Starting phenix.real_space_refine on Fri Mar 6 22:47:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tu6_26127/03_2026/7tu6_26127.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tu6_26127/03_2026/7tu6_26127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tu6_26127/03_2026/7tu6_26127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tu6_26127/03_2026/7tu6_26127.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tu6_26127/03_2026/7tu6_26127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tu6_26127/03_2026/7tu6_26127.map" } resolution = 2.7 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= 0.004 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19278 atoms to isotropic. 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 36 5.49 5 Mg 6 5.21 5 S 48 5.16 5 C 12756 2.51 5 N 3444 2.21 5 O 3738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20028 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 417} Chain breaks: 3 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 6, 'ARG:plan': 2, 'ASP:plan': 9, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 129 Chain: "B" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 417} Chain breaks: 3 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 6, 'ARG:plan': 2, 'ASP:plan': 9, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 129 Chain: "C" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 417} Chain breaks: 3 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 6, 'ARG:plan': 2, 'ASP:plan': 9, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 129 Chain: "D" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 417} Chain breaks: 3 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 6, 'ARG:plan': 2, 'ASP:plan': 9, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 129 Chain: "E" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 417} Chain breaks: 3 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 6, 'ARG:plan': 2, 'ASP:plan': 9, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 129 Chain: "F" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 417} Chain breaks: 3 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 6, 'ARG:plan': 2, 'ASP:plan': 9, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 129 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'DTP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'DTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'DTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'DTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'DTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.04, per 1000 atoms: 0.25 Number of scatterers: 20028 At special positions: 0 Unit cell: (130.48, 137.004, 97.86, 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 48 16.00 P 36 15.00 Mg 6 11.99 O 3738 8.00 N 3444 7.00 C 12756 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: 1.73 Conformation dependent library (CDL) restraints added in 836.7 milliseconds 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4812 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 0 sheets defined 71.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 removed outlier: 3.561A pdb=" N LEU A 7 " --> pdb=" O ASN A 3 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 8 " --> pdb=" O TRP A 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3 through 8' Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.548A pdb=" N GLU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 24 " --> pdb=" O ARG A 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 20 through 24' Processing helix chain 'A' and resid 29 through 41 Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 47 through 50 Processing helix chain 'A' and resid 64 through 91 removed outlier: 3.508A pdb=" N SER A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 115 removed outlier: 4.256A pdb=" N PHE A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 135 removed outlier: 4.261A pdb=" N GLU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 144 Processing helix chain 'A' and resid 148 through 157 Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 243 through 268 Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.602A pdb=" N ALA A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.894A pdb=" N THR A 287 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 288 " --> pdb=" O GLY A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 288' Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 298 through 325 removed outlier: 3.754A pdb=" N ARG A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 345 through 359 Processing helix chain 'A' and resid 362 through 389 removed outlier: 3.960A pdb=" N ASN A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 411 through 426 removed outlier: 3.734A pdb=" N MET A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 439 Processing helix chain 'B' and resid 4 through 8 removed outlier: 3.591A pdb=" N LEU B 8 " --> pdb=" O TRP B 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4 through 8' Processing helix chain 'B' and resid 20 through 24 removed outlier: 3.548A pdb=" N GLU B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 24 " --> pdb=" O ARG B 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 20 through 24' Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 47 through 50 Processing helix chain 'B' and resid 64 through 91 removed outlier: 3.509A pdb=" N SER B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 115 removed outlier: 4.255A pdb=" N PHE B 105 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 135 removed outlier: 4.261A pdb=" N GLU B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS B 129 " --> pdb=" O HIS B 125 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE B 135 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 144 Processing helix chain 'B' and resid 148 through 157 Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'B' and resid 182 through 190 Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 243 through 268 Processing helix chain 'B' and resid 272 through 280 removed outlier: 3.602A pdb=" N ALA B 276 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 288 removed outlier: 3.894A pdb=" N THR B 287 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 288 " --> pdb=" O GLY B 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 284 through 288' Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 298 through 325 removed outlier: 3.754A pdb=" N ARG B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 345 through 359 Processing helix chain 'B' and resid 362 through 389 removed outlier: 3.960A pdb=" N ASN B 389 " --> pdb=" O ARG B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 403 Processing helix chain 'B' and resid 411 through 426 removed outlier: 3.733A pdb=" N MET B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 439 Processing helix chain 'C' and resid 4 through 8 removed outlier: 3.592A pdb=" N LEU C 8 " --> pdb=" O TRP C 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4 through 8' Processing helix chain 'C' and resid 20 through 24 removed outlier: 3.548A pdb=" N GLU C 23 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 20 through 24' Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 47 through 50 Processing helix chain 'C' and resid 64 through 91 removed outlier: 3.509A pdb=" N SER C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 removed outlier: 4.256A pdb=" N PHE C 105 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 106 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 135 removed outlier: 4.261A pdb=" N GLU C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS C 129 " --> pdb=" O HIS C 125 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE C 135 " --> pdb=" O ILE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 144 Processing helix chain 'C' and resid 148 through 157 Processing helix chain 'C' and resid 159 through 169 Processing helix chain 'C' and resid 182 through 190 Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 228 Processing helix chain 'C' and resid 243 through 268 Processing helix chain 'C' and resid 272 through 280 removed outlier: 3.601A pdb=" N ALA C 276 " --> pdb=" O PRO C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 288 removed outlier: 3.894A pdb=" N THR C 287 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE C 288 " --> pdb=" O GLY C 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 288' Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 298 through 325 removed outlier: 3.754A pdb=" N ARG C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 345 through 359 Processing helix chain 'C' and resid 362 through 389 removed outlier: 3.960A pdb=" N ASN C 389 " --> pdb=" O ARG C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 403 Processing helix chain 'C' and resid 411 through 426 removed outlier: 3.734A pdb=" N MET C 426 " --> pdb=" O GLU C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 439 Processing helix chain 'D' and resid 4 through 8 removed outlier: 3.591A pdb=" N LEU D 8 " --> pdb=" O TRP D 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4 through 8' Processing helix chain 'D' and resid 20 through 24 removed outlier: 3.548A pdb=" N GLU D 23 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN D 24 " --> pdb=" O ARG D 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 20 through 24' Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'D' and resid 47 through 50 Processing helix chain 'D' and resid 64 through 91 removed outlier: 3.508A pdb=" N SER D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 115 removed outlier: 4.256A pdb=" N PHE D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 135 removed outlier: 4.262A pdb=" N GLU D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 129 " --> pdb=" O HIS D 125 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE D 135 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 144 Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 159 through 169 Processing helix chain 'D' and resid 182 through 190 Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 216 through 228 Processing helix chain 'D' and resid 243 through 268 Processing helix chain 'D' and resid 272 through 280 removed outlier: 3.602A pdb=" N ALA D 276 " --> pdb=" O PRO D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.894A pdb=" N THR D 287 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE D 288 " --> pdb=" O GLY D 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 284 through 288' Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 298 through 325 removed outlier: 3.753A pdb=" N ARG D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 331 Processing helix chain 'D' and resid 345 through 359 Processing helix chain 'D' and resid 362 through 389 removed outlier: 3.960A pdb=" N ASN D 389 " --> pdb=" O ARG D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'D' and resid 411 through 426 removed outlier: 3.735A pdb=" N MET D 426 " --> pdb=" O GLU D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 439 Processing helix chain 'E' and resid 4 through 8 removed outlier: 3.592A pdb=" N LEU E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4 through 8' Processing helix chain 'E' and resid 20 through 24 removed outlier: 3.548A pdb=" N GLU E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN E 24 " --> pdb=" O ARG E 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 20 through 24' Processing helix chain 'E' and resid 29 through 41 Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'E' and resid 47 through 50 Processing helix chain 'E' and resid 64 through 91 removed outlier: 3.509A pdb=" N SER E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 115 removed outlier: 4.255A pdb=" N PHE E 105 " --> pdb=" O LYS E 101 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY E 106 " --> pdb=" O PHE E 102 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 135 removed outlier: 4.262A pdb=" N GLU E 128 " --> pdb=" O GLY E 124 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS E 129 " --> pdb=" O HIS E 125 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE E 135 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 144 Processing helix chain 'E' and resid 148 through 157 Processing helix chain 'E' and resid 159 through 169 Processing helix chain 'E' and resid 182 through 190 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 228 Processing helix chain 'E' and resid 243 through 268 Processing helix chain 'E' and resid 272 through 280 removed outlier: 3.601A pdb=" N ALA E 276 " --> pdb=" O PRO E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 288 removed outlier: 3.893A pdb=" N THR E 287 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE E 288 " --> pdb=" O GLY E 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 284 through 288' Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 298 through 325 removed outlier: 3.754A pdb=" N ARG E 302 " --> pdb=" O GLU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 331 Processing helix chain 'E' and resid 345 through 359 Processing helix chain 'E' and resid 362 through 389 removed outlier: 3.960A pdb=" N ASN E 389 " --> pdb=" O ARG E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 403 Processing helix chain 'E' and resid 411 through 426 removed outlier: 3.734A pdb=" N MET E 426 " --> pdb=" O GLU E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 439 Processing helix chain 'F' and resid 4 through 8 removed outlier: 3.591A pdb=" N LEU F 8 " --> pdb=" O TRP F 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 4 through 8' Processing helix chain 'F' and resid 20 through 24 removed outlier: 3.547A pdb=" N GLU F 23 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN F 24 " --> pdb=" O ARG F 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 20 through 24' Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 47 through 50 Processing helix chain 'F' and resid 64 through 91 removed outlier: 3.508A pdb=" N SER F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 115 removed outlier: 4.256A pdb=" N PHE F 105 " --> pdb=" O LYS F 101 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA F 115 " --> pdb=" O ALA F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 135 removed outlier: 4.261A pdb=" N GLU F 128 " --> pdb=" O GLY F 124 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS F 129 " --> pdb=" O HIS F 125 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE F 135 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 144 Processing helix chain 'F' and resid 148 through 157 Processing helix chain 'F' and resid 159 through 169 Processing helix chain 'F' and resid 182 through 190 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 216 through 228 Processing helix chain 'F' and resid 243 through 268 Processing helix chain 'F' and resid 272 through 280 removed outlier: 3.601A pdb=" N ALA F 276 " --> pdb=" O PRO F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 288 removed outlier: 3.894A pdb=" N THR F 287 " --> pdb=" O VAL F 284 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 284 through 288' Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 298 through 325 removed outlier: 3.754A pdb=" N ARG F 302 " --> pdb=" O GLU F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 331 Processing helix chain 'F' and resid 345 through 359 Processing helix chain 'F' and resid 362 through 389 removed outlier: 3.960A pdb=" N ASN F 389 " --> pdb=" O ARG F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 403 Processing helix chain 'F' and resid 411 through 426 removed outlier: 3.733A pdb=" N MET F 426 " --> pdb=" O GLU F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 439 1182 hydrogen bonds defined for protein. 3456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3216 1.31 - 1.43: 5461 1.43 - 1.56: 11603 1.56 - 1.68: 66 1.68 - 1.81: 78 Bond restraints: 20424 Sorted by residual: bond pdb=" CA GLN E 52 " pdb=" C GLN E 52 " ideal model delta sigma weight residual 1.526 1.569 -0.043 9.20e-03 1.18e+04 2.14e+01 bond pdb=" CA GLN C 52 " pdb=" C GLN C 52 " ideal model delta sigma weight residual 1.526 1.568 -0.042 9.20e-03 1.18e+04 2.12e+01 bond pdb=" CA GLN F 52 " pdb=" C GLN F 52 " ideal model delta sigma weight residual 1.526 1.568 -0.042 9.20e-03 1.18e+04 2.10e+01 bond pdb=" CA GLN A 52 " pdb=" C GLN A 52 " ideal model delta sigma weight residual 1.526 1.568 -0.042 9.20e-03 1.18e+04 2.10e+01 bond pdb=" CA GLN D 52 " pdb=" C GLN D 52 " ideal model delta sigma weight residual 1.526 1.568 -0.042 9.20e-03 1.18e+04 2.06e+01 ... (remaining 20419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 26128 1.47 - 2.93: 1193 2.93 - 4.40: 267 4.40 - 5.87: 78 5.87 - 7.33: 66 Bond angle restraints: 27732 Sorted by residual: angle pdb=" N LEU B 412 " pdb=" CA LEU B 412 " pdb=" C LEU B 412 " ideal model delta sigma weight residual 111.71 118.90 -7.19 1.15e+00 7.56e-01 3.91e+01 angle pdb=" N LEU C 412 " pdb=" CA LEU C 412 " pdb=" C LEU C 412 " ideal model delta sigma weight residual 111.71 118.89 -7.18 1.15e+00 7.56e-01 3.89e+01 angle pdb=" N LEU F 412 " pdb=" CA LEU F 412 " pdb=" C LEU F 412 " ideal model delta sigma weight residual 111.71 118.88 -7.17 1.15e+00 7.56e-01 3.89e+01 angle pdb=" N LEU A 412 " pdb=" CA LEU A 412 " pdb=" C LEU A 412 " ideal model delta sigma weight residual 111.71 118.87 -7.16 1.15e+00 7.56e-01 3.88e+01 angle pdb=" N LEU D 412 " pdb=" CA LEU D 412 " pdb=" C LEU D 412 " ideal model delta sigma weight residual 111.71 118.86 -7.15 1.15e+00 7.56e-01 3.87e+01 ... (remaining 27727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 11180 17.72 - 35.44: 764 35.44 - 53.16: 260 53.16 - 70.88: 24 70.88 - 88.61: 60 Dihedral angle restraints: 12288 sinusoidal: 4782 harmonic: 7506 Sorted by residual: dihedral pdb=" C TYR B 257 " pdb=" N TYR B 257 " pdb=" CA TYR B 257 " pdb=" CB TYR B 257 " ideal model delta harmonic sigma weight residual -122.60 -132.57 9.97 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C TYR F 257 " pdb=" N TYR F 257 " pdb=" CA TYR F 257 " pdb=" CB TYR F 257 " ideal model delta harmonic sigma weight residual -122.60 -132.56 9.96 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C TYR C 257 " pdb=" N TYR C 257 " pdb=" CA TYR C 257 " pdb=" CB TYR C 257 " ideal model delta harmonic sigma weight residual -122.60 -132.55 9.95 0 2.50e+00 1.60e-01 1.59e+01 ... (remaining 12285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2885 0.085 - 0.169: 163 0.169 - 0.254: 54 0.254 - 0.339: 12 0.339 - 0.423: 12 Chirality restraints: 3126 Sorted by residual: chirality pdb=" CA TYR B 257 " pdb=" N TYR B 257 " pdb=" C TYR B 257 " pdb=" CB TYR B 257 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA TYR E 257 " pdb=" N TYR E 257 " pdb=" C TYR E 257 " pdb=" CB TYR E 257 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CA TYR C 257 " pdb=" N TYR C 257 " pdb=" C TYR C 257 " pdb=" CB TYR C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.46e+00 ... (remaining 3123 not shown) Planarity restraints: 3474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 269 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C GLY B 269 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY B 269 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 270 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 269 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C GLY A 269 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY A 269 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A 270 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 269 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C GLY F 269 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY F 269 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU F 270 " -0.013 2.00e-02 2.50e+03 ... (remaining 3471 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 42 2.49 - 3.10: 13784 3.10 - 3.70: 29177 3.70 - 4.30: 43361 4.30 - 4.90: 73256 Nonbonded interactions: 159620 Sorted by model distance: nonbonded pdb=" NE2 HIS F 116 " pdb="MG MG F 503 " model vdw 1.892 2.250 nonbonded pdb=" NE2 HIS C 116 " pdb="MG MG C 502 " model vdw 1.892 2.250 nonbonded pdb=" NE2 HIS A 116 " pdb="MG MG A 503 " model vdw 1.892 2.250 nonbonded pdb=" NE2 HIS D 116 " pdb="MG MG D 503 " model vdw 1.893 2.250 nonbonded pdb=" NE2 HIS E 116 " pdb="MG MG E 502 " model vdw 1.893 2.250 ... (remaining 159615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 501) selection = (chain 'B' and resid 3 through 501) selection = (chain 'C' and resid 3 through 501) selection = (chain 'D' and resid 3 through 501) selection = (chain 'E' and resid 3 through 501) selection = (chain 'F' and resid 3 through 501) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.570 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.040 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: 0.020 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 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 : 0.007 0.061 20424 Z= 0.448 Angle : 0.790 7.332 27732 Z= 0.532 Chirality : 0.058 0.423 3126 Planarity : 0.005 0.078 3474 Dihedral : 15.187 88.605 7476 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.62 % Allowed : 2.48 % Favored : 96.90 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2532 helix: 1.23 (0.13), residues: 1674 sheet: None (None), residues: 0 loop : -1.75 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 45 TYR 0.014 0.002 TYR C 305 PHE 0.006 0.001 PHE C 61 TRP 0.006 0.001 TRP B 4 HIS 0.007 0.002 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00691 (20424) covalent geometry : angle 0.79027 (27732) hydrogen bonds : bond 0.19349 ( 1182) hydrogen bonds : angle 6.14249 ( 3456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 523 time to evaluate : 0.758 Fit side-chains REVERT: A 102 PHE cc_start: 0.8227 (p90) cc_final: 0.7942 (p90) REVERT: A 253 ASP cc_start: 0.7549 (t70) cc_final: 0.7157 (t0) REVERT: B 28 ARG cc_start: 0.8132 (ttt-90) cc_final: 0.7866 (mmm160) REVERT: B 65 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7240 (tpt170) REVERT: B 117 ASP cc_start: 0.6762 (m-30) cc_final: 0.6531 (m-30) REVERT: B 153 GLN cc_start: 0.8322 (tp40) cc_final: 0.8082 (mm-40) REVERT: B 226 GLU cc_start: 0.6998 (tp30) cc_final: 0.6782 (tp30) REVERT: B 270 LEU cc_start: 0.8442 (mt) cc_final: 0.8214 (mt) REVERT: B 354 LEU cc_start: 0.7965 (tp) cc_final: 0.7749 (tt) REVERT: C 28 ARG cc_start: 0.8145 (ttt-90) cc_final: 0.7927 (mmm160) REVERT: C 65 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7263 (tpt170) REVERT: C 253 ASP cc_start: 0.7473 (t70) cc_final: 0.7227 (t70) REVERT: C 270 LEU cc_start: 0.8229 (mt) cc_final: 0.8014 (mt) REVERT: D 253 ASP cc_start: 0.7660 (t70) cc_final: 0.7207 (t0) REVERT: D 270 LEU cc_start: 0.8634 (mt) cc_final: 0.8393 (mt) REVERT: D 326 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7417 (tm-30) REVERT: E 20 LEU cc_start: 0.8548 (mt) cc_final: 0.8276 (mt) REVERT: E 45 ARG cc_start: 0.8420 (ttm170) cc_final: 0.8184 (ttp80) REVERT: E 86 LYS cc_start: 0.8101 (mtmt) cc_final: 0.7895 (mtmt) REVERT: E 207 ASP cc_start: 0.7376 (p0) cc_final: 0.7086 (p0) REVERT: E 214 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8304 (mm-40) REVERT: E 326 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7406 (tm-30) REVERT: F 20 LEU cc_start: 0.8727 (mt) cc_final: 0.8450 (mt) REVERT: F 45 ARG cc_start: 0.8410 (ttm170) cc_final: 0.8123 (ttp80) REVERT: F 270 LEU cc_start: 0.8460 (mt) cc_final: 0.8248 (mp) REVERT: F 326 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7512 (tm-30) outliers start: 12 outliers final: 1 residues processed: 532 average time/residue: 0.8096 time to fit residues: 473.6732 Evaluate side-chains 435 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 432 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain E residue 411 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 48 GLN A 153 GLN A 343 ASN A 389 ASN A 395 ASN B 3 ASN B 24 GLN B 48 GLN B 52 GLN B 120 ASN B 199 HIS B 267 ASN B 343 ASN B 345 GLN B 389 ASN B 395 ASN C 24 GLN C 48 GLN C 52 GLN C 199 HIS C 267 ASN C 345 GLN C 389 ASN C 395 ASN D 13 GLN D 24 GLN D 48 GLN D 153 GLN D 389 ASN D 395 ASN E 24 GLN E 52 GLN E 120 ASN E 153 GLN E 389 ASN E 395 ASN F 13 GLN F 24 GLN F 48 GLN F 52 GLN F 120 ASN F 137 ASN F 343 ASN F 389 ASN F 395 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115721 restraints weight = 25552.419| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.81 r_work: 0.3315 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20424 Z= 0.222 Angle : 0.581 6.191 27732 Z= 0.317 Chirality : 0.041 0.165 3126 Planarity : 0.004 0.042 3474 Dihedral : 11.751 80.859 3183 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.41 % Allowed : 11.20 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.16), residues: 2532 helix: 1.52 (0.12), residues: 1692 sheet: None (None), residues: 0 loop : -2.00 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 77 TYR 0.032 0.002 TYR B 257 PHE 0.022 0.002 PHE F 220 TRP 0.011 0.002 TRP D 240 HIS 0.008 0.002 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00518 (20424) covalent geometry : angle 0.58088 (27732) hydrogen bonds : bond 0.08404 ( 1182) hydrogen bonds : angle 4.02092 ( 3456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 537 time to evaluate : 0.756 Fit side-chains REVERT: A 101 LYS cc_start: 0.8315 (mttp) cc_final: 0.8094 (mttm) REVERT: A 102 PHE cc_start: 0.8631 (p90) cc_final: 0.8354 (p90) REVERT: A 260 ILE cc_start: 0.8387 (mm) cc_final: 0.8177 (mp) REVERT: B 45 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8057 (ttp80) REVERT: B 226 GLU cc_start: 0.8077 (tp30) cc_final: 0.7802 (tp30) REVERT: B 280 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7249 (mtp) REVERT: B 358 ARG cc_start: 0.8339 (ptp-110) cc_final: 0.8124 (ptm160) REVERT: C 24 GLN cc_start: 0.8080 (mt0) cc_final: 0.7710 (tt0) REVERT: C 45 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.7917 (ttp80) REVERT: C 65 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7968 (tpt170) REVERT: C 117 ASP cc_start: 0.7902 (m-30) cc_final: 0.7669 (m-30) REVERT: C 280 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.6779 (mtp) REVERT: D 101 LYS cc_start: 0.8264 (mttp) cc_final: 0.7861 (mttp) REVERT: D 216 GLU cc_start: 0.7551 (mp0) cc_final: 0.7218 (mp0) REVERT: D 260 ILE cc_start: 0.8415 (mm) cc_final: 0.8207 (mp) REVERT: D 293 TYR cc_start: 0.7719 (t80) cc_final: 0.7498 (t80) REVERT: D 326 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7180 (tm-30) REVERT: E 45 ARG cc_start: 0.8833 (ttm170) cc_final: 0.8600 (ttp80) REVERT: E 260 ILE cc_start: 0.8013 (mm) cc_final: 0.7804 (mp) REVERT: E 270 LEU cc_start: 0.8568 (mt) cc_final: 0.8286 (mp) REVERT: E 415 ASN cc_start: 0.8391 (m-40) cc_final: 0.8119 (m-40) REVERT: F 45 ARG cc_start: 0.8822 (ttm170) cc_final: 0.8602 (ttp80) REVERT: F 155 LEU cc_start: 0.8672 (mt) cc_final: 0.8433 (mm) REVERT: F 270 LEU cc_start: 0.8582 (mt) cc_final: 0.8326 (mp) REVERT: F 326 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7685 (tm-30) outliers start: 66 outliers final: 38 residues processed: 559 average time/residue: 0.7103 time to fit residues: 440.9423 Evaluate side-chains 534 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 491 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 411 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 67 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 235 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 189 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 24 GLN A 48 GLN A 267 ASN B 3 ASN B 13 GLN B 52 GLN B 345 GLN C 52 GLN C 345 GLN D 13 GLN D 24 GLN D 343 ASN E 52 GLN E 137 ASN F 48 GLN F 52 GLN F 137 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.119075 restraints weight = 25722.165| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.72 r_work: 0.3369 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20424 Z= 0.139 Angle : 0.466 5.680 27732 Z= 0.256 Chirality : 0.036 0.155 3126 Planarity : 0.003 0.034 3474 Dihedral : 10.956 89.427 3178 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.30 % Allowed : 15.02 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.17), residues: 2532 helix: 2.09 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -1.52 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 242 TYR 0.024 0.001 TYR B 257 PHE 0.014 0.001 PHE F 61 TRP 0.009 0.001 TRP A 240 HIS 0.005 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00299 (20424) covalent geometry : angle 0.46644 (27732) hydrogen bonds : bond 0.06451 ( 1182) hydrogen bonds : angle 3.81219 ( 3456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 488 time to evaluate : 0.721 Fit side-chains REVERT: A 102 PHE cc_start: 0.8552 (p90) cc_final: 0.8279 (p90) REVERT: A 323 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7928 (mmm) REVERT: B 45 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8018 (ttp80) REVERT: B 65 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7604 (tpt170) REVERT: B 117 ASP cc_start: 0.7795 (m-30) cc_final: 0.7546 (m-30) REVERT: B 136 LYS cc_start: 0.7898 (ttmm) cc_final: 0.7673 (ttmm) REVERT: B 226 GLU cc_start: 0.8043 (tp30) cc_final: 0.7757 (tp30) REVERT: B 373 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7223 (t80) REVERT: C 24 GLN cc_start: 0.8078 (mt0) cc_final: 0.7734 (tt0) REVERT: C 45 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7896 (ttp80) REVERT: C 373 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.6961 (t80) REVERT: D 216 GLU cc_start: 0.7588 (mp0) cc_final: 0.7237 (mp0) REVERT: D 326 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7625 (tm-30) REVERT: E 48 GLN cc_start: 0.8732 (pt0) cc_final: 0.8516 (pt0) REVERT: E 415 ASN cc_start: 0.8343 (m-40) cc_final: 0.8113 (m-40) REVERT: F 45 ARG cc_start: 0.8805 (ttm170) cc_final: 0.8551 (ttp80) REVERT: F 270 LEU cc_start: 0.8515 (mt) cc_final: 0.8278 (mp) REVERT: F 326 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7582 (tm-30) outliers start: 64 outliers final: 31 residues processed: 514 average time/residue: 0.6380 time to fit residues: 367.3398 Evaluate side-chains 524 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 487 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 411 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 74 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 213 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 24 GLN B 3 ASN B 52 GLN B 343 ASN B 345 GLN C 52 GLN C 345 GLN D 13 GLN D 24 GLN D 214 GLN D 267 ASN D 343 ASN D 400 GLN E 24 GLN E 52 GLN E 137 ASN E 267 ASN F 48 GLN F 52 GLN F 137 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.132957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.115185 restraints weight = 25562.572| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.72 r_work: 0.3304 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 20424 Z= 0.233 Angle : 0.555 5.436 27732 Z= 0.303 Chirality : 0.042 0.157 3126 Planarity : 0.004 0.035 3474 Dihedral : 10.957 89.123 3174 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.18 % Allowed : 16.10 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2532 helix: 1.65 (0.13), residues: 1692 sheet: None (None), residues: 0 loop : -2.06 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 65 TYR 0.020 0.002 TYR D 257 PHE 0.022 0.002 PHE F 220 TRP 0.010 0.002 TRP A 240 HIS 0.007 0.002 HIS E 204 Details of bonding type rmsd covalent geometry : bond 0.00556 (20424) covalent geometry : angle 0.55515 (27732) hydrogen bonds : bond 0.08642 ( 1182) hydrogen bonds : angle 4.03930 ( 3456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 529 time to evaluate : 0.683 Fit side-chains REVERT: A 102 PHE cc_start: 0.8640 (p90) cc_final: 0.8378 (p90) REVERT: A 229 LEU cc_start: 0.8383 (mt) cc_final: 0.8157 (mp) REVERT: B 65 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7652 (tpt170) REVERT: B 117 ASP cc_start: 0.7860 (m-30) cc_final: 0.7516 (m-30) REVERT: B 136 LYS cc_start: 0.7958 (ttmm) cc_final: 0.7727 (ttmm) REVERT: B 226 GLU cc_start: 0.8059 (tp30) cc_final: 0.7760 (tp30) REVERT: B 373 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7574 (t80) REVERT: C 24 GLN cc_start: 0.8171 (mt0) cc_final: 0.7898 (tt0) REVERT: C 373 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7185 (t80) REVERT: D 214 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8532 (tp40) REVERT: D 216 GLU cc_start: 0.7673 (mp0) cc_final: 0.7318 (mp0) REVERT: D 326 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7831 (tm-30) REVERT: E 11 LYS cc_start: 0.8244 (ptmt) cc_final: 0.8030 (tttt) REVERT: E 270 LEU cc_start: 0.8486 (mt) cc_final: 0.8247 (mp) REVERT: E 354 LEU cc_start: 0.8512 (tp) cc_final: 0.8210 (tp) REVERT: E 415 ASN cc_start: 0.8382 (m-40) cc_final: 0.8125 (m-40) REVERT: F 45 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8528 (ttp80) REVERT: F 202 SER cc_start: 0.8363 (m) cc_final: 0.8111 (t) REVERT: F 326 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7731 (tm-30) outliers start: 81 outliers final: 49 residues processed: 556 average time/residue: 0.6861 time to fit residues: 424.3295 Evaluate side-chains 567 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 515 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 430 LYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 153 GLN Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain F residue 417 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 236 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 225 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 3 ASN B 52 GLN B 345 GLN C 52 GLN C 345 GLN D 24 GLN D 343 ASN D 434 ASN E 52 GLN E 137 ASN F 52 GLN F 137 ASN F 343 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.137220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119761 restraints weight = 25541.718| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.70 r_work: 0.3381 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20424 Z= 0.121 Angle : 0.448 5.099 27732 Z= 0.247 Chirality : 0.036 0.147 3126 Planarity : 0.003 0.034 3474 Dihedral : 10.190 85.324 3174 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.46 % Allowed : 18.11 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.17), residues: 2532 helix: 2.11 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.77 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 65 TYR 0.017 0.001 TYR B 257 PHE 0.012 0.001 PHE F 220 TRP 0.008 0.001 TRP A 240 HIS 0.004 0.001 HIS E 204 Details of bonding type rmsd covalent geometry : bond 0.00248 (20424) covalent geometry : angle 0.44756 (27732) hydrogen bonds : bond 0.05809 ( 1182) hydrogen bonds : angle 3.76286 ( 3456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 494 time to evaluate : 0.684 Fit side-chains REVERT: A 102 PHE cc_start: 0.8592 (p90) cc_final: 0.8315 (p90) REVERT: B 45 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8018 (ttp80) REVERT: B 65 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7459 (tpt170) REVERT: B 117 ASP cc_start: 0.7869 (m-30) cc_final: 0.7547 (m-30) REVERT: B 136 LYS cc_start: 0.7933 (ttmm) cc_final: 0.7708 (ttmm) REVERT: B 220 PHE cc_start: 0.8039 (t80) cc_final: 0.7696 (t80) REVERT: B 226 GLU cc_start: 0.7965 (tp30) cc_final: 0.7675 (tp30) REVERT: B 373 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.7235 (t80) REVERT: C 24 GLN cc_start: 0.8108 (mt0) cc_final: 0.7872 (tt0) REVERT: C 129 LYS cc_start: 0.8357 (mmtt) cc_final: 0.8152 (mmtt) REVERT: C 226 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7134 (tt0) REVERT: C 373 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.6894 (t80) REVERT: D 216 GLU cc_start: 0.7631 (mp0) cc_final: 0.7251 (mp0) REVERT: D 326 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7667 (tm-30) REVERT: E 11 LYS cc_start: 0.8246 (ptmt) cc_final: 0.7965 (tttt) REVERT: E 270 LEU cc_start: 0.8426 (mt) cc_final: 0.8192 (mp) REVERT: E 354 LEU cc_start: 0.8529 (tp) cc_final: 0.8205 (tp) REVERT: E 415 ASN cc_start: 0.8333 (m-40) cc_final: 0.8066 (m-40) REVERT: F 45 ARG cc_start: 0.8797 (ttm170) cc_final: 0.8547 (ttp80) REVERT: F 202 SER cc_start: 0.8273 (m) cc_final: 0.8022 (p) REVERT: F 207 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7568 (p0) REVERT: F 326 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7540 (tm-30) outliers start: 67 outliers final: 31 residues processed: 520 average time/residue: 0.6464 time to fit residues: 375.5159 Evaluate side-chains 528 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 491 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 257 TYR Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 411 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 155 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 254 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 200 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 3 ASN B 52 GLN B 343 ASN B 345 GLN C 343 ASN D 24 GLN D 343 ASN E 24 GLN E 52 GLN E 137 ASN F 48 GLN F 52 GLN F 137 ASN F 343 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.135540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117540 restraints weight = 25470.696| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.78 r_work: 0.3344 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20424 Z= 0.156 Angle : 0.485 5.535 27732 Z= 0.265 Chirality : 0.038 0.153 3126 Planarity : 0.003 0.033 3474 Dihedral : 9.978 81.793 3174 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.46 % Allowed : 19.14 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.17), residues: 2532 helix: 1.98 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.89 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 65 TYR 0.019 0.001 TYR B 257 PHE 0.016 0.001 PHE F 220 TRP 0.007 0.001 TRP A 240 HIS 0.005 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00350 (20424) covalent geometry : angle 0.48479 (27732) hydrogen bonds : bond 0.06780 ( 1182) hydrogen bonds : angle 3.79133 ( 3456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 503 time to evaluate : 0.683 Fit side-chains REVERT: A 102 PHE cc_start: 0.8634 (p90) cc_final: 0.8357 (p90) REVERT: B 65 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7482 (tpt170) REVERT: B 117 ASP cc_start: 0.7939 (m-30) cc_final: 0.7556 (m-30) REVERT: B 136 LYS cc_start: 0.7956 (ttmm) cc_final: 0.7712 (ttmm) REVERT: B 226 GLU cc_start: 0.7998 (tp30) cc_final: 0.7690 (tp30) REVERT: B 373 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7324 (t80) REVERT: C 11 LYS cc_start: 0.8199 (ptmt) cc_final: 0.7969 (ptmt) REVERT: C 24 GLN cc_start: 0.8117 (mt0) cc_final: 0.7878 (tt0) REVERT: C 226 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: C 373 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7019 (t80) REVERT: D 216 GLU cc_start: 0.7698 (mp0) cc_final: 0.7291 (mp0) REVERT: D 293 TYR cc_start: 0.7773 (t80) cc_final: 0.7573 (t80) REVERT: D 326 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7748 (tm-30) REVERT: E 11 LYS cc_start: 0.8280 (ptmt) cc_final: 0.8010 (tttt) REVERT: E 270 LEU cc_start: 0.8409 (mt) cc_final: 0.8158 (mp) REVERT: E 354 LEU cc_start: 0.8457 (tp) cc_final: 0.8147 (tp) REVERT: E 415 ASN cc_start: 0.8378 (m-40) cc_final: 0.8107 (m-40) REVERT: F 45 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8570 (ttp80) REVERT: F 202 SER cc_start: 0.8246 (m) cc_final: 0.7967 (p) REVERT: F 207 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7525 (p0) REVERT: F 326 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7629 (tm-30) outliers start: 67 outliers final: 43 residues processed: 524 average time/residue: 0.6825 time to fit residues: 398.9646 Evaluate side-chains 546 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 498 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 430 LYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 257 TYR Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 411 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 182 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 250 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 chunk 214 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 3 ASN B 52 GLN B 343 ASN B 345 GLN C 52 GLN C 343 ASN C 345 GLN D 24 GLN D 343 ASN E 48 GLN E 52 GLN E 137 ASN F 24 GLN F 137 ASN F 343 ASN F 400 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.133583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.115624 restraints weight = 25347.422| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.77 r_work: 0.3314 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20424 Z= 0.202 Angle : 0.527 5.779 27732 Z= 0.288 Chirality : 0.040 0.157 3126 Planarity : 0.003 0.032 3474 Dihedral : 10.132 84.164 3174 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.51 % Allowed : 19.50 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.17), residues: 2532 helix: 1.81 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.97 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.025 0.002 TYR B 257 PHE 0.020 0.002 PHE F 220 TRP 0.008 0.002 TRP A 240 HIS 0.005 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00474 (20424) covalent geometry : angle 0.52691 (27732) hydrogen bonds : bond 0.07893 ( 1182) hydrogen bonds : angle 3.92321 ( 3456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 513 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 102 PHE cc_start: 0.8688 (p90) cc_final: 0.8417 (p90) REVERT: A 229 LEU cc_start: 0.8368 (mt) cc_final: 0.8129 (mp) REVERT: B 65 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7566 (tpt170) REVERT: B 117 ASP cc_start: 0.7961 (m-30) cc_final: 0.7590 (m-30) REVERT: B 226 GLU cc_start: 0.7995 (tp30) cc_final: 0.7688 (tp30) REVERT: B 373 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7473 (t80) REVERT: C 11 LYS cc_start: 0.8245 (ptmt) cc_final: 0.7991 (ptmt) REVERT: C 24 GLN cc_start: 0.8186 (mt0) cc_final: 0.7929 (tt0) REVERT: C 226 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7173 (tt0) REVERT: C 373 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7105 (t80) REVERT: D 216 GLU cc_start: 0.7702 (mp0) cc_final: 0.7300 (mp0) REVERT: D 326 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7833 (tm-30) REVERT: E 11 LYS cc_start: 0.8287 (ptmt) cc_final: 0.8028 (tttt) REVERT: E 270 LEU cc_start: 0.8480 (mt) cc_final: 0.8240 (mp) REVERT: E 354 LEU cc_start: 0.8462 (tp) cc_final: 0.8167 (tp) REVERT: E 415 ASN cc_start: 0.8390 (m-40) cc_final: 0.8145 (m-40) REVERT: F 45 ARG cc_start: 0.8850 (ttm110) cc_final: 0.8562 (ttp80) REVERT: F 202 SER cc_start: 0.8303 (m) cc_final: 0.8082 (t) REVERT: F 207 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7611 (p0) REVERT: F 326 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7650 (tm-30) outliers start: 68 outliers final: 46 residues processed: 534 average time/residue: 0.6823 time to fit residues: 405.8274 Evaluate side-chains 566 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 515 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 257 TYR Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 417 ILE Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 65 optimal weight: 7.9990 chunk 247 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 254 optimal weight: 0.0670 chunk 46 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 145 optimal weight: 0.7980 chunk 176 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN B 52 GLN C 52 GLN D 24 GLN D 343 ASN E 52 GLN E 137 ASN F 24 GLN F 137 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.138988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121644 restraints weight = 25680.827| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.70 r_work: 0.3412 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20424 Z= 0.107 Angle : 0.435 5.336 27732 Z= 0.239 Chirality : 0.035 0.163 3126 Planarity : 0.003 0.029 3474 Dihedral : 9.346 71.529 3174 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.89 % Allowed : 20.49 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.17), residues: 2532 helix: 2.25 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.75 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 65 TYR 0.016 0.001 TYR B 257 PHE 0.009 0.001 PHE E 220 TRP 0.008 0.001 TRP A 240 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00214 (20424) covalent geometry : angle 0.43530 (27732) hydrogen bonds : bond 0.05076 ( 1182) hydrogen bonds : angle 3.65904 ( 3456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 495 time to evaluate : 0.703 Fit side-chains REVERT: A 102 PHE cc_start: 0.8582 (p90) cc_final: 0.8353 (p90) REVERT: A 217 ARG cc_start: 0.8254 (ttt-90) cc_final: 0.7927 (ttt-90) REVERT: B 220 PHE cc_start: 0.8019 (t80) cc_final: 0.7698 (t80) REVERT: B 226 GLU cc_start: 0.7946 (tp30) cc_final: 0.7671 (tp30) REVERT: B 373 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.7014 (t80) REVERT: C 12 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8161 (mtt180) REVERT: C 24 GLN cc_start: 0.8131 (mt0) cc_final: 0.7912 (tt0) REVERT: C 45 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.7866 (ttp80) REVERT: C 354 LEU cc_start: 0.8581 (tp) cc_final: 0.8376 (tt) REVERT: C 373 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.6772 (t80) REVERT: D 216 GLU cc_start: 0.7680 (mp0) cc_final: 0.7283 (mp0) REVERT: D 305 TYR cc_start: 0.7912 (t80) cc_final: 0.7707 (t80) REVERT: E 48 GLN cc_start: 0.8712 (pt0) cc_final: 0.8491 (pt0) REVERT: E 52 GLN cc_start: 0.7983 (tp40) cc_final: 0.7278 (tp-100) REVERT: E 270 LEU cc_start: 0.8421 (mt) cc_final: 0.8184 (mp) REVERT: E 354 LEU cc_start: 0.8505 (tp) cc_final: 0.8205 (tp) REVERT: E 415 ASN cc_start: 0.8344 (m-40) cc_final: 0.8089 (m-40) REVERT: F 45 ARG cc_start: 0.8776 (ttm170) cc_final: 0.8561 (ttp80) REVERT: F 65 ARG cc_start: 0.7651 (mmt90) cc_final: 0.7444 (mmt180) REVERT: F 202 SER cc_start: 0.8221 (m) cc_final: 0.8010 (p) REVERT: F 207 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7559 (p0) REVERT: F 323 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7532 (mmm) REVERT: F 326 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7549 (tm-30) REVERT: F 411 SER cc_start: 0.7713 (OUTLIER) cc_final: 0.7387 (m) outliers start: 56 outliers final: 33 residues processed: 516 average time/residue: 0.6781 time to fit residues: 390.7748 Evaluate side-chains 524 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 484 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 430 LYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 257 TYR Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 99 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 245 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 65 optimal weight: 0.0270 chunk 44 optimal weight: 6.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 343 ASN B 3 ASN B 343 ASN B 345 GLN C 52 GLN C 153 GLN C 343 ASN C 345 GLN C 434 ASN D 24 GLN D 343 ASN E 137 ASN F 137 ASN F 343 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120524 restraints weight = 25587.961| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.70 r_work: 0.3393 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20424 Z= 0.121 Angle : 0.460 6.306 27732 Z= 0.250 Chirality : 0.036 0.168 3126 Planarity : 0.003 0.030 3474 Dihedral : 9.174 67.975 3174 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.37 % Allowed : 21.67 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.17), residues: 2532 helix: 2.40 (0.13), residues: 1644 sheet: None (None), residues: 0 loop : -1.43 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 65 TYR 0.018 0.001 TYR A 257 PHE 0.012 0.001 PHE F 220 TRP 0.007 0.001 TRP A 240 HIS 0.004 0.001 HIS E 204 Details of bonding type rmsd covalent geometry : bond 0.00254 (20424) covalent geometry : angle 0.46038 (27732) hydrogen bonds : bond 0.05586 ( 1182) hydrogen bonds : angle 3.65387 ( 3456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 494 time to evaluate : 0.749 Fit side-chains REVERT: A 102 PHE cc_start: 0.8595 (p90) cc_final: 0.8366 (p90) REVERT: A 217 ARG cc_start: 0.8281 (ttt-90) cc_final: 0.7952 (ttt-90) REVERT: B 45 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8019 (ttp80) REVERT: B 52 GLN cc_start: 0.7991 (tp40) cc_final: 0.7680 (tp-100) REVERT: B 226 GLU cc_start: 0.7958 (tp30) cc_final: 0.7690 (tp30) REVERT: B 373 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7187 (t80) REVERT: C 12 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8181 (mtt180) REVERT: C 24 GLN cc_start: 0.8143 (mt0) cc_final: 0.7917 (tt0) REVERT: C 45 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7901 (ttp80) REVERT: C 52 GLN cc_start: 0.7982 (tp40) cc_final: 0.7674 (tp-100) REVERT: C 354 LEU cc_start: 0.8593 (tp) cc_final: 0.8386 (tt) REVERT: C 373 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.6873 (t80) REVERT: C 437 LYS cc_start: 0.7151 (mtpt) cc_final: 0.6941 (mtpt) REVERT: D 216 GLU cc_start: 0.7673 (mp0) cc_final: 0.7280 (mp0) REVERT: D 305 TYR cc_start: 0.7888 (t80) cc_final: 0.7680 (t80) REVERT: E 48 GLN cc_start: 0.8720 (pt0) cc_final: 0.8506 (pt0) REVERT: E 270 LEU cc_start: 0.8399 (mt) cc_final: 0.8162 (mp) REVERT: E 330 LEU cc_start: 0.8569 (tp) cc_final: 0.8312 (mt) REVERT: E 354 LEU cc_start: 0.8505 (tp) cc_final: 0.8201 (tp) REVERT: E 415 ASN cc_start: 0.8369 (m-40) cc_final: 0.8102 (m-40) REVERT: F 45 ARG cc_start: 0.8793 (ttm110) cc_final: 0.8579 (ttp80) REVERT: F 65 ARG cc_start: 0.7720 (mmt90) cc_final: 0.7499 (mmt180) REVERT: F 207 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7560 (p0) REVERT: F 263 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6958 (pt0) REVERT: F 323 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7601 (mmm) REVERT: F 326 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7566 (tm-30) REVERT: F 411 SER cc_start: 0.7790 (OUTLIER) cc_final: 0.7459 (m) outliers start: 46 outliers final: 28 residues processed: 513 average time/residue: 0.6918 time to fit residues: 395.7171 Evaluate side-chains 519 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 482 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 257 TYR Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 213 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 3 ASN B 343 ASN C 343 ASN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 343 ASN E 137 ASN F 137 ASN F 343 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.131589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114034 restraints weight = 25431.268| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.69 r_work: 0.3289 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 20424 Z= 0.304 Angle : 0.629 6.788 27732 Z= 0.342 Chirality : 0.046 0.180 3126 Planarity : 0.004 0.106 3474 Dihedral : 10.064 81.678 3174 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.37 % Allowed : 22.14 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.16), residues: 2532 helix: 1.61 (0.12), residues: 1680 sheet: None (None), residues: 0 loop : -2.06 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 65 TYR 0.027 0.003 TYR C 257 PHE 0.023 0.003 PHE F 220 TRP 0.008 0.002 TRP A 240 HIS 0.007 0.002 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00746 (20424) covalent geometry : angle 0.62889 (27732) hydrogen bonds : bond 0.09417 ( 1182) hydrogen bonds : angle 4.08231 ( 3456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 533 time to evaluate : 0.728 Fit side-chains REVERT: A 25 ASP cc_start: 0.7109 (m-30) cc_final: 0.6826 (m-30) REVERT: A 102 PHE cc_start: 0.8719 (p90) cc_final: 0.8479 (p90) REVERT: B 52 GLN cc_start: 0.8004 (tp40) cc_final: 0.7720 (tp-100) REVERT: B 220 PHE cc_start: 0.8145 (t80) cc_final: 0.7695 (t80) REVERT: B 226 GLU cc_start: 0.8002 (tp30) cc_final: 0.7697 (tp30) REVERT: B 345 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8072 (mm-40) REVERT: B 373 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.7679 (t80) REVERT: C 24 GLN cc_start: 0.8259 (mt0) cc_final: 0.8000 (tt0) REVERT: C 373 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7313 (t80) REVERT: D 216 GLU cc_start: 0.7696 (mp0) cc_final: 0.7339 (mp0) REVERT: E 11 LYS cc_start: 0.8267 (ptmt) cc_final: 0.8066 (tttt) REVERT: E 225 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: E 330 LEU cc_start: 0.8653 (tp) cc_final: 0.8386 (mt) REVERT: E 354 LEU cc_start: 0.8523 (tp) cc_final: 0.8218 (tp) REVERT: E 415 ASN cc_start: 0.8439 (m-40) cc_final: 0.8149 (m-40) REVERT: F 45 ARG cc_start: 0.8838 (ttm110) cc_final: 0.8569 (ttp80) REVERT: F 226 GLU cc_start: 0.7789 (tp30) cc_final: 0.7494 (tt0) REVERT: F 260 ILE cc_start: 0.8118 (mm) cc_final: 0.7848 (mt) REVERT: F 270 LEU cc_start: 0.8495 (mt) cc_final: 0.8291 (mp) REVERT: F 326 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7683 (tm-30) outliers start: 46 outliers final: 34 residues processed: 549 average time/residue: 0.6830 time to fit residues: 417.6798 Evaluate side-chains 564 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 527 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 251 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN B 415 ASN C 343 ASN C 345 GLN D 343 ASN E 137 ASN F 52 GLN F 137 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.117857 restraints weight = 25492.793| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.69 r_work: 0.3358 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20424 Z= 0.145 Angle : 0.499 5.952 27732 Z= 0.273 Chirality : 0.038 0.163 3126 Planarity : 0.003 0.047 3474 Dihedral : 9.513 74.604 3174 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.01 % Allowed : 22.45 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.17), residues: 2532 helix: 1.90 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -2.05 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 65 TYR 0.018 0.001 TYR A 257 PHE 0.012 0.001 PHE F 220 TRP 0.010 0.001 TRP A 240 HIS 0.004 0.001 HIS E 204 Details of bonding type rmsd covalent geometry : bond 0.00319 (20424) covalent geometry : angle 0.49865 (27732) hydrogen bonds : bond 0.06536 ( 1182) hydrogen bonds : angle 3.81963 ( 3456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8288.01 seconds wall clock time: 141 minutes 9.07 seconds (8469.07 seconds total)