Starting phenix.real_space_refine on Thu Mar 5 13:43:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uiv_20788/03_2026/6uiv_20788.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uiv_20788/03_2026/6uiv_20788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uiv_20788/03_2026/6uiv_20788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uiv_20788/03_2026/6uiv_20788.map" model { file = "/net/cci-nas-00/data/ceres_data/6uiv_20788/03_2026/6uiv_20788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uiv_20788/03_2026/6uiv_20788.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 14861 2.51 5 N 4191 2.21 5 O 3773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22902 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 2, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "B" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 2, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 2, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "D" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 2, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "E" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 2, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "F" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 2, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "G" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 2, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "H" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 2, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "I" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 2, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "J" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 2, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "K" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 2, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Time building chain proxies: 4.72, per 1000 atoms: 0.21 Number of scatterers: 22902 At special positions: 0 Unit cell: (145.692, 146.718, 103.626, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 3773 8.00 N 4191 7.00 C 14861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 130 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 162 " distance=2.02 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 130 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 162 " distance=2.02 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 130 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 162 " distance=2.02 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 130 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 130 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 162 " distance=2.02 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 130 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 162 " distance=2.03 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 130 " distance=2.03 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 162 " distance=2.03 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 130 " distance=2.03 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 162 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 975.5 milliseconds 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5984 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 11 sheets defined 77.4% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 20 through 38 removed outlier: 3.520A pdb=" N LEU A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 75 removed outlier: 3.533A pdb=" N TYR A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.564A pdb=" N ARG A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 124 removed outlier: 3.519A pdb=" N LEU A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA A 113 " --> pdb=" O ARG A 109 " (cutoff:3.500A) Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.532A pdb=" N SER A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE A 156 " --> pdb=" O HIS A 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 169 through 209 Processing helix chain 'A' and resid 214 through 251 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 274 through 282 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'B' and resid 21 through 38 removed outlier: 3.520A pdb=" N LEU B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 75 removed outlier: 3.533A pdb=" N TYR B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 77 through 89 removed outlier: 3.563A pdb=" N ARG B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 124 removed outlier: 3.519A pdb=" N LEU B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 125 through 133 removed outlier: 3.533A pdb=" N SER B 133 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE B 156 " --> pdb=" O HIS B 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 169 through 209 Processing helix chain 'B' and resid 214 through 251 Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'C' and resid 21 through 38 removed outlier: 3.521A pdb=" N LEU C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 75 removed outlier: 3.534A pdb=" N TYR C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 77 through 89 removed outlier: 3.564A pdb=" N ARG C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 124 removed outlier: 3.519A pdb=" N LEU C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Proline residue: C 114 - end of helix Processing helix chain 'C' and resid 125 through 133 removed outlier: 3.532A pdb=" N SER C 133 " --> pdb=" O VAL C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.547A pdb=" N ILE C 156 " --> pdb=" O HIS C 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 169 through 209 Processing helix chain 'C' and resid 214 through 251 Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 274 through 282 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'D' and resid 21 through 38 removed outlier: 3.520A pdb=" N LEU D 38 " --> pdb=" O GLY D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 75 removed outlier: 3.533A pdb=" N TYR D 56 " --> pdb=" O ARG D 52 " (cutoff:3.500A) Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 77 through 89 removed outlier: 3.563A pdb=" N ARG D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 124 removed outlier: 3.519A pdb=" N LEU D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Proline residue: D 114 - end of helix Processing helix chain 'D' and resid 125 through 133 removed outlier: 3.532A pdb=" N SER D 133 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE D 156 " --> pdb=" O HIS D 152 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 169 through 209 Processing helix chain 'D' and resid 214 through 251 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 274 through 282 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'E' and resid 21 through 38 removed outlier: 3.520A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.533A pdb=" N TYR E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Proline residue: E 64 - end of helix Processing helix chain 'E' and resid 77 through 89 removed outlier: 3.565A pdb=" N ARG E 89 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 124 removed outlier: 3.519A pdb=" N LEU E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA E 113 " --> pdb=" O ARG E 109 " (cutoff:3.500A) Proline residue: E 114 - end of helix Processing helix chain 'E' and resid 125 through 133 removed outlier: 3.532A pdb=" N SER E 133 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 149 through 151 No H-bonds generated for 'chain 'E' and resid 149 through 151' Processing helix chain 'E' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE E 156 " --> pdb=" O HIS E 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 169 through 209 Processing helix chain 'E' and resid 214 through 251 Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 274 through 282 Processing helix chain 'E' and resid 297 through 306 Processing helix chain 'F' and resid 21 through 38 removed outlier: 3.520A pdb=" N LEU F 38 " --> pdb=" O GLY F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 75 removed outlier: 3.534A pdb=" N TYR F 56 " --> pdb=" O ARG F 52 " (cutoff:3.500A) Proline residue: F 64 - end of helix Processing helix chain 'F' and resid 77 through 89 removed outlier: 3.564A pdb=" N ARG F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 124 removed outlier: 3.520A pdb=" N LEU F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA F 113 " --> pdb=" O ARG F 109 " (cutoff:3.500A) Proline residue: F 114 - end of helix Processing helix chain 'F' and resid 125 through 133 removed outlier: 3.532A pdb=" N SER F 133 " --> pdb=" O VAL F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'F' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE F 156 " --> pdb=" O HIS F 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 163 Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 169 through 209 Processing helix chain 'F' and resid 214 through 251 Processing helix chain 'F' and resid 257 through 267 Processing helix chain 'F' and resid 274 through 282 Processing helix chain 'F' and resid 297 through 306 Processing helix chain 'G' and resid 21 through 38 removed outlier: 3.520A pdb=" N LEU G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 75 removed outlier: 3.533A pdb=" N TYR G 56 " --> pdb=" O ARG G 52 " (cutoff:3.500A) Proline residue: G 64 - end of helix Processing helix chain 'G' and resid 77 through 89 removed outlier: 3.564A pdb=" N ARG G 89 " --> pdb=" O GLU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 124 removed outlier: 3.520A pdb=" N LEU G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ALA G 113 " --> pdb=" O ARG G 109 " (cutoff:3.500A) Proline residue: G 114 - end of helix Processing helix chain 'G' and resid 125 through 133 removed outlier: 3.532A pdb=" N SER G 133 " --> pdb=" O VAL G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 136 No H-bonds generated for 'chain 'G' and resid 134 through 136' Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'G' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE G 156 " --> pdb=" O HIS G 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 163 Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 169 through 209 Processing helix chain 'G' and resid 214 through 251 Processing helix chain 'G' and resid 257 through 267 Processing helix chain 'G' and resid 274 through 282 Processing helix chain 'G' and resid 297 through 306 Processing helix chain 'H' and resid 21 through 38 removed outlier: 3.520A pdb=" N LEU H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 75 removed outlier: 3.533A pdb=" N TYR H 56 " --> pdb=" O ARG H 52 " (cutoff:3.500A) Proline residue: H 64 - end of helix Processing helix chain 'H' and resid 77 through 89 removed outlier: 3.564A pdb=" N ARG H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 124 removed outlier: 3.519A pdb=" N LEU H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA H 113 " --> pdb=" O ARG H 109 " (cutoff:3.500A) Proline residue: H 114 - end of helix Processing helix chain 'H' and resid 125 through 133 removed outlier: 3.532A pdb=" N SER H 133 " --> pdb=" O VAL H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 136 No H-bonds generated for 'chain 'H' and resid 134 through 136' Processing helix chain 'H' and resid 149 through 151 No H-bonds generated for 'chain 'H' and resid 149 through 151' Processing helix chain 'H' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE H 156 " --> pdb=" O HIS H 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 163 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 169 through 209 Processing helix chain 'H' and resid 214 through 251 Processing helix chain 'H' and resid 257 through 267 Processing helix chain 'H' and resid 274 through 282 Processing helix chain 'H' and resid 297 through 306 Processing helix chain 'I' and resid 21 through 38 removed outlier: 3.520A pdb=" N LEU I 38 " --> pdb=" O GLY I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 75 removed outlier: 3.533A pdb=" N TYR I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'I' and resid 77 through 89 removed outlier: 3.564A pdb=" N ARG I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 124 removed outlier: 3.520A pdb=" N LEU I 101 " --> pdb=" O ALA I 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA I 113 " --> pdb=" O ARG I 109 " (cutoff:3.500A) Proline residue: I 114 - end of helix Processing helix chain 'I' and resid 125 through 133 removed outlier: 3.533A pdb=" N SER I 133 " --> pdb=" O VAL I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'I' and resid 149 through 151 No H-bonds generated for 'chain 'I' and resid 149 through 151' Processing helix chain 'I' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE I 156 " --> pdb=" O HIS I 152 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG I 159 " --> pdb=" O GLU I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 163 Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 209 Processing helix chain 'I' and resid 214 through 251 Processing helix chain 'I' and resid 257 through 267 Processing helix chain 'I' and resid 274 through 282 Processing helix chain 'I' and resid 297 through 306 Processing helix chain 'J' and resid 21 through 38 removed outlier: 3.521A pdb=" N LEU J 38 " --> pdb=" O GLY J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 75 removed outlier: 3.534A pdb=" N TYR J 56 " --> pdb=" O ARG J 52 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.564A pdb=" N ARG J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 124 removed outlier: 3.519A pdb=" N LEU J 101 " --> pdb=" O ALA J 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA J 113 " --> pdb=" O ARG J 109 " (cutoff:3.500A) Proline residue: J 114 - end of helix Processing helix chain 'J' and resid 125 through 133 removed outlier: 3.533A pdb=" N SER J 133 " --> pdb=" O VAL J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 136 No H-bonds generated for 'chain 'J' and resid 134 through 136' Processing helix chain 'J' and resid 149 through 151 No H-bonds generated for 'chain 'J' and resid 149 through 151' Processing helix chain 'J' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE J 156 " --> pdb=" O HIS J 152 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG J 159 " --> pdb=" O GLU J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 163 Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 169 through 209 Processing helix chain 'J' and resid 214 through 251 Processing helix chain 'J' and resid 257 through 267 Processing helix chain 'J' and resid 274 through 282 Processing helix chain 'J' and resid 297 through 306 Processing helix chain 'K' and resid 21 through 38 removed outlier: 3.520A pdb=" N LEU K 38 " --> pdb=" O GLY K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 75 removed outlier: 3.533A pdb=" N TYR K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 77 through 89 removed outlier: 3.564A pdb=" N ARG K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 124 removed outlier: 3.519A pdb=" N LEU K 101 " --> pdb=" O ALA K 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA K 113 " --> pdb=" O ARG K 109 " (cutoff:3.500A) Proline residue: K 114 - end of helix Processing helix chain 'K' and resid 125 through 133 removed outlier: 3.532A pdb=" N SER K 133 " --> pdb=" O VAL K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 136 No H-bonds generated for 'chain 'K' and resid 134 through 136' Processing helix chain 'K' and resid 149 through 151 No H-bonds generated for 'chain 'K' and resid 149 through 151' Processing helix chain 'K' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE K 156 " --> pdb=" O HIS K 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 163 Processing helix chain 'K' and resid 166 through 168 No H-bonds generated for 'chain 'K' and resid 166 through 168' Processing helix chain 'K' and resid 169 through 209 Processing helix chain 'K' and resid 214 through 251 Processing helix chain 'K' and resid 257 through 267 Processing helix chain 'K' and resid 274 through 282 Processing helix chain 'K' and resid 297 through 306 Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 290 Processing sheet with id=AA2, first strand: chain 'B' and resid 289 through 290 Processing sheet with id=AA3, first strand: chain 'C' and resid 289 through 290 Processing sheet with id=AA4, first strand: chain 'D' and resid 289 through 290 Processing sheet with id=AA5, first strand: chain 'E' and resid 289 through 290 Processing sheet with id=AA6, first strand: chain 'F' and resid 289 through 290 Processing sheet with id=AA7, first strand: chain 'G' and resid 289 through 290 Processing sheet with id=AA8, first strand: chain 'H' and resid 289 through 290 Processing sheet with id=AA9, first strand: chain 'I' and resid 289 through 290 Processing sheet with id=AB1, first strand: chain 'J' and resid 289 through 290 Processing sheet with id=AB2, first strand: chain 'K' and resid 289 through 290 1695 hydrogen bonds defined for protein. 5019 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7472 1.34 - 1.46: 5166 1.46 - 1.58: 10814 1.58 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 23529 Sorted by residual: bond pdb=" N THR G 272 " pdb=" CA THR G 272 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.23e-02 6.61e+03 9.65e+00 bond pdb=" N THR F 272 " pdb=" CA THR F 272 " ideal model delta sigma weight residual 1.454 1.491 -0.038 1.23e-02 6.61e+03 9.50e+00 bond pdb=" N THR K 272 " pdb=" CA THR K 272 " ideal model delta sigma weight residual 1.454 1.491 -0.038 1.23e-02 6.61e+03 9.45e+00 bond pdb=" N THR J 272 " pdb=" CA THR J 272 " ideal model delta sigma weight residual 1.454 1.491 -0.038 1.23e-02 6.61e+03 9.45e+00 bond pdb=" N THR H 272 " pdb=" CA THR H 272 " ideal model delta sigma weight residual 1.454 1.491 -0.038 1.23e-02 6.61e+03 9.45e+00 ... (remaining 23524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 30285 1.66 - 3.32: 1677 3.32 - 4.98: 213 4.98 - 6.64: 85 6.64 - 8.31: 25 Bond angle restraints: 32285 Sorted by residual: angle pdb=" C GLN E 36 " pdb=" N GLU E 37 " pdb=" CA GLU E 37 " ideal model delta sigma weight residual 120.28 126.20 -5.92 1.34e+00 5.57e-01 1.95e+01 angle pdb=" C GLN A 36 " pdb=" N GLU A 37 " pdb=" CA GLU A 37 " ideal model delta sigma weight residual 120.28 126.18 -5.90 1.34e+00 5.57e-01 1.94e+01 angle pdb=" C GLN F 36 " pdb=" N GLU F 37 " pdb=" CA GLU F 37 " ideal model delta sigma weight residual 120.28 126.15 -5.87 1.34e+00 5.57e-01 1.92e+01 angle pdb=" C GLN C 36 " pdb=" N GLU C 37 " pdb=" CA GLU C 37 " ideal model delta sigma weight residual 120.28 126.13 -5.85 1.34e+00 5.57e-01 1.91e+01 angle pdb=" C ALA I 43 " pdb=" N PHE I 44 " pdb=" CA PHE I 44 " ideal model delta sigma weight residual 121.54 113.23 8.31 1.91e+00 2.74e-01 1.89e+01 ... (remaining 32280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 12384 16.44 - 32.88: 1080 32.88 - 49.32: 176 49.32 - 65.76: 11 65.76 - 82.20: 33 Dihedral angle restraints: 13684 sinusoidal: 4433 harmonic: 9251 Sorted by residual: dihedral pdb=" CA ALA J 96 " pdb=" C ALA J 96 " pdb=" N ALA J 97 " pdb=" CA ALA J 97 " ideal model delta harmonic sigma weight residual -180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA ALA H 96 " pdb=" C ALA H 96 " pdb=" N ALA H 97 " pdb=" CA ALA H 97 " ideal model delta harmonic sigma weight residual -180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA ALA F 96 " pdb=" C ALA F 96 " pdb=" N ALA F 97 " pdb=" CA ALA F 97 " ideal model delta harmonic sigma weight residual 180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 13681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2952 0.066 - 0.132: 656 0.132 - 0.199: 88 0.199 - 0.265: 0 0.265 - 0.331: 11 Chirality restraints: 3707 Sorted by residual: chirality pdb=" CB VAL J 83 " pdb=" CA VAL J 83 " pdb=" CG1 VAL J 83 " pdb=" CG2 VAL J 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB VAL G 83 " pdb=" CA VAL G 83 " pdb=" CG1 VAL G 83 " pdb=" CG2 VAL G 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB VAL I 83 " pdb=" CA VAL I 83 " pdb=" CG1 VAL I 83 " pdb=" CG2 VAL I 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 3704 not shown) Planarity restraints: 4169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 97 " 0.054 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO E 98 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 98 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 98 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 97 " -0.054 5.00e-02 4.00e+02 8.18e-02 1.07e+01 pdb=" N PRO I 98 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO I 98 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO I 98 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 97 " -0.054 5.00e-02 4.00e+02 8.18e-02 1.07e+01 pdb=" N PRO H 98 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO H 98 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO H 98 " -0.045 5.00e-02 4.00e+02 ... (remaining 4166 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3715 2.75 - 3.29: 22524 3.29 - 3.83: 39959 3.83 - 4.36: 43001 4.36 - 4.90: 75811 Nonbonded interactions: 185010 Sorted by model distance: nonbonded pdb=" N GLN B 273 " pdb=" OE1 GLN B 273 " model vdw 2.218 3.120 nonbonded pdb=" N GLN I 273 " pdb=" OE1 GLN I 273 " model vdw 2.219 3.120 nonbonded pdb=" N GLN D 273 " pdb=" OE1 GLN D 273 " model vdw 2.219 3.120 nonbonded pdb=" N GLN G 273 " pdb=" OE1 GLN G 273 " model vdw 2.219 3.120 nonbonded pdb=" N GLN H 273 " pdb=" OE1 GLN H 273 " model vdw 2.219 3.120 ... (remaining 185005 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.320 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 0.068 23551 Z= 0.366 Angle : 0.890 8.305 32329 Z= 0.541 Chirality : 0.056 0.331 3707 Planarity : 0.008 0.082 4169 Dihedral : 13.351 82.197 7634 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.13 % Allowed : 11.25 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.10), residues: 3135 helix: -2.00 (0.07), residues: 2211 sheet: None (None), residues: 0 loop : -2.74 (0.17), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 298 TYR 0.013 0.003 TYR F 287 PHE 0.011 0.002 PHE F 253 TRP 0.007 0.002 TRP E 80 HIS 0.009 0.001 HIS F 88 Details of bonding type rmsd covalent geometry : bond 0.00715 (23529) covalent geometry : angle 0.88952 (32285) SS BOND : bond 0.00440 ( 22) SS BOND : angle 1.29002 ( 44) hydrogen bonds : bond 0.08526 ( 1695) hydrogen bonds : angle 5.52873 ( 5019) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 281 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ILE cc_start: 0.9198 (tp) cc_final: 0.8808 (tp) REVERT: B 156 ILE cc_start: 0.9187 (tp) cc_final: 0.8749 (tp) REVERT: D 156 ILE cc_start: 0.9187 (tp) cc_final: 0.8822 (tp) REVERT: E 156 ILE cc_start: 0.9189 (tp) cc_final: 0.8835 (tp) REVERT: F 71 ILE cc_start: 0.9483 (mt) cc_final: 0.9281 (mt) REVERT: F 156 ILE cc_start: 0.9178 (tp) cc_final: 0.8789 (tp) REVERT: G 156 ILE cc_start: 0.9225 (tp) cc_final: 0.8838 (tp) REVERT: H 156 ILE cc_start: 0.9232 (tp) cc_final: 0.8832 (tp) REVERT: I 156 ILE cc_start: 0.9182 (tp) cc_final: 0.8741 (tp) REVERT: I 222 GLN cc_start: 0.8322 (mt0) cc_final: 0.8121 (mt0) REVERT: K 156 ILE cc_start: 0.9187 (tp) cc_final: 0.8787 (tp) outliers start: 22 outliers final: 1 residues processed: 303 average time/residue: 0.1221 time to fit residues: 63.6071 Evaluate side-chains 200 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 247 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.0670 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 226 ASN A 279 ASN B 185 GLN B 216 GLN B 226 ASN B 279 ASN C 185 GLN C 216 GLN C 226 ASN C 279 ASN D 185 GLN D 216 GLN D 226 ASN D 279 ASN E 185 GLN E 226 ASN E 279 ASN F 185 GLN F 226 ASN F 279 ASN G 185 GLN G 226 ASN G 279 ASN H 185 GLN H 226 ASN H 279 ASN I 185 GLN I 216 GLN I 226 ASN I 279 ASN J 185 GLN J 226 ASN J 279 ASN K 185 GLN K 226 ASN K 279 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.090925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.068294 restraints weight = 74266.929| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.19 r_work: 0.3233 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23551 Z= 0.115 Angle : 0.538 5.632 32329 Z= 0.287 Chirality : 0.037 0.116 3707 Planarity : 0.005 0.059 4169 Dihedral : 4.529 23.593 3455 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.36 % Allowed : 13.25 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 3135 helix: 0.63 (0.10), residues: 2233 sheet: None (None), residues: 0 loop : -2.07 (0.18), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 233 TYR 0.011 0.001 TYR J 223 PHE 0.009 0.001 PHE G 69 TRP 0.006 0.001 TRP H 220 HIS 0.023 0.002 HIS J 152 Details of bonding type rmsd covalent geometry : bond 0.00249 (23529) covalent geometry : angle 0.53815 (32285) SS BOND : bond 0.00086 ( 22) SS BOND : angle 0.64797 ( 44) hydrogen bonds : bond 0.03183 ( 1695) hydrogen bonds : angle 3.67745 ( 5019) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 239 time to evaluate : 0.835 Fit side-chains REVERT: A 229 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8426 (tm-30) REVERT: C 227 GLU cc_start: 0.8879 (tt0) cc_final: 0.8676 (tt0) REVERT: D 296 TYR cc_start: 0.9213 (m-80) cc_final: 0.8949 (m-80) REVERT: F 71 ILE cc_start: 0.9501 (mt) cc_final: 0.9291 (mt) REVERT: I 222 GLN cc_start: 0.9031 (mt0) cc_final: 0.8787 (mt0) REVERT: K 229 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8469 (tm-30) outliers start: 7 outliers final: 5 residues processed: 245 average time/residue: 0.1193 time to fit residues: 51.8307 Evaluate side-chains 212 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 207 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain J residue 201 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 174 optimal weight: 4.9990 chunk 56 optimal weight: 80.0000 chunk 82 optimal weight: 4.9990 chunk 140 optimal weight: 80.0000 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 246 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 287 optimal weight: 0.4980 chunk 153 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 207 HIS C 207 HIS E 207 HIS F 207 HIS I 207 HIS K 207 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.089680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.066943 restraints weight = 74942.779| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.17 r_work: 0.3197 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23551 Z= 0.147 Angle : 0.519 5.793 32329 Z= 0.276 Chirality : 0.038 0.163 3707 Planarity : 0.004 0.053 4169 Dihedral : 4.117 18.633 3454 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.46 % Allowed : 16.38 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.15), residues: 3135 helix: 1.76 (0.10), residues: 2233 sheet: None (None), residues: 0 loop : -1.45 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 233 TYR 0.010 0.001 TYR A 54 PHE 0.010 0.001 PHE D 69 TRP 0.007 0.001 TRP H 302 HIS 0.002 0.001 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00325 (23529) covalent geometry : angle 0.51883 (32285) SS BOND : bond 0.00193 ( 22) SS BOND : angle 0.66550 ( 44) hydrogen bonds : bond 0.03183 ( 1695) hydrogen bonds : angle 3.32474 ( 5019) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 193 time to evaluate : 0.605 Fit side-chains REVERT: E 152 HIS cc_start: 0.7846 (t-90) cc_final: 0.7573 (t70) REVERT: E 229 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8483 (tm-30) REVERT: F 71 ILE cc_start: 0.9496 (mt) cc_final: 0.9280 (mt) REVERT: F 126 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8547 (pm20) REVERT: G 152 HIS cc_start: 0.7995 (t-90) cc_final: 0.7781 (t70) REVERT: H 152 HIS cc_start: 0.7980 (t-90) cc_final: 0.7712 (t70) REVERT: K 152 HIS cc_start: 0.8183 (t-90) cc_final: 0.7879 (t70) outliers start: 9 outliers final: 7 residues processed: 201 average time/residue: 0.1127 time to fit residues: 40.4909 Evaluate side-chains 190 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 182 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain J residue 201 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 258 optimal weight: 7.9990 chunk 262 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 230 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 HIS D 207 HIS ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.088729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.066177 restraints weight = 75409.442| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.05 r_work: 0.3211 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23551 Z= 0.137 Angle : 0.502 5.744 32329 Z= 0.264 Chirality : 0.038 0.165 3707 Planarity : 0.004 0.051 4169 Dihedral : 3.922 18.067 3454 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.98 % Allowed : 17.57 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.15), residues: 3135 helix: 2.34 (0.11), residues: 2244 sheet: None (None), residues: 0 loop : -1.29 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 233 TYR 0.009 0.001 TYR D 54 PHE 0.010 0.001 PHE B 69 TRP 0.005 0.001 TRP J 220 HIS 0.005 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00306 (23529) covalent geometry : angle 0.50247 (32285) SS BOND : bond 0.00167 ( 22) SS BOND : angle 0.50037 ( 44) hydrogen bonds : bond 0.03048 ( 1695) hydrogen bonds : angle 3.14536 ( 5019) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: D 229 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8539 (tm-30) REVERT: E 152 HIS cc_start: 0.7867 (t-90) cc_final: 0.7637 (t70) REVERT: E 229 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8385 (tm-30) REVERT: F 71 ILE cc_start: 0.9502 (mt) cc_final: 0.9267 (mt) REVERT: G 152 HIS cc_start: 0.7970 (t-90) cc_final: 0.7738 (t70) outliers start: 19 outliers final: 15 residues processed: 195 average time/residue: 0.1163 time to fit residues: 40.2014 Evaluate side-chains 196 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 260 ASP Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 281 ILE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 218 optimal weight: 1.9990 chunk 135 optimal weight: 0.0770 chunk 65 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 303 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 266 optimal weight: 0.0270 chunk 120 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 256 optimal weight: 0.0980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 HIS C 152 HIS C 216 GLN D 152 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 HIS ** H 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 HIS I 216 GLN J 152 HIS ** K 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.090044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.067837 restraints weight = 75535.400| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.99 r_work: 0.3260 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23551 Z= 0.101 Angle : 0.480 7.402 32329 Z= 0.249 Chirality : 0.037 0.178 3707 Planarity : 0.004 0.051 4169 Dihedral : 3.754 16.581 3454 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.31 % Allowed : 18.13 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.15), residues: 3135 helix: 2.63 (0.11), residues: 2244 sheet: None (None), residues: 0 loop : -1.13 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 233 TYR 0.013 0.001 TYR G 287 PHE 0.008 0.001 PHE C 69 TRP 0.005 0.001 TRP C 302 HIS 0.004 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00222 (23529) covalent geometry : angle 0.47992 (32285) SS BOND : bond 0.00141 ( 22) SS BOND : angle 0.47105 ( 44) hydrogen bonds : bond 0.02751 ( 1695) hydrogen bonds : angle 3.00155 ( 5019) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9242 (tt) REVERT: A 229 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8341 (tm-30) REVERT: C 229 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8502 (tm-30) REVERT: D 198 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9278 (tt) REVERT: D 229 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8418 (tm-30) REVERT: E 229 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8356 (tm-30) REVERT: F 71 ILE cc_start: 0.9489 (mt) cc_final: 0.9272 (mt) REVERT: G 198 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9261 (tt) REVERT: H 198 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9247 (tt) REVERT: I 198 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9271 (tt) REVERT: K 198 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9228 (tt) REVERT: K 229 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8414 (tm-30) outliers start: 45 outliers final: 32 residues processed: 237 average time/residue: 0.1171 time to fit residues: 48.6225 Evaluate side-chains 221 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 152 HIS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 281 ILE Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 213 SER Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 213 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 221 optimal weight: 0.0010 chunk 120 optimal weight: 4.9990 chunk 294 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 HIS D 152 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 HIS ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 HIS ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 GLN ** H 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.088401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.065694 restraints weight = 75578.198| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.11 r_work: 0.3187 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23551 Z= 0.165 Angle : 0.525 6.640 32329 Z= 0.276 Chirality : 0.039 0.173 3707 Planarity : 0.004 0.052 4169 Dihedral : 3.789 16.803 3454 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.39 % Allowed : 18.28 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.15), residues: 3135 helix: 2.79 (0.11), residues: 2244 sheet: None (None), residues: 0 loop : -1.05 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 233 TYR 0.009 0.001 TYR H 287 PHE 0.010 0.001 PHE K 69 TRP 0.006 0.001 TRP C 302 HIS 0.019 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00369 (23529) covalent geometry : angle 0.52477 (32285) SS BOND : bond 0.00195 ( 22) SS BOND : angle 0.49040 ( 44) hydrogen bonds : bond 0.03067 ( 1695) hydrogen bonds : angle 3.01761 ( 5019) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 186 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9247 (tt) REVERT: A 229 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8318 (tm-30) REVERT: C 229 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8557 (tm-30) REVERT: D 198 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9227 (tt) REVERT: D 229 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8591 (tm-30) REVERT: E 229 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8405 (tm-30) REVERT: F 71 ILE cc_start: 0.9503 (mt) cc_final: 0.9292 (mt) REVERT: F 198 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9230 (tt) REVERT: G 198 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9235 (tt) REVERT: H 198 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9239 (tt) REVERT: I 198 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9211 (tp) REVERT: K 198 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9234 (tt) REVERT: K 229 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8445 (tm-30) outliers start: 66 outliers final: 52 residues processed: 241 average time/residue: 0.1132 time to fit residues: 47.5378 Evaluate side-chains 237 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 178 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 260 ASP Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 281 ILE Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 213 SER Chi-restraints excluded: chain J residue 281 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 272 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 29 optimal weight: 0.0070 chunk 81 optimal weight: 7.9990 chunk 288 optimal weight: 6.9990 chunk 84 optimal weight: 80.0000 chunk 97 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 276 optimal weight: 6.9990 chunk 252 optimal weight: 80.0000 chunk 79 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 overall best weight: 2.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS B 76 ASN B 152 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 HIS ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.087315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.064606 restraints weight = 75918.280| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.93 r_work: 0.3173 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23551 Z= 0.212 Angle : 0.557 6.213 32329 Z= 0.294 Chirality : 0.040 0.180 3707 Planarity : 0.004 0.052 4169 Dihedral : 3.892 19.074 3454 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.16 % Allowed : 19.36 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.15), residues: 3135 helix: 2.75 (0.11), residues: 2244 sheet: None (None), residues: 0 loop : -1.11 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 233 TYR 0.012 0.001 TYR E 287 PHE 0.011 0.001 PHE C 69 TRP 0.006 0.001 TRP J 220 HIS 0.020 0.001 HIS E 152 Details of bonding type rmsd covalent geometry : bond 0.00468 (23529) covalent geometry : angle 0.55660 (32285) SS BOND : bond 0.00209 ( 22) SS BOND : angle 0.51044 ( 44) hydrogen bonds : bond 0.03347 ( 1695) hydrogen bonds : angle 3.12442 ( 5019) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 184 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9256 (tt) REVERT: A 229 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8341 (tm-30) REVERT: D 198 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9231 (tt) REVERT: D 229 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8611 (tm-30) REVERT: E 229 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8428 (tm-30) REVERT: F 71 ILE cc_start: 0.9512 (mt) cc_final: 0.9301 (mt) REVERT: H 229 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8537 (tm-30) REVERT: K 198 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9210 (tt) outliers start: 81 outliers final: 66 residues processed: 254 average time/residue: 0.1155 time to fit residues: 50.7112 Evaluate side-chains 247 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 178 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 88 HIS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 182 TYR Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 213 SER Chi-restraints excluded: chain J residue 281 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 182 TYR Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 272 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 266 optimal weight: 0.0070 chunk 161 optimal weight: 0.5980 chunk 298 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 148 optimal weight: 0.9980 chunk 241 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS B 76 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 HIS ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 HIS ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.088995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.066911 restraints weight = 75219.602| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.92 r_work: 0.3233 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23551 Z= 0.116 Angle : 0.516 9.706 32329 Z= 0.268 Chirality : 0.038 0.195 3707 Planarity : 0.004 0.052 4169 Dihedral : 3.782 16.339 3454 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.85 % Allowed : 20.13 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.15), residues: 3135 helix: 2.88 (0.11), residues: 2244 sheet: None (None), residues: 0 loop : -1.02 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 233 TYR 0.007 0.001 TYR B 287 PHE 0.008 0.001 PHE B 69 TRP 0.005 0.001 TRP J 220 HIS 0.003 0.001 HIS G 88 Details of bonding type rmsd covalent geometry : bond 0.00263 (23529) covalent geometry : angle 0.51566 (32285) SS BOND : bond 0.00141 ( 22) SS BOND : angle 0.45331 ( 44) hydrogen bonds : bond 0.02942 ( 1695) hydrogen bonds : angle 3.03081 ( 5019) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 187 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8245 (tm-30) REVERT: D 229 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8507 (tm-30) REVERT: E 229 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8394 (tm-30) REVERT: F 71 ILE cc_start: 0.9493 (mt) cc_final: 0.9280 (mt) REVERT: G 198 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9236 (tt) REVERT: H 198 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9239 (tt) REVERT: H 229 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8516 (tm-30) REVERT: I 198 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9218 (tp) outliers start: 75 outliers final: 57 residues processed: 256 average time/residue: 0.1232 time to fit residues: 54.0100 Evaluate side-chains 246 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 186 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 182 TYR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 88 HIS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 182 TYR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 182 TYR Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 260 ASP Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 182 TYR Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 213 SER Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 182 TYR Chi-restraints excluded: chain K residue 213 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 196 optimal weight: 80.0000 chunk 243 optimal weight: 0.0570 chunk 226 optimal weight: 0.3980 chunk 283 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 220 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 271 optimal weight: 0.9990 chunk 211 optimal weight: 10.0000 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 HIS ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.089783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.067688 restraints weight = 75710.624| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.96 r_work: 0.3256 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23551 Z= 0.109 Angle : 0.518 10.020 32329 Z= 0.266 Chirality : 0.037 0.192 3707 Planarity : 0.004 0.052 4169 Dihedral : 3.687 16.082 3454 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.49 % Allowed : 20.34 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.15), residues: 3135 helix: 2.99 (0.11), residues: 2244 sheet: None (None), residues: 0 loop : -0.97 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 233 TYR 0.016 0.001 TYR C 214 PHE 0.008 0.001 PHE C 69 TRP 0.005 0.001 TRP A 80 HIS 0.027 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00249 (23529) covalent geometry : angle 0.51763 (32285) SS BOND : bond 0.00159 ( 22) SS BOND : angle 0.45115 ( 44) hydrogen bonds : bond 0.02818 ( 1695) hydrogen bonds : angle 2.95717 ( 5019) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 194 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 229 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8508 (tm-30) REVERT: E 229 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8362 (tm-30) REVERT: F 71 ILE cc_start: 0.9458 (mt) cc_final: 0.9222 (mt) REVERT: H 198 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9246 (tt) REVERT: H 229 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8511 (tm-30) outliers start: 68 outliers final: 56 residues processed: 254 average time/residue: 0.1224 time to fit residues: 53.4908 Evaluate side-chains 239 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 182 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 182 TYR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 88 HIS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 182 TYR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 182 TYR Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 182 TYR Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 281 ILE Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 213 SER Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 182 TYR Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 213 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 249 optimal weight: 0.3980 chunk 187 optimal weight: 7.9990 chunk 284 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 177 optimal weight: 0.4980 chunk 234 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 281 optimal weight: 0.9990 chunk 293 optimal weight: 10.0000 chunk 297 optimal weight: 0.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 HIS ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 HIS ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.089751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.067782 restraints weight = 75943.189| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.97 r_work: 0.3258 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23551 Z= 0.111 Angle : 0.523 10.474 32329 Z= 0.268 Chirality : 0.037 0.194 3707 Planarity : 0.004 0.052 4169 Dihedral : 3.642 16.084 3454 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.13 % Allowed : 20.85 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.15), residues: 3135 helix: 3.01 (0.11), residues: 2244 sheet: None (None), residues: 0 loop : -0.91 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 233 TYR 0.018 0.001 TYR D 214 PHE 0.008 0.001 PHE C 69 TRP 0.006 0.001 TRP D 80 HIS 0.003 0.000 HIS G 88 Details of bonding type rmsd covalent geometry : bond 0.00255 (23529) covalent geometry : angle 0.52319 (32285) SS BOND : bond 0.00155 ( 22) SS BOND : angle 0.45577 ( 44) hydrogen bonds : bond 0.02799 ( 1695) hydrogen bonds : angle 2.92044 ( 5019) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 189 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8372 (tm-30) REVERT: E 229 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8333 (tm-30) REVERT: F 71 ILE cc_start: 0.9457 (mt) cc_final: 0.9218 (mt) REVERT: H 198 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9250 (tt) REVERT: H 229 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8496 (tm-30) REVERT: J 273 GLN cc_start: 0.7623 (mp10) cc_final: 0.7402 (mp10) outliers start: 61 outliers final: 57 residues processed: 244 average time/residue: 0.1161 time to fit residues: 48.6913 Evaluate side-chains 236 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 182 TYR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 88 HIS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 182 TYR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 182 TYR Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 272 THR Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 182 TYR Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 281 ILE Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 213 SER Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 182 TYR Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 213 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 244 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 203 optimal weight: 8.9990 chunk 282 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 65 optimal weight: 0.3980 chunk 140 optimal weight: 80.0000 chunk 119 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** H 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.089050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.066893 restraints weight = 75576.791| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.95 r_work: 0.3236 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23551 Z= 0.138 Angle : 0.537 8.610 32329 Z= 0.279 Chirality : 0.039 0.201 3707 Planarity : 0.004 0.052 4169 Dihedral : 3.706 19.172 3454 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.29 % Allowed : 21.21 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.15), residues: 3135 helix: 2.99 (0.11), residues: 2255 sheet: None (None), residues: 0 loop : -1.11 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 233 TYR 0.013 0.001 TYR C 214 PHE 0.009 0.001 PHE A 69 TRP 0.005 0.001 TRP D 80 HIS 0.029 0.001 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00312 (23529) covalent geometry : angle 0.53741 (32285) SS BOND : bond 0.00178 ( 22) SS BOND : angle 0.50544 ( 44) hydrogen bonds : bond 0.02956 ( 1695) hydrogen bonds : angle 2.93481 ( 5019) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5071.89 seconds wall clock time: 87 minutes 35.44 seconds (5255.44 seconds total)