Starting phenix.real_space_refine on Mon Jul 6 11:58:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tu6_26127/07_2026/7tu6_26127.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tu6_26127/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tu6_26127/07_2026/7tu6_26127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tu6_26127/07_2026/7tu6_26127.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tu6_26127/07_2026/7tu6_26127.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tu6_26127/07_2026/7tu6_26127.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tu6_26127/07_2026/7tu6_26127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tu6_26127/07_2026/7tu6_26127.cif" } 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-6108/lib/python3.11/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: 3.97, per 1000 atoms: 0.20 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: 1.53 Conformation dependent library (CDL) restraints added in 725.1 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: 0.55 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: 3.14 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 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: 11060 17.72 - 35.44: 680 35.44 - 53.16: 170 53.16 - 70.88: 24 70.88 - 88.61: 30 Dihedral angle restraints: 11964 sinusoidal: 4458 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 11961 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.550 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 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 : 13.431 88.605 7152 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/Z covalent geometry : bond 0.00691 / 0.45 (20424) covalent geometry : angle 0.79027 / 0.53 (27732) hydrogen bonds : bond 0.19349 / 12.90 ( 1182) hydrogen bonds : angle 6.14249 / 4.37 ( 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 : 0.568 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: 0.6731 time to fit residues: 396.2877 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 : 0.722 ------------------------------------------------------------------------------- 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... 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 267 ASN 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 267 ASN F 343 ASN F 389 ASN F 395 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115934 restraints weight = 25543.995| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.73 r_work: 0.3322 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2269 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= 0.223 Angle : 0.580 5.735 27732 Z= 0.317 Chirality : 0.041 0.169 3126 Planarity : 0.004 0.042 3474 Dihedral : 5.326 44.502 2859 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.35 % Allowed : 11.25 % 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: 0.61 (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 B 358 TYR 0.032 0.002 TYR B 257 PHE 0.023 0.002 PHE F 220 TRP 0.011 0.002 TRP D 240 HIS 0.007 0.002 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (20424) covalent geometry : angle 0.57987 / 0.32 (27732) hydrogen bonds : bond 0.08510 / 5.86 ( 1182) hydrogen bonds : angle 4.02405 / 2.83 ( 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 601 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 536 time to evaluate : 0.776 Fit side-chains REVERT: A 101 LYS cc_start: 0.8326 (mttp) cc_final: 0.7947 (mttm) REVERT: A 102 PHE cc_start: 0.8631 (p90) cc_final: 0.8328 (p90) REVERT: A 260 ILE cc_start: 0.8427 (mm) cc_final: 0.8222 (mp) REVERT: B 45 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8044 (ttp80) REVERT: B 226 GLU cc_start: 0.8064 (tp30) cc_final: 0.7785 (tp30) REVERT: C 24 GLN cc_start: 0.8109 (mt0) cc_final: 0.7734 (tt0) REVERT: C 65 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7952 (tpt170) REVERT: C 117 ASP cc_start: 0.7859 (m-30) cc_final: 0.7625 (m-30) REVERT: C 280 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6813 (mtp) REVERT: D 101 LYS cc_start: 0.8278 (mttp) cc_final: 0.7884 (mttp) REVERT: D 216 GLU cc_start: 0.7543 (mp0) cc_final: 0.7223 (mp0) REVERT: D 293 TYR cc_start: 0.7764 (t80) cc_final: 0.7534 (t80) REVERT: D 326 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7190 (tm-30) REVERT: E 45 ARG cc_start: 0.8819 (ttm170) cc_final: 0.8598 (ttp80) REVERT: E 214 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8657 (mm-40) REVERT: E 270 LEU cc_start: 0.8575 (mt) cc_final: 0.8305 (mp) REVERT: E 415 ASN cc_start: 0.8373 (m-40) cc_final: 0.8096 (m-40) REVERT: F 45 ARG cc_start: 0.8807 (ttm170) cc_final: 0.8602 (ttp80) REVERT: F 155 LEU cc_start: 0.8701 (mt) cc_final: 0.8470 (mm) REVERT: F 270 LEU cc_start: 0.8603 (mt) cc_final: 0.8356 (mp) REVERT: F 326 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7689 (tm-30) outliers start: 65 outliers final: 38 residues processed: 557 average time/residue: 0.6102 time to fit residues: 380.0096 Evaluate side-chains 528 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 487 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR 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 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 323 MET 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 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 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 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: 3.9990 chunk 77 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.132405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114538 restraints weight = 25491.930| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.72 r_work: 0.3300 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 20424 Z= 0.249 Angle : 0.575 5.478 27732 Z= 0.314 Chirality : 0.042 0.157 3126 Planarity : 0.004 0.037 3474 Dihedral : 4.897 37.608 2854 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.23 % Allowed : 14.04 % Favored : 81.73 % 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: 0.53 (0.16), residues: 2532 helix: 1.49 (0.12), residues: 1692 sheet: None (None), residues: 0 loop : -2.12 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 37 TYR 0.026 0.002 TYR B 257 PHE 0.022 0.002 PHE A 220 TRP 0.011 0.002 TRP A 240 HIS 0.007 0.002 HIS E 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.25 (20424) covalent geometry : angle 0.57484 / 0.31 (27732) hydrogen bonds : bond 0.08995 / 6.19 ( 1182) hydrogen bonds : angle 4.10841 / 2.89 ( 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 617 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 535 time to evaluate : 0.611 Fit side-chains REVERT: A 101 LYS cc_start: 0.8314 (mttp) cc_final: 0.8111 (mptp) REVERT: A 102 PHE cc_start: 0.8689 (p90) cc_final: 0.8439 (p90) REVERT: A 229 LEU cc_start: 0.8376 (mt) cc_final: 0.8175 (mp) REVERT: A 260 ILE cc_start: 0.8470 (mm) cc_final: 0.8267 (mp) REVERT: B 65 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7697 (tpt170) REVERT: B 117 ASP cc_start: 0.7815 (m-30) cc_final: 0.7510 (m-30) REVERT: B 136 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7750 (ttmm) REVERT: B 226 GLU cc_start: 0.8052 (tp30) cc_final: 0.7783 (tp30) REVERT: B 280 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7191 (mtp) REVERT: B 373 TYR cc_start: 0.8210 (OUTLIER) cc_final: 0.7586 (t80) REVERT: C 24 GLN cc_start: 0.8179 (mt0) cc_final: 0.7894 (tt0) REVERT: C 45 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8017 (ttp80) REVERT: C 373 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7224 (t80) REVERT: D 216 GLU cc_start: 0.7635 (mp0) cc_final: 0.7296 (mp0) REVERT: D 326 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7799 (tm-30) REVERT: E 11 LYS cc_start: 0.8262 (ptmt) cc_final: 0.8019 (tttt) REVERT: E 45 ARG cc_start: 0.8821 (ttm170) cc_final: 0.8520 (ttp80) REVERT: E 260 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7708 (mt) REVERT: E 270 LEU cc_start: 0.8523 (mt) cc_final: 0.8293 (mp) REVERT: F 155 LEU cc_start: 0.8690 (mt) cc_final: 0.8468 (mm) REVERT: F 202 SER cc_start: 0.8398 (m) cc_final: 0.8122 (t) REVERT: F 326 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7619 (tm-30) outliers start: 82 outliers final: 45 residues processed: 563 average time/residue: 0.5777 time to fit residues: 365.0066 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 : 0.787 ------------------------------------------------------------------------------- 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 225 GLN Chi-restraints excluded: chain A residue 238 VAL 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 65 ARG Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 280 MET 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 62 VAL 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 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 263 GLU Chi-restraints excluded: chain D residue 373 TYR 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 260 ILE 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 12 ARG Chi-restraints excluded: chain F residue 225 GLN 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 74 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 213 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 GLN B 3 ASN B 52 GLN B 345 GLN C 52 GLN C 345 GLN D 24 GLN D 343 ASN E 48 GLN E 52 GLN E 137 ASN F 137 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.136541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118866 restraints weight = 25598.707| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.72 r_work: 0.3367 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20424 Z= 0.129 Angle : 0.456 5.129 27732 Z= 0.253 Chirality : 0.036 0.143 3126 Planarity : 0.003 0.034 3474 Dihedral : 4.179 37.661 2850 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.25 % Allowed : 17.34 % Favored : 79.41 % 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: 1.41 (0.17), residues: 2532 helix: 2.16 (0.13), residues: 1644 sheet: None (None), residues: 0 loop : -1.54 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 242 TYR 0.016 0.001 TYR C 257 PHE 0.013 0.001 PHE F 220 TRP 0.010 0.001 TRP A 240 HIS 0.005 0.001 HIS E 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (20424) covalent geometry : angle 0.45590 / 0.25 (27732) hydrogen bonds : bond 0.06211 / 4.30 ( 1182) hydrogen bonds : angle 3.81824 / 2.69 ( 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 563 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 500 time to evaluate : 0.755 Fit side-chains REVERT: A 102 PHE cc_start: 0.8623 (p90) cc_final: 0.8359 (p90) REVERT: A 326 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7192 (tm-30) REVERT: B 45 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8030 (ttp80) REVERT: B 65 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7590 (tpt170) REVERT: B 117 ASP cc_start: 0.7832 (m-30) cc_final: 0.7540 (m-30) REVERT: B 136 LYS cc_start: 0.7944 (ttmm) cc_final: 0.7731 (ttmm) REVERT: B 226 GLU cc_start: 0.7985 (tp30) cc_final: 0.7701 (tp30) REVERT: B 373 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.7224 (t80) REVERT: C 24 GLN cc_start: 0.8113 (mt0) cc_final: 0.7868 (tt0) REVERT: C 45 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7857 (ttp80) REVERT: C 129 LYS cc_start: 0.8373 (mmtt) cc_final: 0.8161 (mmtt) REVERT: C 373 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.6952 (t80) REVERT: D 216 GLU cc_start: 0.7618 (mp0) cc_final: 0.7240 (mp0) REVERT: D 326 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7708 (tm-30) REVERT: E 45 ARG cc_start: 0.8796 (ttm170) cc_final: 0.8507 (ttp80) REVERT: E 260 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7853 (mp) REVERT: E 270 LEU cc_start: 0.8478 (mt) cc_final: 0.8224 (mp) REVERT: E 415 ASN cc_start: 0.8342 (m-40) cc_final: 0.8089 (m-40) REVERT: F 326 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7583 (tm-30) outliers start: 63 outliers final: 31 residues processed: 522 average time/residue: 0.5782 time to fit residues: 339.1925 Evaluate side-chains 530 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 493 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 87 LEU 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 441 LEU Chi-restraints excluded: chain B residue 45 ARG 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 C residue 45 ARG 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 207 ASP Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 263 GLU 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 263 GLU Chi-restraints excluded: chain E residue 257 TYR Chi-restraints excluded: chain E residue 260 ILE 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 153 GLN Chi-restraints excluded: chain F residue 205 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 236 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 225 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN B 3 ASN B 345 GLN C 52 GLN D 24 GLN D 343 ASN E 24 GLN E 52 GLN E 137 ASN F 52 GLN F 137 ASN F 343 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.136165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118547 restraints weight = 25392.089| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.71 r_work: 0.3360 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20424 Z= 0.146 Angle : 0.472 5.184 27732 Z= 0.258 Chirality : 0.037 0.147 3126 Planarity : 0.003 0.032 3474 Dihedral : 4.080 37.275 2850 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.56 % Allowed : 18.32 % Favored : 78.12 % 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: 1.10 (0.17), residues: 2532 helix: 1.97 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.94 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 242 TYR 0.018 0.001 TYR B 257 PHE 0.015 0.001 PHE F 220 TRP 0.008 0.001 TRP A 240 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (20424) covalent geometry : angle 0.47209 / 0.26 (27732) hydrogen bonds : bond 0.06557 / 4.54 ( 1182) hydrogen bonds : angle 3.80395 / 2.68 ( 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 564 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 495 time to evaluate : 0.767 Fit side-chains REVERT: A 102 PHE cc_start: 0.8627 (p90) cc_final: 0.8371 (p90) REVERT: A 326 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 65 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7461 (tpt170) REVERT: B 117 ASP cc_start: 0.7876 (m-30) cc_final: 0.7522 (m-30) REVERT: B 136 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7732 (ttmm) REVERT: B 226 GLU cc_start: 0.7990 (tp30) cc_final: 0.7686 (tp30) REVERT: B 373 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.7294 (t80) REVERT: C 24 GLN cc_start: 0.8134 (mt0) cc_final: 0.7891 (tt0) REVERT: C 226 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: C 280 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6798 (mtp) REVERT: C 373 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.6985 (t80) REVERT: D 216 GLU cc_start: 0.7678 (mp0) cc_final: 0.7288 (mp0) REVERT: D 326 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7730 (tm-30) REVERT: E 11 LYS cc_start: 0.8243 (ptmt) cc_final: 0.7958 (tttt) REVERT: E 45 ARG cc_start: 0.8804 (ttm110) cc_final: 0.8518 (ttp80) REVERT: E 260 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7896 (mp) REVERT: E 270 LEU cc_start: 0.8456 (mt) cc_final: 0.8218 (mp) REVERT: E 415 ASN cc_start: 0.8364 (m-40) cc_final: 0.8091 (m-40) REVERT: F 202 SER cc_start: 0.8153 (t) cc_final: 0.7921 (p) REVERT: F 326 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7614 (tm-30) outliers start: 69 outliers final: 39 residues processed: 519 average time/residue: 0.6020 time to fit residues: 350.5707 Evaluate side-chains 540 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 495 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 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 270 LEU 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 207 ASP Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 280 MET 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 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 128 GLU Chi-restraints excluded: chain E residue 155 LEU 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 260 ILE 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 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 373 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 155 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 200 optimal weight: 0.7980 chunk 230 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN B 3 ASN B 52 GLN B 343 ASN B 345 GLN C 52 GLN C 343 ASN C 345 GLN C 434 ASN D 24 GLN D 343 ASN E 24 GLN E 137 ASN F 137 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.134693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.117070 restraints weight = 25320.991| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.70 r_work: 0.3339 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20424 Z= 0.169 Angle : 0.494 5.411 27732 Z= 0.271 Chirality : 0.038 0.150 3126 Planarity : 0.003 0.031 3474 Dihedral : 4.145 37.014 2850 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.61 % Allowed : 18.27 % Favored : 78.12 % 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: 1.02 (0.17), residues: 2532 helix: 1.91 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.96 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 65 TYR 0.020 0.002 TYR B 257 PHE 0.018 0.001 PHE F 220 TRP 0.008 0.001 TRP A 240 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (20424) covalent geometry : angle 0.49399 / 0.27 (27732) hydrogen bonds : bond 0.07159 / 4.94 ( 1182) hydrogen bonds : angle 3.85361 / 2.72 ( 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 572 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 502 time to evaluate : 0.798 Fit side-chains REVERT: A 102 PHE cc_start: 0.8647 (p90) cc_final: 0.8394 (p90) REVERT: A 229 LEU cc_start: 0.8398 (mt) cc_final: 0.8175 (mp) REVERT: B 45 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8102 (ttp80) REVERT: B 65 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7505 (tpt170) REVERT: B 117 ASP cc_start: 0.7909 (m-30) cc_final: 0.7535 (m-30) REVERT: B 226 GLU cc_start: 0.7990 (tp30) cc_final: 0.7687 (tp30) REVERT: B 373 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7412 (t80) REVERT: C 24 GLN cc_start: 0.8170 (mt0) cc_final: 0.7894 (tt0) REVERT: C 226 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7125 (tt0) REVERT: C 373 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7060 (t80) REVERT: D 216 GLU cc_start: 0.7688 (mp0) cc_final: 0.7328 (mp0) REVERT: D 326 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7786 (tm-30) REVERT: E 11 LYS cc_start: 0.8257 (ptmt) cc_final: 0.7974 (tttt) REVERT: E 45 ARG cc_start: 0.8804 (ttm110) cc_final: 0.8509 (ttp80) REVERT: E 260 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7733 (mt) REVERT: E 270 LEU cc_start: 0.8476 (mt) cc_final: 0.8244 (mp) REVERT: E 280 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7310 (mtp) REVERT: E 415 ASN cc_start: 0.8375 (m-40) cc_final: 0.8111 (m-40) REVERT: F 202 SER cc_start: 0.8108 (t) cc_final: 0.7901 (p) REVERT: F 326 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7662 (tm-30) outliers start: 70 outliers final: 48 residues processed: 523 average time/residue: 0.5953 time to fit residues: 349.7963 Evaluate side-chains 555 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 500 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 45 ARG 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 358 ARG Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 374 GLU 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 207 ASP 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 88 LEU Chi-restraints excluded: chain D residue 263 GLU 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 155 LEU 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 260 ILE Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 280 MET 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 153 GLN Chi-restraints excluded: chain F residue 155 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 182 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 250 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 218 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN B 3 ASN B 52 GLN B 343 ASN C 52 GLN C 345 GLN D 24 GLN D 343 ASN E 137 ASN F 24 GLN F 137 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.134983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117465 restraints weight = 25315.220| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.70 r_work: 0.3343 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20424 Z= 0.167 Angle : 0.495 5.714 27732 Z= 0.270 Chirality : 0.038 0.155 3126 Planarity : 0.003 0.034 3474 Dihedral : 4.149 36.872 2850 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.82 % Allowed : 18.89 % Favored : 77.30 % 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: 1.02 (0.17), residues: 2532 helix: 1.91 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.99 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.019 0.001 TYR B 257 PHE 0.017 0.001 PHE F 220 TRP 0.009 0.001 TRP A 240 HIS 0.005 0.001 HIS F 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (20424) covalent geometry : angle 0.49534 / 0.27 (27732) hydrogen bonds : bond 0.07045 / 4.87 ( 1182) hydrogen bonds : angle 3.84240 / 2.71 ( 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 572 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 498 time to evaluate : 0.561 Fit side-chains REVERT: A 102 PHE cc_start: 0.8639 (p90) cc_final: 0.8384 (p90) REVERT: A 229 LEU cc_start: 0.8370 (mt) cc_final: 0.8143 (mp) REVERT: B 45 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8077 (ttp80) REVERT: B 65 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7485 (tpt170) REVERT: B 117 ASP cc_start: 0.7919 (m-30) cc_final: 0.7572 (m-30) REVERT: B 226 GLU cc_start: 0.7991 (tp30) cc_final: 0.7698 (tp30) REVERT: B 373 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7397 (t80) REVERT: C 24 GLN cc_start: 0.8180 (mt0) cc_final: 0.7914 (tt0) REVERT: C 45 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.7993 (ttp80) REVERT: C 280 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6817 (mtp) REVERT: C 373 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7076 (t80) REVERT: D 216 GLU cc_start: 0.7697 (mp0) cc_final: 0.7330 (mp0) REVERT: D 326 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7782 (tm-30) REVERT: E 11 LYS cc_start: 0.8261 (ptmt) cc_final: 0.7972 (tttt) REVERT: E 45 ARG cc_start: 0.8803 (ttm110) cc_final: 0.8522 (ttp80) REVERT: E 260 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7877 (mm) REVERT: E 270 LEU cc_start: 0.8477 (mt) cc_final: 0.8242 (mp) REVERT: E 280 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7312 (mtp) REVERT: E 415 ASN cc_start: 0.8372 (m-40) cc_final: 0.8109 (m-40) REVERT: F 65 ARG cc_start: 0.7817 (mmt90) cc_final: 0.7411 (mmt180) REVERT: F 202 SER cc_start: 0.8053 (t) cc_final: 0.7798 (p) REVERT: F 326 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7631 (tm-30) outliers start: 74 outliers final: 50 residues processed: 520 average time/residue: 0.5990 time to fit residues: 348.7302 Evaluate side-chains 555 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 497 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 257 TYR 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 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 45 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 280 MET 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 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 417 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 155 LEU 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 260 ILE Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 280 MET 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 155 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 65 optimal weight: 0.0870 chunk 247 optimal weight: 8.9990 chunk 202 optimal weight: 1.9990 chunk 254 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 177 optimal weight: 0.0570 chunk 145 optimal weight: 1.9990 chunk 176 optimal weight: 0.2980 chunk 83 optimal weight: 0.1980 chunk 160 optimal weight: 0.9980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 3 ASN D 24 GLN D 343 ASN E 137 ASN F 24 GLN F 137 ASN F 400 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.141209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124034 restraints weight = 25730.820| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.69 r_work: 0.3451 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20424 Z= 0.096 Angle : 0.418 5.326 27732 Z= 0.228 Chirality : 0.035 0.164 3126 Planarity : 0.003 0.029 3474 Dihedral : 3.712 36.782 2850 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.73 % Allowed : 20.64 % 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: 1.55 (0.17), residues: 2532 helix: 2.32 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.76 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 302 TYR 0.016 0.001 TYR A 257 PHE 0.008 0.001 PHE A 262 TRP 0.006 0.001 TRP A 240 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.10 (20424) covalent geometry : angle 0.41797 / 0.23 (27732) hydrogen bonds : bond 0.04429 / 3.08 ( 1182) hydrogen bonds : angle 3.60101 / 2.55 ( 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 541 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 488 time to evaluate : 0.708 Fit side-chains REVERT: A 102 PHE cc_start: 0.8545 (p90) cc_final: 0.8332 (p90) REVERT: A 305 TYR cc_start: 0.7607 (t80) cc_final: 0.7387 (t80) REVERT: B 226 GLU cc_start: 0.7919 (tp30) cc_final: 0.7653 (tp30) REVERT: B 373 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.6856 (t80) REVERT: C 24 GLN cc_start: 0.8117 (mt0) cc_final: 0.7882 (tt0) REVERT: C 373 TYR cc_start: 0.7574 (OUTLIER) cc_final: 0.6787 (t80) REVERT: D 216 GLU cc_start: 0.7651 (mp0) cc_final: 0.7232 (mp0) REVERT: D 305 TYR cc_start: 0.7788 (t80) cc_final: 0.7527 (t80) REVERT: E 45 ARG cc_start: 0.8760 (ttm110) cc_final: 0.8543 (ttp80) REVERT: E 260 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7712 (mm) REVERT: E 270 LEU cc_start: 0.8411 (mt) cc_final: 0.8179 (mp) REVERT: E 330 LEU cc_start: 0.8577 (tp) cc_final: 0.8332 (mt) REVERT: E 415 ASN cc_start: 0.8337 (m-40) cc_final: 0.8084 (m-40) REVERT: F 52 GLN cc_start: 0.7963 (tp40) cc_final: 0.7400 (tp-100) REVERT: F 202 SER cc_start: 0.8041 (t) cc_final: 0.7801 (p) REVERT: F 263 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6872 (pt0) REVERT: F 323 MET cc_start: 0.7738 (tpt) cc_final: 0.7537 (mmm) REVERT: F 326 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7407 (tm-30) REVERT: F 411 SER cc_start: 0.7620 (OUTLIER) cc_final: 0.7327 (m) outliers start: 53 outliers final: 23 residues processed: 511 average time/residue: 0.5645 time to fit residues: 324.7103 Evaluate side-chains 502 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 474 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain B residue 62 VAL 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 373 TYR Chi-restraints excluded: chain C residue 430 LYS 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 257 TYR Chi-restraints excluded: chain E residue 260 ILE 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 257 TYR Chi-restraints excluded: chain F residue 263 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: 0.9980 chunk 226 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 113 optimal weight: 0.0000 chunk 20 optimal weight: 0.7980 chunk 243 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN A 343 ASN B 3 ASN B 52 GLN B 343 ASN B 345 GLN C 52 GLN C 153 GLN C 343 ASN C 345 GLN D 24 GLN D 63 HIS D 343 ASN E 52 GLN E 137 ASN F 137 ASN F 343 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.139079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121816 restraints weight = 25578.927| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.68 r_work: 0.3418 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 0.002 0.035 20424 Z= 0.111 Angle : 0.444 5.419 27732 Z= 0.240 Chirality : 0.035 0.168 3126 Planarity : 0.003 0.029 3474 Dihedral : 3.698 36.435 2850 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.12 % Allowed : 22.14 % Favored : 75.75 % 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: 1.79 (0.17), residues: 2532 helix: 2.46 (0.13), residues: 1644 sheet: None (None), residues: 0 loop : -1.39 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 65 TYR 0.017 0.001 TYR B 257 PHE 0.011 0.001 PHE F 220 TRP 0.007 0.001 TRP A 240 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (20424) covalent geometry : angle 0.44378 / 0.24 (27732) hydrogen bonds : bond 0.05102 / 3.55 ( 1182) hydrogen bonds : angle 3.60674 / 2.56 ( 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 524 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 483 time to evaluate : 0.668 Fit side-chains REVERT: A 102 PHE cc_start: 0.8569 (p90) cc_final: 0.8321 (p90) REVERT: A 266 ILE cc_start: 0.7461 (mt) cc_final: 0.7004 (tt) REVERT: A 326 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7559 (tm-30) REVERT: B 226 GLU cc_start: 0.7947 (tp30) cc_final: 0.7675 (tp30) REVERT: B 354 LEU cc_start: 0.8697 (tp) cc_final: 0.8492 (tt) REVERT: B 373 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.6986 (t80) REVERT: C 24 GLN cc_start: 0.8141 (mt0) cc_final: 0.7901 (tt0) REVERT: C 373 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.6812 (t80) REVERT: D 216 GLU cc_start: 0.7671 (mp0) cc_final: 0.7268 (mp0) REVERT: D 293 TYR cc_start: 0.7700 (t80) cc_final: 0.7491 (t80) REVERT: D 305 TYR cc_start: 0.7830 (t80) cc_final: 0.7555 (t80) REVERT: E 263 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6981 (pt0) REVERT: E 270 LEU cc_start: 0.8388 (mt) cc_final: 0.8161 (mp) REVERT: E 330 LEU cc_start: 0.8580 (tp) cc_final: 0.8339 (mt) REVERT: E 415 ASN cc_start: 0.8358 (m-40) cc_final: 0.8088 (m-40) REVERT: F 202 SER cc_start: 0.8019 (t) cc_final: 0.7818 (p) REVERT: F 263 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6878 (pt0) REVERT: F 323 MET cc_start: 0.7815 (tpt) cc_final: 0.7550 (mmm) REVERT: F 326 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7533 (tm-30) REVERT: F 411 SER cc_start: 0.7702 (OUTLIER) cc_final: 0.7406 (m) outliers start: 41 outliers final: 25 residues processed: 500 average time/residue: 0.5967 time to fit residues: 335.4344 Evaluate side-chains 506 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 476 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 263 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 D residue 27 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 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 257 TYR Chi-restraints excluded: chain F residue 263 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 0.0980 chunk 254 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 236 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 3 ASN B 343 ASN B 345 GLN C 52 GLN C 343 ASN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 343 ASN E 137 ASN F 24 GLN F 137 ASN F 343 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.116213 restraints weight = 25472.526| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.70 r_work: 0.3327 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20424 Z= 0.207 Angle : 0.549 6.159 27732 Z= 0.297 Chirality : 0.041 0.169 3126 Planarity : 0.003 0.034 3474 Dihedral : 4.159 36.212 2850 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.86 % Allowed : 23.01 % Favored : 75.13 % 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: 1.02 (0.17), residues: 2532 helix: 1.88 (0.13), residues: 1686 sheet: None (None), residues: 0 loop : -1.94 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 65 TYR 0.023 0.002 TYR B 257 PHE 0.018 0.002 PHE F 220 TRP 0.008 0.002 TRP A 240 HIS 0.006 0.001 HIS E 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (20424) covalent geometry : angle 0.54864 / 0.30 (27732) hydrogen bonds : bond 0.07778 / 5.38 ( 1182) hydrogen bonds : angle 3.90429 / 2.76 ( 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 545 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 509 time to evaluate : 0.714 Fit side-chains REVERT: A 25 ASP cc_start: 0.7089 (m-30) cc_final: 0.6821 (m-30) REVERT: A 102 PHE cc_start: 0.8703 (p90) cc_final: 0.8447 (p90) REVERT: A 229 LEU cc_start: 0.8414 (mt) cc_final: 0.8187 (mp) REVERT: B 52 GLN cc_start: 0.7950 (tp40) cc_final: 0.7711 (tp-100) REVERT: B 226 GLU cc_start: 0.7994 (tp30) cc_final: 0.7705 (tp30) REVERT: B 373 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7564 (t80) REVERT: C 24 GLN cc_start: 0.8200 (mt0) cc_final: 0.7966 (tt0) REVERT: C 373 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7147 (t80) REVERT: D 216 GLU cc_start: 0.7681 (mp0) cc_final: 0.7320 (mp0) REVERT: E 11 LYS cc_start: 0.8259 (ptmt) cc_final: 0.7974 (tttt) REVERT: E 270 LEU cc_start: 0.8452 (mt) cc_final: 0.8232 (mp) REVERT: E 330 LEU cc_start: 0.8634 (tp) cc_final: 0.8361 (mt) REVERT: E 415 ASN cc_start: 0.8406 (m-40) cc_final: 0.8197 (m-40) REVERT: F 202 SER cc_start: 0.8037 (t) cc_final: 0.7749 (p) REVERT: F 226 GLU cc_start: 0.7737 (tp30) cc_final: 0.7460 (tt0) REVERT: F 326 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7661 (tm-30) outliers start: 36 outliers final: 29 residues processed: 522 average time/residue: 0.6044 time to fit residues: 354.1165 Evaluate side-chains 536 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 505 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 263 GLU 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 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 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 398 ILE Chi-restraints excluded: chain E residue 427 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 251 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 245 optimal weight: 0.5980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 3 ASN B 343 ASN C 345 GLN D 343 ASN E 137 ASN F 137 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118340 restraints weight = 25442.245| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.70 r_work: 0.3361 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3089 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= 0.149 Angle : 0.491 5.932 27732 Z= 0.268 Chirality : 0.038 0.165 3126 Planarity : 0.003 0.044 3474 Dihedral : 4.024 36.255 2850 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 1.10 (0.17), residues: 2532 helix: 1.98 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.96 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 65 TYR 0.017 0.001 TYR A 257 PHE 0.013 0.001 PHE F 220 TRP 0.009 0.001 TRP A 240 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (20424) covalent geometry : angle 0.49138 / 0.27 (27732) hydrogen bonds : bond 0.06505 / 4.51 ( 1182) hydrogen bonds : angle 3.80215 / 2.69 ( 3456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7527.32 seconds wall clock time: 128 minutes 18.14 seconds (7698.14 seconds total)