-chains 143 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 128 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN A 371 HIS ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS B 73 HIS B 128 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN B 371 HIS C 12 ASN C 40 HIS C 128 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN C 371 HIS D 12 ASN D 40 HIS ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN D 371 HIS E 12 ASN E 40 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN E 371 HIS P 83 HIS P 102 GLN P 144 GLN P 206 HIS P 256 ASN P 317 GLN P 355 ASN P 366 ASN P 442 ASN P 486 HIS P 507 HIS P 563 ASN P 589 ASN ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 624 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.030667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.023288 restraints weight = 212624.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.024100 restraints weight = 129998.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.024659 restraints weight = 91305.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.025091 restraints weight = 70028.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.025381 restraints weight = 56894.498| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 21382 Z= 0.264 Angle : 0.771 8.248 28875 Z= 0.395 Chirality : 0.045 0.209 3073 Planarity : 0.005 0.057 3802 Dihedral : 7.258 108.431 3039 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.57 % Allowed : 6.54 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -1.89 (0.15), residues: 2738 helix: -0.35 (0.14), residues: 1273 sheet: -1.55 (0.26), residues: 390 loop : -2.17 (0.17), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 335 TYR 0.019 0.002 TYR C 143 PHE 0.020 0.002 PHE P 31 TRP 0.016 0.002 TRP B 340 HIS 0.010 0.002 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00557 (21382) covalent geometry : angle 0.77060 (28875) hydrogen bonds : bond 0.03855 ( 989) hydrogen bonds : angle 5.74017 ( 2778) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.893 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: A 190 MET cc_start: 0.9199 (ptm) cc_final: 0.8941 (ptp) REVERT: A 269 MET cc_start: 0.8441 (tmm) cc_final: 0.7955 (tmm) REVERT: A 375 PHE cc_start: 0.8003 (m-80) cc_final: 0.7344 (m-80) REVERT: B 82 MET cc_start: 0.9272 (tpp) cc_final: 0.9029 (tpp) REVERT: B 176 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7174 (mpp) REVERT: B 227 MET cc_start: 0.9048 (mmm) cc_final: 0.8702 (mmm) REVERT: B 283 MET cc_start: 0.9295 (mmm) cc_final: 0.9089 (mmp) REVERT: B 299 MET cc_start: 0.8656 (ttt) cc_final: 0.8155 (tmm) REVERT: B 313 MET cc_start: 0.9392 (mmm) cc_final: 0.9013 (mmm) REVERT: C 82 MET cc_start: 0.9205 (tpp) cc_final: 0.8950 (tpp) REVERT: C 123 MET cc_start: 0.9306 (mmm) cc_final: 0.9097 (mmt) REVERT: C 190 MET cc_start: 0.9126 (ttm) cc_final: 0.8871 (ttp) REVERT: C 194 THR cc_start: 0.9462 (OUTLIER) cc_final: 0.9230 (p) REVERT: C 227 MET cc_start: 0.9349 (mmm) cc_final: 0.9044 (mmm) REVERT: C 299 MET cc_start: 0.8660 (ttp) cc_final: 0.8361 (ptm) REVERT: C 305 MET cc_start: 0.8382 (mpp) cc_final: 0.8090 (mpp) REVERT: C 335 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8234 (ptt-90) REVERT: D 39 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8639 (ptt-90) REVERT: D 44 MET cc_start: 0.8973 (mmm) cc_final: 0.8613 (mmm) REVERT: D 47 MET cc_start: 0.8710 (tpp) cc_final: 0.8171 (mmm) REVERT: D 82 MET cc_start: 0.9366 (tpp) cc_final: 0.9076 (tpp) REVERT: E 82 MET cc_start: 0.9500 (tpp) cc_final: 0.9254 (tpp) REVERT: E 123 MET cc_start: 0.9166 (mmp) cc_final: 0.8629 (mmp) REVERT: E 176 MET cc_start: 0.7802 (tmm) cc_final: 0.7560 (tmm) REVERT: E 190 MET cc_start: 0.9259 (ttp) cc_final: 0.8937 (tmm) REVERT: E 227 MET cc_start: 0.9142 (mmm) cc_final: 0.8760 (mmm) REVERT: E 313 MET cc_start: 0.9737 (tpt) cc_final: 0.9389 (mmm) REVERT: P 383 MET cc_start: 0.9531 (tmm) cc_final: 0.9315 (ppp) REVERT: P 447 ASP cc_start: 0.9688 (t0) cc_final: 0.9433 (m-30) REVERT: P 493 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8646 (mmp) outliers start: 34 outliers final: 9 residues processed: 162 average time/residue: 0.1504 time to fit residues: 38.0256 Evaluate side-chains 140 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 493 MET Chi-restraints excluded: chain P residue 499 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 191 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 255 optimal weight: 50.0000 chunk 72 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN D 12 ASN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 317 GLN ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 689 ASN ** 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 = 0.3023 r_free = 0.3023 target = 0.030452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.023051 restraints weight = 218777.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.023885 restraints weight = 129390.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.024459 restraints weight = 89011.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.024872 restraints weight = 67451.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.025152 restraints weight = 54620.977| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 21382 Z= 0.228 Angle : 0.690 8.911 28875 Z= 0.352 Chirality : 0.044 0.143 3073 Planarity : 0.005 0.065 3802 Dihedral : 6.908 108.937 3039 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.41 % Favored : 94.56 % Rotamer: Outliers : 1.34 % Allowed : 7.32 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -1.09 (0.16), residues: 2738 helix: 0.58 (0.14), residues: 1277 sheet: -1.79 (0.24), residues: 420 loop : -1.85 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 335 TYR 0.017 0.001 TYR P 47 PHE 0.010 0.001 PHE P 31 TRP 0.015 0.002 TRP A 79 HIS 0.008 0.002 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00480 (21382) covalent geometry : angle 0.68956 (28875) hydrogen bonds : bond 0.03456 ( 989) hydrogen bonds : angle 5.17066 ( 2778) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8985 (p0) cc_final: 0.8778 (p0) REVERT: A 119 MET cc_start: 0.9431 (ttp) cc_final: 0.8611 (tmm) REVERT: A 123 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8875 (mmp) REVERT: A 132 MET cc_start: 0.8823 (tmm) cc_final: 0.8420 (tmm) REVERT: A 176 MET cc_start: 0.8616 (tpp) cc_final: 0.8272 (tpp) REVERT: A 269 MET cc_start: 0.8495 (tmm) cc_final: 0.8151 (tmm) REVERT: A 375 PHE cc_start: 0.8238 (m-80) cc_final: 0.7522 (m-80) REVERT: B 82 MET cc_start: 0.9165 (tpp) cc_final: 0.8890 (tpp) REVERT: B 176 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7176 (mpp) REVERT: B 227 MET cc_start: 0.9033 (mmm) cc_final: 0.8622 (mmm) REVERT: B 299 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8112 (tmm) REVERT: B 313 MET cc_start: 0.9254 (mmm) cc_final: 0.8730 (mmm) REVERT: B 335 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8299 (ptt90) REVERT: C 39 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8691 (ptp90) REVERT: C 82 MET cc_start: 0.9148 (tpp) cc_final: 0.8945 (tpp) REVERT: C 227 MET cc_start: 0.9326 (mmm) cc_final: 0.8991 (mmm) REVERT: C 299 MET cc_start: 0.8515 (ttp) cc_final: 0.8270 (ptm) REVERT: D 82 MET cc_start: 0.9164 (tpp) cc_final: 0.8876 (tpp) REVERT: D 227 MET cc_start: 0.9354 (mmm) cc_final: 0.9128 (mmm) REVERT: D 263 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: D 299 MET cc_start: 0.8752 (ttm) cc_final: 0.8076 (tmm) REVERT: D 335 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8231 (ptt-90) REVERT: E 44 MET cc_start: 0.8801 (mmm) cc_final: 0.8391 (mmm) REVERT: E 82 MET cc_start: 0.9451 (tpp) cc_final: 0.9176 (tpp) REVERT: E 123 MET cc_start: 0.9294 (mmp) cc_final: 0.8770 (mmp) REVERT: E 176 MET cc_start: 0.8043 (tmm) cc_final: 0.7690 (tmm) REVERT: E 190 MET cc_start: 0.9221 (ttp) cc_final: 0.8985 (tmm) REVERT: E 227 MET cc_start: 0.9256 (mmm) cc_final: 0.8946 (mmm) REVERT: E 299 MET cc_start: 0.8541 (ppp) cc_final: 0.8036 (ppp) REVERT: E 313 MET cc_start: 0.9736 (tpt) cc_final: 0.9349 (mmm) REVERT: P 422 GLU cc_start: 0.9716 (tt0) cc_final: 0.9491 (pt0) REVERT: P 447 ASP cc_start: 0.9657 (t0) cc_final: 0.9403 (m-30) REVERT: P 459 MET cc_start: 0.9470 (mmm) cc_final: 0.9009 (mmt) REVERT: P 582 MET cc_start: 0.9329 (mmt) cc_final: 0.9014 (mmp) outliers start: 29 outliers final: 10 residues processed: 147 average time/residue: 0.1528 time to fit residues: 35.0067 Evaluate side-chains 135 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 499 PHE Chi-restraints excluded: chain P residue 585 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 181 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 268 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN D 12 ASN D 263 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.030640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.023168 restraints weight = 217408.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.024021 restraints weight = 127302.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.024601 restraints weight = 87123.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.025031 restraints weight = 65861.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.025340 restraints weight = 53135.566| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21382 Z= 0.160 Angle : 0.637 8.072 28875 Z= 0.319 Chirality : 0.043 0.145 3073 Planarity : 0.004 0.054 3802 Dihedral : 6.520 101.846 3039 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.55 % Favored : 94.41 % Rotamer: Outliers : 1.34 % Allowed : 8.06 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.43 (0.16), residues: 2738 helix: 1.23 (0.15), residues: 1253 sheet: -1.82 (0.24), residues: 418 loop : -1.43 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 335 TYR 0.015 0.001 TYR P 47 PHE 0.010 0.001 PHE D 266 TRP 0.013 0.002 TRP A 79 HIS 0.006 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00344 (21382) covalent geometry : angle 0.63715 (28875) hydrogen bonds : bond 0.03114 ( 989) hydrogen bonds : angle 4.84401 ( 2778) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.758 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: A 51 ASP cc_start: 0.8951 (p0) cc_final: 0.8653 (t0) REVERT: A 123 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8935 (mmp) REVERT: A 176 MET cc_start: 0.8578 (tpp) cc_final: 0.8285 (tpp) REVERT: A 375 PHE cc_start: 0.8281 (m-80) cc_final: 0.7632 (m-80) REVERT: B 82 MET cc_start: 0.9152 (tpp) cc_final: 0.8846 (tpp) REVERT: B 176 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7056 (mpp) REVERT: B 227 MET cc_start: 0.9005 (mmm) cc_final: 0.8630 (mmm) REVERT: B 299 MET cc_start: 0.8411 (ttt) cc_final: 0.8099 (tmm) REVERT: B 313 MET cc_start: 0.9150 (mmm) cc_final: 0.8643 (mmm) REVERT: C 39 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8551 (ptt-90) REVERT: C 47 MET cc_start: 0.7648 (tpp) cc_final: 0.7160 (tmm) REVERT: C 82 MET cc_start: 0.9045 (tpp) cc_final: 0.8774 (tpp) REVERT: C 227 MET cc_start: 0.9338 (mmm) cc_final: 0.9004 (mmm) REVERT: C 305 MET cc_start: 0.8320 (mpp) cc_final: 0.8065 (mpp) REVERT: D 82 MET cc_start: 0.9160 (tpp) cc_final: 0.8856 (tpp) REVERT: D 227 MET cc_start: 0.9316 (mmm) cc_final: 0.9053 (mmm) REVERT: D 269 MET cc_start: 0.8813 (ttp) cc_final: 0.8610 (ttp) REVERT: D 313 MET cc_start: 0.9474 (mmm) cc_final: 0.9184 (mmm) REVERT: E 82 MET cc_start: 0.9447 (tpp) cc_final: 0.9134 (tpp) REVERT: E 123 MET cc_start: 0.9295 (mmp) cc_final: 0.8850 (mmp) REVERT: E 190 MET cc_start: 0.9185 (ttp) cc_final: 0.8962 (tmm) REVERT: E 227 MET cc_start: 0.9276 (mmm) cc_final: 0.8921 (mmm) REVERT: E 299 MET cc_start: 0.8530 (ppp) cc_final: 0.7929 (ppp) REVERT: E 313 MET cc_start: 0.9709 (OUTLIER) cc_final: 0.9339 (mmm) REVERT: P 447 ASP cc_start: 0.9644 (t0) cc_final: 0.9411 (m-30) REVERT: P 459 MET cc_start: 0.9457 (mmm) cc_final: 0.8974 (mmt) REVERT: P 582 MET cc_start: 0.9349 (mmt) cc_final: 0.8826 (mmp) outliers start: 29 outliers final: 9 residues processed: 145 average time/residue: 0.1480 time to fit residues: 33.8900 Evaluate side-chains 132 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain P residue 35 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 148 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 232 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 12 ASN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN D 12 ASN ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 408 ASN ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.029324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.022006 restraints weight = 223941.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.022818 restraints weight = 130734.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.023391 restraints weight = 89370.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.023796 restraints weight = 67325.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.024076 restraints weight = 54455.105| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 21382 Z= 0.290 Angle : 0.738 9.174 28875 Z= 0.372 Chirality : 0.044 0.171 3073 Planarity : 0.004 0.057 3802 Dihedral : 6.510 104.369 3039 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.50 % Favored : 93.46 % Rotamer: Outliers : 1.52 % Allowed : 8.98 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.35 (0.17), residues: 2738 helix: 1.23 (0.15), residues: 1255 sheet: -1.87 (0.24), residues: 423 loop : -1.25 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 227 TYR 0.018 0.002 TYR P 169 PHE 0.021 0.002 PHE P 176 TRP 0.017 0.002 TRP B 79 HIS 0.010 0.002 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00612 (21382) covalent geometry : angle 0.73846 (28875) hydrogen bonds : bond 0.03478 ( 989) hydrogen bonds : angle 5.03003 ( 2778) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8997 (p0) cc_final: 0.8739 (p0) REVERT: A 123 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.9040 (mmp) REVERT: A 176 MET cc_start: 0.8617 (tpp) cc_final: 0.8292 (tpp) REVERT: A 375 PHE cc_start: 0.8540 (m-80) cc_final: 0.8207 (m-80) REVERT: B 82 MET cc_start: 0.9119 (tpp) cc_final: 0.8802 (tpp) REVERT: B 176 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7017 (mpp) REVERT: B 227 MET cc_start: 0.9024 (mmm) cc_final: 0.8718 (mmm) REVERT: B 299 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8432 (ppp) REVERT: B 313 MET cc_start: 0.9080 (mmm) cc_final: 0.8682 (mmm) REVERT: C 39 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8694 (ptp90) REVERT: C 47 MET cc_start: 0.7756 (tpp) cc_final: 0.7273 (tmm) REVERT: C 227 MET cc_start: 0.9323 (mmm) cc_final: 0.9004 (mmm) REVERT: C 299 MET cc_start: 0.8640 (ppp) cc_final: 0.7490 (ppp) REVERT: C 375 PHE cc_start: 0.8439 (m-80) cc_final: 0.8096 (m-80) REVERT: D 82 MET cc_start: 0.9137 (tpp) cc_final: 0.8857 (tpp) REVERT: D 227 MET cc_start: 0.9324 (mmm) cc_final: 0.9043 (mmm) REVERT: D 313 MET cc_start: 0.9583 (mmm) cc_final: 0.9331 (mmm) REVERT: E 44 MET cc_start: 0.8613 (mmm) cc_final: 0.7069 (tpp) REVERT: E 47 MET cc_start: 0.8090 (mmm) cc_final: 0.6919 (mmm) REVERT: E 82 MET cc_start: 0.9421 (tpp) cc_final: 0.9118 (tpp) REVERT: E 119 MET cc_start: 0.9690 (ttp) cc_final: 0.9124 (ptp) REVERT: E 123 MET cc_start: 0.9374 (mmp) cc_final: 0.8995 (mmp) REVERT: E 190 MET cc_start: 0.9173 (ttp) cc_final: 0.8932 (tmm) REVERT: E 227 MET cc_start: 0.9286 (mmm) cc_final: 0.8916 (mmm) REVERT: E 299 MET cc_start: 0.8636 (ppp) cc_final: 0.7954 (ppp) REVERT: E 313 MET cc_start: 0.9737 (tpt) cc_final: 0.9307 (mmm) REVERT: P 447 ASP cc_start: 0.9621 (t0) cc_final: 0.9341 (m-30) REVERT: P 459 MET cc_start: 0.9486 (mmm) cc_final: 0.9005 (mmt) REVERT: P 582 MET cc_start: 0.9250 (mmt) cc_final: 0.9018 (mmp) outliers start: 33 outliers final: 15 residues processed: 143 average time/residue: 0.1248 time to fit residues: 29.3624 Evaluate side-chains 131 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 171 ASP Chi-restraints excluded: chain P residue 261 VAL Chi-restraints excluded: chain P residue 499 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 226 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.029418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.022122 restraints weight = 221486.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.022928 restraints weight = 128814.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.023507 restraints weight = 88389.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.023910 restraints weight = 66544.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.024208 restraints weight = 53810.871| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 21382 Z= 0.234 Angle : 0.678 8.210 28875 Z= 0.341 Chirality : 0.044 0.165 3073 Planarity : 0.004 0.048 3802 Dihedral : 6.180 104.722 3039 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.06 % Favored : 93.90 % Rotamer: Outliers : 1.43 % Allowed : 9.35 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.13 (0.17), residues: 2738 helix: 1.40 (0.15), residues: 1257 sheet: -1.78 (0.25), residues: 418 loop : -1.14 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 379 TYR 0.015 0.001 TYR P 169 PHE 0.015 0.001 PHE P 499 TRP 0.016 0.002 TRP A 79 HIS 0.008 0.002 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00496 (21382) covalent geometry : angle 0.67782 (28875) hydrogen bonds : bond 0.03289 ( 989) hydrogen bonds : angle 4.86784 ( 2778) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.889 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: A 51 ASP cc_start: 0.9058 (p0) cc_final: 0.8795 (p0) REVERT: A 176 MET cc_start: 0.8664 (tpp) cc_final: 0.8210 (tpp) REVERT: A 375 PHE cc_start: 0.8711 (m-80) cc_final: 0.8378 (m-80) REVERT: B 39 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8517 (ptp-170) REVERT: B 82 MET cc_start: 0.9086 (tpp) cc_final: 0.8802 (tpp) REVERT: B 176 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7066 (mpp) REVERT: B 227 MET cc_start: 0.9046 (mmm) cc_final: 0.8735 (mmm) REVERT: B 299 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8315 (tmm) REVERT: B 313 MET cc_start: 0.9008 (mmm) cc_final: 0.8608 (mmm) REVERT: C 47 MET cc_start: 0.7472 (tpp) cc_final: 0.6808 (tmm) REVERT: C 227 MET cc_start: 0.9318 (mmm) cc_final: 0.8998 (mmm) REVERT: C 299 MET cc_start: 0.8626 (ppp) cc_final: 0.7567 (ppp) REVERT: C 305 MET cc_start: 0.8545 (mpp) cc_final: 0.8130 (mpp) REVERT: C 375 PHE cc_start: 0.8525 (m-80) cc_final: 0.8140 (m-80) REVERT: D 47 MET cc_start: 0.8724 (mmm) cc_final: 0.8498 (mmm) REVERT: D 82 MET cc_start: 0.9144 (tpp) cc_final: 0.8868 (tpp) REVERT: D 227 MET cc_start: 0.9320 (mmm) cc_final: 0.9025 (mmm) REVERT: D 269 MET cc_start: 0.8883 (ttp) cc_final: 0.8651 (ttp) REVERT: D 313 MET cc_start: 0.9528 (mmm) cc_final: 0.9321 (mmm) REVERT: E 44 MET cc_start: 0.8389 (mmm) cc_final: 0.7036 (tpp) REVERT: E 47 MET cc_start: 0.8223 (mmm) cc_final: 0.7393 (mmm) REVERT: E 82 MET cc_start: 0.9440 (tpp) cc_final: 0.9117 (tpp) REVERT: E 119 MET cc_start: 0.9682 (ttp) cc_final: 0.9078 (ptp) REVERT: E 123 MET cc_start: 0.9384 (mmp) cc_final: 0.9017 (mmp) REVERT: E 190 MET cc_start: 0.9159 (ttp) cc_final: 0.8924 (tmm) REVERT: E 227 MET cc_start: 0.9248 (mmm) cc_final: 0.8832 (mmm) REVERT: E 299 MET cc_start: 0.8636 (ppp) cc_final: 0.7893 (ppp) REVERT: E 313 MET cc_start: 0.9716 (tpt) cc_final: 0.9285 (mmm) REVERT: P 447 ASP cc_start: 0.9631 (t0) cc_final: 0.9355 (m-30) REVERT: P 533 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8677 (pt) outliers start: 31 outliers final: 15 residues processed: 137 average time/residue: 0.1327 time to fit residues: 29.7903 Evaluate side-chains 131 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 171 ASP Chi-restraints excluded: chain P residue 499 PHE Chi-restraints excluded: chain P residue 533 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 143 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.030032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.022709 restraints weight = 215898.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.023547 restraints weight = 125334.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.024129 restraints weight = 85446.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.024540 restraints weight = 64291.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.024842 restraints weight = 52002.181| |-----------------------------------------------------------------------------| r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21382 Z= 0.119 Angle : 0.634 9.178 28875 Z= 0.311 Chirality : 0.043 0.196 3073 Planarity : 0.003 0.046 3802 Dihedral : 5.747 94.205 3039 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.01 % Allowed : 10.04 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: 0.21 (0.17), residues: 2738 helix: 1.72 (0.15), residues: 1261 sheet: -1.70 (0.25), residues: 418 loop : -0.97 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 39 TYR 0.014 0.001 TYR A 143 PHE 0.009 0.001 PHE D 262 TRP 0.011 0.002 TRP B 79 HIS 0.008 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00261 (21382) covalent geometry : angle 0.63397 (28875) hydrogen bonds : bond 0.02867 ( 989) hydrogen bonds : angle 4.52854 ( 2778) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8221 (mpp80) REVERT: A 51 ASP cc_start: 0.9016 (p0) cc_final: 0.8681 (t0) REVERT: A 71 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9150 (tt) REVERT: A 176 MET cc_start: 0.8565 (tpp) cc_final: 0.8328 (tpp) REVERT: A 190 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.9072 (ptp) REVERT: A 375 PHE cc_start: 0.8609 (m-80) cc_final: 0.8007 (m-80) REVERT: B 82 MET cc_start: 0.9077 (tpp) cc_final: 0.8777 (tpp) REVERT: B 176 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.6916 (mpp) REVERT: B 227 MET cc_start: 0.9008 (mmm) cc_final: 0.8689 (mmm) REVERT: B 283 MET cc_start: 0.9021 (mmm) cc_final: 0.8676 (mmp) REVERT: B 299 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8090 (tmm) REVERT: B 313 MET cc_start: 0.9062 (mmm) cc_final: 0.8628 (mmm) REVERT: C 227 MET cc_start: 0.9308 (mmm) cc_final: 0.8972 (mmm) REVERT: C 299 MET cc_start: 0.8609 (ppp) cc_final: 0.7543 (ppp) REVERT: C 375 PHE cc_start: 0.8515 (m-80) cc_final: 0.7971 (m-80) REVERT: D 82 MET cc_start: 0.9156 (tpp) cc_final: 0.8869 (tpp) REVERT: D 132 MET cc_start: 0.9100 (tmm) cc_final: 0.8696 (tmm) REVERT: D 269 MET cc_start: 0.8757 (ttp) cc_final: 0.8411 (ptm) REVERT: D 313 MET cc_start: 0.9515 (mmm) cc_final: 0.9314 (mmm) REVERT: E 44 MET cc_start: 0.8329 (mmm) cc_final: 0.6779 (tpp) REVERT: E 47 MET cc_start: 0.8009 (mmm) cc_final: 0.7335 (mmm) REVERT: E 82 MET cc_start: 0.9416 (tpp) cc_final: 0.9062 (tpp) REVERT: E 119 MET cc_start: 0.9640 (ttp) cc_final: 0.9079 (ptp) REVERT: E 123 MET cc_start: 0.9272 (mmp) cc_final: 0.8937 (mmp) REVERT: E 190 MET cc_start: 0.9145 (ttp) cc_final: 0.8913 (tmm) REVERT: E 227 MET cc_start: 0.9224 (mmm) cc_final: 0.8834 (mmm) REVERT: E 299 MET cc_start: 0.8600 (ppp) cc_final: 0.7801 (ppp) REVERT: E 313 MET cc_start: 0.9678 (OUTLIER) cc_final: 0.9265 (mmm) REVERT: P 447 ASP cc_start: 0.9587 (t0) cc_final: 0.9345 (m-30) REVERT: P 459 MET cc_start: 0.9302 (mmm) cc_final: 0.9041 (mmm) REVERT: P 533 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8641 (pt) outliers start: 22 outliers final: 9 residues processed: 132 average time/residue: 0.1387 time to fit residues: 29.5407 Evaluate side-chains 128 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain P residue 533 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 12 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 265 optimal weight: 30.0000 chunk 183 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 254 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 11 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 HIS D 12 ASN ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.029164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.021938 restraints weight = 221570.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.022740 restraints weight = 129471.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.023305 restraints weight = 88726.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.023714 restraints weight = 66973.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.024006 restraints weight = 54025.375| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 21382 Z= 0.282 Angle : 0.736 14.443 28875 Z= 0.366 Chirality : 0.044 0.227 3073 Planarity : 0.004 0.084 3802 Dihedral : 5.885 100.551 3039 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.50 % Favored : 93.46 % Rotamer: Outliers : 1.24 % Allowed : 10.23 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: 0.05 (0.17), residues: 2738 helix: 1.55 (0.15), residues: 1258 sheet: -1.78 (0.24), residues: 418 loop : -0.99 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 682 TYR 0.025 0.002 TYR A 143 PHE 0.015 0.002 PHE D 262 TRP 0.014 0.002 TRP A 79 HIS 0.009 0.002 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00592 (21382) covalent geometry : angle 0.73640 (28875) hydrogen bonds : bond 0.03315 ( 989) hydrogen bonds : angle 4.84529 ( 2778) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8256 (mpp80) REVERT: A 51 ASP cc_start: 0.9067 (p0) cc_final: 0.8724 (p0) REVERT: A 123 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8956 (mmp) REVERT: A 176 MET cc_start: 0.8670 (tpp) cc_final: 0.8439 (tpp) REVERT: B 39 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8335 (ptt-90) REVERT: B 82 MET cc_start: 0.9057 (tpp) cc_final: 0.8780 (tpp) REVERT: B 227 MET cc_start: 0.9074 (mmm) cc_final: 0.8758 (mmm) REVERT: B 313 MET cc_start: 0.8997 (mmm) cc_final: 0.8559 (mmm) REVERT: C 227 MET cc_start: 0.9315 (mmm) cc_final: 0.9004 (mmm) REVERT: C 299 MET cc_start: 0.8695 (ppp) cc_final: 0.7759 (ppp) REVERT: C 375 PHE cc_start: 0.8584 (m-80) cc_final: 0.8145 (m-80) REVERT: D 82 MET cc_start: 0.9091 (tpp) cc_final: 0.8821 (tpp) REVERT: D 269 MET cc_start: 0.8810 (ttp) cc_final: 0.8487 (tmm) REVERT: E 82 MET cc_start: 0.9417 (tpp) cc_final: 0.9105 (tpp) REVERT: E 119 MET cc_start: 0.9662 (ttp) cc_final: 0.9132 (ptp) REVERT: E 123 MET cc_start: 0.9313 (mmp) cc_final: 0.9041 (mmp) REVERT: E 227 MET cc_start: 0.9244 (mmm) cc_final: 0.8853 (mmm) REVERT: E 299 MET cc_start: 0.8640 (ppp) cc_final: 0.7908 (ppp) REVERT: E 313 MET cc_start: 0.9688 (tpt) cc_final: 0.9215 (mmm) REVERT: P 533 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8461 (pt) REVERT: P 582 MET cc_start: 0.9144 (mmm) cc_final: 0.8725 (mmp) outliers start: 27 outliers final: 13 residues processed: 133 average time/residue: 0.1319 time to fit residues: 28.5683 Evaluate side-chains 126 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain P residue 499 PHE Chi-restraints excluded: chain P residue 533 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 75 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 139 optimal weight: 0.0570 chunk 102 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.029806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.022553 restraints weight = 216002.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.023384 restraints weight = 125389.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.023955 restraints weight = 85437.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.024365 restraints weight = 64391.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.024678 restraints weight = 51988.720| |-----------------------------------------------------------------------------| r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21382 Z= 0.132 Angle : 0.675 10.235 28875 Z= 0.329 Chirality : 0.044 0.220 3073 Planarity : 0.004 0.041 3802 Dihedral : 5.745 93.730 3039 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.83 % Allowed : 10.73 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % 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 are not related in a simple way. whole: 0.23 (0.17), residues: 2738 helix: 1.70 (0.15), residues: 1259 sheet: -1.71 (0.24), residues: 419 loop : -0.89 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 39 TYR 0.022 0.001 TYR A 143 PHE 0.013 0.001 PHE D 262 TRP 0.013 0.002 TRP B 79 HIS 0.010 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00290 (21382) covalent geometry : angle 0.67549 (28875) hydrogen bonds : bond 0.02886 ( 989) hydrogen bonds : angle 4.55593 ( 2778) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.827 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: A 37 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8174 (mpp80) REVERT: A 51 ASP cc_start: 0.9004 (p0) cc_final: 0.8765 (t0) REVERT: A 123 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8918 (mmp) REVERT: A 176 MET cc_start: 0.8652 (tpp) cc_final: 0.8421 (tpp) REVERT: A 190 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.9074 (ptp) REVERT: A 375 PHE cc_start: 0.8760 (m-80) cc_final: 0.8075 (m-80) REVERT: B 82 MET cc_start: 0.9078 (tpp) cc_final: 0.8784 (tpp) REVERT: B 176 MET cc_start: 0.7665 (mpp) cc_final: 0.7165 (mpp) REVERT: B 227 MET cc_start: 0.9029 (mmm) cc_final: 0.8702 (mmm) REVERT: B 299 MET cc_start: 0.8320 (tmm) cc_final: 0.8090 (ppp) REVERT: B 313 MET cc_start: 0.8950 (mmm) cc_final: 0.8666 (mmm) REVERT: C 227 MET cc_start: 0.9303 (mmm) cc_final: 0.8961 (mmm) REVERT: C 299 MET cc_start: 0.8759 (ppp) cc_final: 0.7855 (ppp) REVERT: C 375 PHE cc_start: 0.8579 (m-80) cc_final: 0.8019 (m-80) REVERT: D 47 MET cc_start: 0.8716 (mmm) cc_final: 0.8103 (mmm) REVERT: D 82 MET cc_start: 0.9152 (tpp) cc_final: 0.8874 (tpp) REVERT: D 227 MET cc_start: 0.9387 (mmm) cc_final: 0.8950 (mmm) REVERT: D 269 MET cc_start: 0.8905 (ttp) cc_final: 0.8487 (tmm) REVERT: D 313 MET cc_start: 0.9120 (mmm) cc_final: 0.8593 (mmm) REVERT: E 82 MET cc_start: 0.9406 (tpp) cc_final: 0.9058 (tpp) REVERT: E 119 MET cc_start: 0.9645 (ttp) cc_final: 0.9092 (ptp) REVERT: E 123 MET cc_start: 0.9287 (mmp) cc_final: 0.8951 (mmp) REVERT: E 227 MET cc_start: 0.9194 (mmm) cc_final: 0.8785 (mmm) REVERT: E 299 MET cc_start: 0.8618 (ppp) cc_final: 0.7831 (ppp) REVERT: E 313 MET cc_start: 0.9676 (tpt) cc_final: 0.9261 (mmm) REVERT: P 447 ASP cc_start: 0.9682 (t0) cc_final: 0.9367 (m-30) REVERT: P 459 MET cc_start: 0.9291 (mmm) cc_final: 0.8913 (mmm) REVERT: P 493 MET cc_start: 0.8863 (mmt) cc_final: 0.8596 (mmp) REVERT: P 533 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8447 (pt) REVERT: P 582 MET cc_start: 0.9222 (mmm) cc_final: 0.8803 (mmp) outliers start: 18 outliers final: 12 residues processed: 127 average time/residue: 0.1350 time to fit residues: 28.2251 Evaluate side-chains 127 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain P residue 499 PHE Chi-restraints excluded: chain P residue 533 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 93 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 24 optimal weight: 0.0270 chunk 238 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 270 optimal weight: 50.0000 chunk 121 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 195 optimal weight: 9.9990 chunk 185 optimal weight: 30.0000 chunk 101 optimal weight: 5.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.029414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.022153 restraints weight = 220594.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.022984 restraints weight = 126237.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.023567 restraints weight = 85639.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.023980 restraints weight = 64219.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.024266 restraints weight = 51600.856| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 21382 Z= 0.221 Angle : 0.725 10.900 28875 Z= 0.355 Chirality : 0.044 0.204 3073 Planarity : 0.004 0.041 3802 Dihedral : 5.797 94.299 3039 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.14 % Favored : 93.83 % Rotamer: Outliers : 0.88 % Allowed : 10.59 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % 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 are not related in a simple way. whole: 0.28 (0.17), residues: 2738 helix: 1.66 (0.15), residues: 1253 sheet: -1.76 (0.24), residues: 418 loop : -0.70 (0.21), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 628 TYR 0.027 0.001 TYR A 143 PHE 0.017 0.001 PHE D 262 TRP 0.014 0.002 TRP B 79 HIS 0.009 0.002 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00470 (21382) covalent geometry : angle 0.72492 (28875) hydrogen bonds : bond 0.03107 ( 989) hydrogen bonds : angle 4.69120 ( 2778) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8216 (mpp80) REVERT: A 51 ASP cc_start: 0.9084 (p0) cc_final: 0.8734 (p0) REVERT: A 123 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.9006 (mmp) REVERT: A 176 MET cc_start: 0.8781 (tpp) cc_final: 0.8564 (tpp) REVERT: B 39 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8585 (ptp-170) REVERT: B 82 MET cc_start: 0.9110 (tpp) cc_final: 0.8820 (tpp) REVERT: B 176 MET cc_start: 0.7892 (mpp) cc_final: 0.7309 (mpp) REVERT: B 227 MET cc_start: 0.9063 (mmm) cc_final: 0.8734 (mmm) REVERT: B 313 MET cc_start: 0.9103 (mmm) cc_final: 0.8804 (mmm) REVERT: C 123 MET cc_start: 0.8697 (tpp) cc_final: 0.8407 (tpp) REVERT: C 227 MET cc_start: 0.9300 (mmm) cc_final: 0.8964 (mmm) REVERT: C 299 MET cc_start: 0.8841 (ppp) cc_final: 0.7924 (ppp) REVERT: C 305 MET cc_start: 0.8589 (mpp) cc_final: 0.8197 (mpp) REVERT: C 375 PHE cc_start: 0.8655 (m-80) cc_final: 0.8052 (m-80) REVERT: D 82 MET cc_start: 0.9145 (tpp) cc_final: 0.8839 (tpp) REVERT: D 227 MET cc_start: 0.9374 (mmm) cc_final: 0.8938 (mmm) REVERT: D 269 MET cc_start: 0.8983 (ttp) cc_final: 0.8702 (tmm) REVERT: D 313 MET cc_start: 0.9186 (mmm) cc_final: 0.8705 (mmm) REVERT: E 82 MET cc_start: 0.9424 (tpp) cc_final: 0.9071 (tpp) REVERT: E 119 MET cc_start: 0.9661 (ttp) cc_final: 0.9145 (ptp) REVERT: E 123 MET cc_start: 0.9351 (mmp) cc_final: 0.9024 (mmp) REVERT: E 227 MET cc_start: 0.9201 (mmm) cc_final: 0.8831 (mmm) REVERT: E 299 MET cc_start: 0.8652 (ppp) cc_final: 0.7872 (ppp) REVERT: E 313 MET cc_start: 0.9711 (tpt) cc_final: 0.9259 (mmm) REVERT: P 447 ASP cc_start: 0.9695 (t0) cc_final: 0.9297 (m-30) REVERT: P 459 MET cc_start: 0.9341 (mmm) cc_final: 0.8960 (mmm) REVERT: P 493 MET cc_start: 0.8911 (mmt) cc_final: 0.8668 (mmp) REVERT: P 533 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8470 (pt) REVERT: P 582 MET cc_start: 0.9239 (mmm) cc_final: 0.8822 (mmp) outliers start: 19 outliers final: 13 residues processed: 126 average time/residue: 0.1367 time to fit residues: 28.2529 Evaluate side-chains 127 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain P residue 499 PHE Chi-restraints excluded: chain P residue 533 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 176 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 224 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 219 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 217 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.029936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.022722 restraints weight = 214539.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.023559 restraints weight = 124705.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.024138 restraints weight = 84976.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.024543 restraints weight = 63838.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.024853 restraints weight = 51565.550| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21382 Z= 0.122 Angle : 0.675 15.881 28875 Z= 0.324 Chirality : 0.043 0.201 3073 Planarity : 0.003 0.039 3802 Dihedral : 5.624 84.988 3039 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.88 % Allowed : 10.64 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.38 % 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 are not related in a simple way. whole: 0.50 (0.17), residues: 2738 helix: 1.87 (0.15), residues: 1254 sheet: -1.69 (0.24), residues: 419 loop : -0.60 (0.21), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 39 TYR 0.019 0.001 TYR A 143 PHE 0.012 0.001 PHE D 262 TRP 0.013 0.002 TRP B 79 HIS 0.008 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00270 (21382) covalent geometry : angle 0.67529 (28875) hydrogen bonds : bond 0.02782 ( 989) hydrogen bonds : angle 4.44106 ( 2778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2972.13 seconds wall clock time: 52 minutes 39.61 seconds (3159.61 seconds total)