Starting phenix.real_space_refine on Wed Mar 4 21:56:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sss_25413/03_2026/7sss_25413.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sss_25413/03_2026/7sss_25413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sss_25413/03_2026/7sss_25413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sss_25413/03_2026/7sss_25413.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sss_25413/03_2026/7sss_25413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sss_25413/03_2026/7sss_25413.map" } resolution = 2.4 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5095 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 72 5.16 5 C 7695 2.51 5 N 2009 2.21 5 O 2394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 12190 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1446 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 181, 1437 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 181, 1437 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 1457 Chain: "B" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 181, 1441 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 181, 1441 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 1449 Chain: "C" Number of atoms: 1449 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 181, 1440 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 181, 1440 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 1459 Chain: "D" Number of atoms: 1457 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 181, 1437 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 181, 1437 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 1445 Chain: "E" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1341 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 173, 1341 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1356 Chain: "F" Number of atoms: 1354 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1345 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 173, 1345 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 1360 Chain: "G" Number of atoms: 1354 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1345 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 173, 1345 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 1360 Chain: "H" Number of atoms: 1354 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1345 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 173, 1345 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 1360 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'PEV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEV:plan-1': 2, 'PEV:plan-2': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {'8PP': 1, 'PEV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEV:plan-1': 1, 'PEV:plan-2': 1, '8PP:plan-8': 1, '8PP:plan-9': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Unusual residues: {'PEV': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEV:plan-1': 2, 'PEV:plan-2': 2} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'PEV': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEV:plan-1': 3, 'PEV:plan-2': 3} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 166 Unusual residues: {'8PP': 1, 'NAD': 1, 'PEV': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'8PP:plan-7': 1, '8PP:plan-8': 1, '8PP:plan-9': 1, 'PEV:plan-1': 1, 'PEV:plan-2': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Unusual residues: {'NAD': 1, 'PEV': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEV:plan-1': 3, 'PEV:plan-2': 3} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 107 Unusual residues: {'8PP': 1, 'PEV': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'8PP:plan-7': 1, '8PP:plan-8': 1, '8PP:plan-9': 1, 'PEV:plan-1': 2, 'PEV:plan-2': 2} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 133 Unusual residues: {'8PP': 1, 'PEV': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'8PP:plan-7': 1, '8PP:plan-8': 1, '8PP:plan-9': 1, 'PEV:plan-1': 2, 'PEV:plan-2': 2} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N AGLN A 152 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 152 " occ=0.50 residue: pdb=" N AGLN B 152 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 152 " occ=0.50 residue: pdb=" N AARG B 276 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 276 " occ=0.50 residue: pdb=" N AGLN C 152 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 152 " occ=0.50 residue: pdb=" N AGLN D 152 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN D 152 " occ=0.50 residue: pdb=" N AARG D 276 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 276 " occ=0.50 residue: pdb=" N ALYS E 96 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS E 96 " occ=0.50 residue: pdb=" N ALYS F 96 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS F 96 " occ=0.50 residue: pdb=" N ALYS G 96 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS G 96 " occ=0.50 residue: pdb=" N ALYS H 96 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS H 96 " occ=0.50 Time building chain proxies: 5.01, per 1000 atoms: 0.41 Number of scatterers: 12190 At special positions: 0 Unit cell: (95.795, 104.125, 92.463, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 20 15.00 O 2394 8.00 N 2009 7.00 C 7695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 767.7 milliseconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 82.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 95 through 108 removed outlier: 3.802A pdb=" N LEU A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.701A pdb=" N ILE A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 170 Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 192 through 197 Proline residue: A 195 - end of helix No H-bonds generated for 'chain 'A' and resid 192 through 197' Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 212 through 231 Processing helix chain 'A' and resid 238 through 260 removed outlier: 3.681A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 266 through 282 removed outlier: 3.558A pdb=" N ASN A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 108 removed outlier: 3.615A pdb=" N LEU B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.781A pdb=" N ILE B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 171 removed outlier: 3.586A pdb=" N LEU B 170 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 191 Processing helix chain 'B' and resid 192 through 197 Proline residue: B 195 - end of helix No H-bonds generated for 'chain 'B' and resid 192 through 197' Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 212 through 231 Processing helix chain 'B' and resid 238 through 260 removed outlier: 3.677A pdb=" N GLN B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 266 through 281 Processing helix chain 'C' and resid 96 through 108 removed outlier: 3.580A pdb=" N LEU C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 127 removed outlier: 3.832A pdb=" N ILE C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 170 removed outlier: 3.569A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 191 Processing helix chain 'C' and resid 192 through 197 Proline residue: C 195 - end of helix No H-bonds generated for 'chain 'C' and resid 192 through 197' Processing helix chain 'C' and resid 199 through 208 Processing helix chain 'C' and resid 212 through 231 Processing helix chain 'C' and resid 238 through 260 removed outlier: 3.677A pdb=" N GLN C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 266 through 282 Processing helix chain 'D' and resid 97 through 108 removed outlier: 3.629A pdb=" N LEU D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 117 through 127 removed outlier: 3.722A pdb=" N ILE D 121 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 170 Processing helix chain 'D' and resid 177 through 191 Processing helix chain 'D' and resid 192 through 197 Proline residue: D 195 - end of helix No H-bonds generated for 'chain 'D' and resid 192 through 197' Processing helix chain 'D' and resid 199 through 208 Processing helix chain 'D' and resid 212 through 231 Processing helix chain 'D' and resid 238 through 260 removed outlier: 3.679A pdb=" N GLN D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 266 through 282 Processing helix chain 'E' and resid 46 through 75 removed outlier: 3.568A pdb=" N VAL E 73 " --> pdb=" O GLY E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 105 Processing helix chain 'E' and resid 111 through 126 removed outlier: 3.564A pdb=" N PHE E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 157 Processing helix chain 'E' and resid 164 through 178 Processing helix chain 'E' and resid 193 through 215 Processing helix chain 'F' and resid 46 through 74 Processing helix chain 'F' and resid 79 through 105 Processing helix chain 'F' and resid 111 through 126 removed outlier: 3.570A pdb=" N VAL F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 160 removed outlier: 3.987A pdb=" N GLU F 158 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU F 159 " --> pdb=" O THR F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 178 removed outlier: 3.512A pdb=" N LEU F 168 " --> pdb=" O TYR F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 217 removed outlier: 3.500A pdb=" N VAL F 198 " --> pdb=" O PRO F 194 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG F 216 " --> pdb=" O TYR F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 74 Processing helix chain 'G' and resid 79 through 105 Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.546A pdb=" N VAL G 117 " --> pdb=" O PRO G 113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE G 120 " --> pdb=" O ASN G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 157 Processing helix chain 'G' and resid 164 through 178 Processing helix chain 'G' and resid 193 through 217 removed outlier: 4.012A pdb=" N ARG G 216 " --> pdb=" O TYR G 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 74 Processing helix chain 'H' and resid 79 through 105 Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.543A pdb=" N VAL H 117 " --> pdb=" O PRO H 113 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE H 120 " --> pdb=" O ASN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 160 removed outlier: 3.661A pdb=" N GLU H 159 " --> pdb=" O THR H 155 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP H 160 " --> pdb=" O LEU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 178 removed outlier: 3.537A pdb=" N LEU H 168 " --> pdb=" O TYR H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 217 removed outlier: 3.506A pdb=" N VAL H 198 " --> pdb=" O PRO H 194 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG H 216 " --> pdb=" O TYR H 212 " (cutoff:3.500A) 878 hydrogen bonds defined for protein. 2644 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: 1.68 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1921 1.32 - 1.44: 3132 1.44 - 1.56: 7000 1.56 - 1.68: 40 1.68 - 1.81: 132 Bond restraints: 12225 Sorted by residual: bond pdb=" N ILE A 250 " pdb=" CA ILE A 250 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 6.94e+00 bond pdb=" N AARG B 276 " pdb=" CA AARG B 276 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.19e-02 7.06e+03 6.05e+00 bond pdb=" O3 NAD E 306 " pdb=" PA NAD E 306 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" O3 NAD F 306 " pdb=" PA NAD F 306 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 5.95e+00 bond pdb=" C1 PEV C 405 " pdb=" O3P PEV C 405 " ideal model delta sigma weight residual 1.407 1.454 -0.047 2.00e-02 2.50e+03 5.57e+00 ... (remaining 12220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 16157 1.99 - 3.98: 222 3.98 - 5.97: 45 5.97 - 7.96: 2 7.96 - 9.95: 16 Bond angle restraints: 16442 Sorted by residual: angle pdb=" O3P PEV H 301 " pdb=" P PEV H 301 " pdb=" O4P PEV H 301 " ideal model delta sigma weight residual 93.57 103.52 -9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" O3P PEV C 401 " pdb=" P PEV C 401 " pdb=" O4P PEV C 401 " ideal model delta sigma weight residual 93.57 103.49 -9.92 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CA AARG B 276 " pdb=" C AARG B 276 " pdb=" O AARG B 276 " ideal model delta sigma weight residual 120.82 117.35 3.47 1.05e+00 9.07e-01 1.09e+01 angle pdb=" O3P PEV H 302 " pdb=" P PEV H 302 " pdb=" O4P PEV H 302 " ideal model delta sigma weight residual 93.57 103.40 -9.83 3.00e+00 1.11e-01 1.07e+01 angle pdb=" O3P PEV C 403 " pdb=" P PEV C 403 " pdb=" O4P PEV C 403 " ideal model delta sigma weight residual 93.57 103.22 -9.65 3.00e+00 1.11e-01 1.03e+01 ... (remaining 16437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 7201 35.86 - 71.73: 274 71.73 - 107.59: 16 107.59 - 143.45: 2 143.45 - 179.32: 8 Dihedral angle restraints: 7501 sinusoidal: 3337 harmonic: 4164 Sorted by residual: dihedral pdb=" C3 PEV C 403 " pdb=" C1 PEV C 403 " pdb=" C2 PEV C 403 " pdb=" O3P PEV C 403 " ideal model delta sinusoidal sigma weight residual 292.80 113.48 179.32 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PEV G 303 " pdb=" C1 PEV G 303 " pdb=" C2 PEV G 303 " pdb=" O3P PEV G 303 " ideal model delta sinusoidal sigma weight residual 292.80 116.80 176.00 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PEV H 301 " pdb=" C1 PEV H 301 " pdb=" C2 PEV H 301 " pdb=" O3P PEV H 301 " ideal model delta sinusoidal sigma weight residual -67.20 103.39 -170.59 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 7498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1285 0.039 - 0.079: 407 0.079 - 0.118: 76 0.118 - 0.158: 8 0.158 - 0.197: 2 Chirality restraints: 1778 Sorted by residual: chirality pdb=" C2 PEV E 304 " pdb=" C1 PEV E 304 " pdb=" C3 PEV E 304 " pdb=" O2 PEV E 304 " both_signs ideal model delta sigma weight residual False 2.36 2.56 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CA ILE A 250 " pdb=" N ILE A 250 " pdb=" C ILE A 250 " pdb=" CB ILE A 250 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" C1D NAD E 306 " pdb=" C2D NAD E 306 " pdb=" N1N NAD E 306 " pdb=" O4D NAD E 306 " both_signs ideal model delta sigma weight residual False 2.41 2.57 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 1775 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C32 8PP B 403 " 0.338 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C33 8PP B 403 " -0.502 2.00e-02 2.50e+03 pdb=" C34 8PP B 403 " -0.108 2.00e-02 2.50e+03 pdb=" C35 8PP B 403 " 0.109 2.00e-02 2.50e+03 pdb=" C36 8PP B 403 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 8PP G 302 " 0.335 2.00e-02 2.50e+03 2.85e-01 1.01e+03 pdb=" C23 8PP G 302 " -0.495 2.00e-02 2.50e+03 pdb=" C24 8PP G 302 " -0.105 2.00e-02 2.50e+03 pdb=" C25 8PP G 302 " 0.167 2.00e-02 2.50e+03 pdb=" C26 8PP G 302 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 8PP B 403 " -0.317 2.00e-02 2.50e+03 2.70e-01 9.12e+02 pdb=" C18 8PP B 403 " 0.467 2.00e-02 2.50e+03 pdb=" C19 8PP B 403 " 0.098 2.00e-02 2.50e+03 pdb=" C20 8PP B 403 " -0.068 2.00e-02 2.50e+03 pdb=" C21 8PP B 403 " -0.179 2.00e-02 2.50e+03 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3838 2.84 - 3.35: 11471 3.35 - 3.87: 20898 3.87 - 4.38: 26733 4.38 - 4.90: 42144 Nonbonded interactions: 105084 Sorted by model distance: nonbonded pdb=" ND1 HIS B 211 " pdb=" OG SER E 201 " model vdw 2.323 3.120 nonbonded pdb=" ND1 HIS A 211 " pdb=" OG SER G 201 " model vdw 2.329 3.120 nonbonded pdb=" ND1 HIS D 211 " pdb=" OG SER H 201 " model vdw 2.330 3.120 nonbonded pdb=" OD2 ASP F 50 " pdb=" O HOH F 401 " model vdw 2.332 3.040 nonbonded pdb=" ND1 HIS C 211 " pdb=" OG SER F 201 " model vdw 2.333 3.120 ... (remaining 105079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 95 through 151 or resid 153 through 162 or (resid 163 and \ (name N or name CA or name C or name O or name CB )) or resid 164 through 209 or \ (resid 210 and (name N or name CA or name C or name O or name CB or name CD )) \ or resid 211 through 275 or resid 277 through 283)) selection = (chain 'B' and (resid 95 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 151 or resid 153 through 162 or (r \ esid 163 and (name N or name CA or name C or name O or name CB )) or resid 164 t \ hrough 209 or (resid 210 and (name N or name CA or name C or name O or name CB o \ r name CD )) or resid 211 through 275 or resid 277 through 283)) selection = (chain 'C' and (resid 95 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 151 or resid 153 through 162 or (r \ esid 163 and (name N or name CA or name C or name O or name CB )) or resid 164 t \ hrough 275 or resid 277 through 283)) selection = (chain 'D' and (resid 95 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 151 or resid 153 through 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB or name CD )) or \ resid 211 through 275 or resid 277 through 283)) } ncs_group { reference = (chain 'E' and (resid 45 through 95 or resid 97 through 217 or (resid 301 and (n \ ame C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 o \ r name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 \ or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O \ 3P or name O4P or name P )) or (resid 305 and (name C18 or name C19 or name C20 \ or name C21 or name C22)))) selection = (chain 'F' and (resid 45 through 95 or resid 97 through 182 or (resid 183 and (n \ ame N or name CA or name C or name O or name CB )) or resid 184 through 213 or ( \ resid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 217 or (resid 301 and (name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name O11 or name O1P or name O2 or name O2P \ or name O3 or name O31 or name O3P or name O4P or name P )) or (resid 305 and (n \ ame C17 or name C18 or name C19 or name C20 or name C21)))) selection = (chain 'G' and (resid 45 through 95 or resid 97 through 182 or (resid 183 and (n \ ame N or name CA or name C or name O or name CB )) or resid 184 through 213 or ( \ resid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 217 or (resid 301 and (name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name O11 or name O1P or name O2 or name O2P \ or name O3 or name O31 or name O3P or name O4P or name P )) or (resid 305 and (n \ ame C18 or name C19 or name C20 or name C21 or name C22)))) selection = (chain 'H' and (resid 45 through 95 or resid 97 through 182 or (resid 183 and (n \ ame N or name CA or name C or name O or name CB )) or resid 184 through 213 or ( \ resid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 217 or (resid 301 and (name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name O11 or name O1P or name O2 or name O2P \ or name O3 or name O31 or name O3P or name O4P or name P )) or (resid 305 and (n \ ame C18 or name C19 or name C20 or name C21 or name C22)))) } 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=0.50 max=1.00 mean=0.99 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.480 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.006 0.049 12225 Z= 0.268 Angle : 0.661 9.948 16442 Z= 0.318 Chirality : 0.039 0.197 1778 Planarity : 0.019 0.288 2066 Dihedral : 17.639 179.315 4801 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: 0.01 (0.22), residues: 1422 helix: 0.36 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -1.12 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 156 TYR 0.008 0.001 TYR F 67 PHE 0.006 0.001 PHE D 149 TRP 0.012 0.002 TRP A 200 HIS 0.003 0.001 HIS C 211 Details of bonding type rmsd covalent geometry : bond 0.00559 (12225) covalent geometry : angle 0.66092 (16442) hydrogen bonds : bond 0.21359 ( 878) hydrogen bonds : angle 6.18914 ( 2644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.470 Fit side-chains REVERT: A 109 GLU cc_start: 0.5345 (mt-10) cc_final: 0.4907 (tp30) REVERT: A 169 GLN cc_start: 0.6424 (mt0) cc_final: 0.6081 (mt0) REVERT: A 179 ASP cc_start: 0.7380 (p0) cc_final: 0.7021 (p0) REVERT: A 202 ARG cc_start: 0.7391 (tpt90) cc_final: 0.7179 (tpm170) REVERT: A 223 MET cc_start: 0.8782 (ttp) cc_final: 0.8568 (ttp) REVERT: A 271 ARG cc_start: 0.7151 (ttm110) cc_final: 0.6800 (mtm-85) REVERT: A 274 GLU cc_start: 0.7701 (tt0) cc_final: 0.7356 (tt0) REVERT: A 276 ARG cc_start: 0.7448 (mmm-85) cc_final: 0.6569 (mpp-170) REVERT: A 279 ASP cc_start: 0.6740 (m-30) cc_final: 0.6468 (m-30) REVERT: B 109 GLU cc_start: 0.5412 (mt-10) cc_final: 0.4882 (tp30) REVERT: B 164 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6687 (mt-10) REVERT: B 169 GLN cc_start: 0.6480 (mt0) cc_final: 0.5845 (pt0) REVERT: B 179 ASP cc_start: 0.7349 (p0) cc_final: 0.7074 (p0) REVERT: B 202 ARG cc_start: 0.7383 (tpt90) cc_final: 0.7175 (tpm170) REVERT: B 223 MET cc_start: 0.8702 (ttp) cc_final: 0.8449 (ttp) REVERT: B 271 ARG cc_start: 0.7139 (ttm110) cc_final: 0.6771 (mtm-85) REVERT: B 274 GLU cc_start: 0.7715 (tt0) cc_final: 0.7412 (tt0) REVERT: B 279 ASP cc_start: 0.6710 (m-30) cc_final: 0.6428 (m-30) REVERT: C 109 GLU cc_start: 0.5437 (mt-10) cc_final: 0.4900 (tp30) REVERT: C 162 GLU cc_start: 0.6608 (pt0) cc_final: 0.6272 (pt0) REVERT: C 177 LYS cc_start: 0.6948 (mtpp) cc_final: 0.6402 (mmtt) REVERT: C 179 ASP cc_start: 0.7301 (p0) cc_final: 0.6971 (p0) REVERT: C 202 ARG cc_start: 0.7193 (tpt90) cc_final: 0.6970 (tpm170) REVERT: C 223 MET cc_start: 0.8677 (ttp) cc_final: 0.8457 (ttp) REVERT: C 234 GLN cc_start: 0.7822 (mt0) cc_final: 0.7613 (mt0) REVERT: C 271 ARG cc_start: 0.7092 (ttm110) cc_final: 0.6753 (mtm-85) REVERT: C 274 GLU cc_start: 0.7708 (tt0) cc_final: 0.7358 (tt0) REVERT: C 276 ARG cc_start: 0.7496 (mmm-85) cc_final: 0.6615 (mpp-170) REVERT: C 279 ASP cc_start: 0.6722 (m-30) cc_final: 0.6457 (m-30) REVERT: D 109 GLU cc_start: 0.5304 (mt-10) cc_final: 0.4836 (tp30) REVERT: D 167 LEU cc_start: 0.6675 (mt) cc_final: 0.6382 (mt) REVERT: D 177 LYS cc_start: 0.6968 (mtpp) cc_final: 0.6450 (mmtt) REVERT: D 179 ASP cc_start: 0.7312 (p0) cc_final: 0.6977 (p0) REVERT: D 202 ARG cc_start: 0.7430 (tpt90) cc_final: 0.7191 (tpm170) REVERT: D 223 MET cc_start: 0.8763 (ttp) cc_final: 0.8544 (ttp) REVERT: D 271 ARG cc_start: 0.7131 (ttm110) cc_final: 0.6780 (mtm-85) REVERT: D 274 GLU cc_start: 0.7712 (tt0) cc_final: 0.7402 (tt0) REVERT: D 279 ASP cc_start: 0.6735 (m-30) cc_final: 0.6437 (m-30) REVERT: D 281 MET cc_start: 0.6329 (mmp) cc_final: 0.6116 (mmm) REVERT: D 283 MET cc_start: 0.3367 (ttp) cc_final: 0.3059 (ptt) REVERT: E 71 MET cc_start: 0.8547 (tpt) cc_final: 0.8289 (tpt) REVERT: E 99 GLU cc_start: 0.7731 (mt-10) cc_final: 0.6984 (mp0) REVERT: E 132 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6592 (tt0) REVERT: E 143 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6651 (tt0) REVERT: E 147 HIS cc_start: 0.7719 (t-90) cc_final: 0.7355 (t-90) REVERT: E 180 GLU cc_start: 0.5548 (tp30) cc_final: 0.5212 (tm-30) REVERT: E 199 LEU cc_start: 0.7323 (tp) cc_final: 0.7100 (tp) REVERT: E 211 ILE cc_start: 0.8496 (mm) cc_final: 0.8250 (mt) REVERT: F 50 ASP cc_start: 0.7087 (m-30) cc_final: 0.6694 (m-30) REVERT: F 71 MET cc_start: 0.8474 (tpt) cc_final: 0.8224 (tpt) REVERT: F 99 GLU cc_start: 0.7732 (mt-10) cc_final: 0.6998 (mp0) REVERT: F 143 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6672 (tt0) REVERT: F 147 HIS cc_start: 0.7721 (t-90) cc_final: 0.7370 (t-90) REVERT: F 199 LEU cc_start: 0.7387 (tp) cc_final: 0.7170 (tp) REVERT: F 211 ILE cc_start: 0.8479 (mm) cc_final: 0.8227 (mt) REVERT: F 215 GLU cc_start: 0.7692 (pt0) cc_final: 0.7365 (pt0) REVERT: G 99 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7006 (mp0) REVERT: G 143 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6678 (tt0) REVERT: G 147 HIS cc_start: 0.7712 (t-90) cc_final: 0.7360 (t-90) REVERT: G 157 MET cc_start: 0.5043 (mtt) cc_final: 0.4818 (mtm) REVERT: G 175 ARG cc_start: 0.7936 (tmm-80) cc_final: 0.7716 (tmm160) REVERT: G 180 GLU cc_start: 0.5544 (tp30) cc_final: 0.5233 (tm-30) REVERT: G 199 LEU cc_start: 0.7355 (tp) cc_final: 0.7150 (tp) REVERT: G 208 ARG cc_start: 0.7028 (mtt-85) cc_final: 0.6719 (mmt90) REVERT: G 211 ILE cc_start: 0.8539 (mm) cc_final: 0.8291 (mt) REVERT: G 215 GLU cc_start: 0.7700 (pt0) cc_final: 0.7347 (pt0) REVERT: H 71 MET cc_start: 0.8490 (tpt) cc_final: 0.8171 (tpt) REVERT: H 99 GLU cc_start: 0.7719 (mt-10) cc_final: 0.6969 (mp0) REVERT: H 132 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6559 (tt0) REVERT: H 143 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6679 (tt0) REVERT: H 147 HIS cc_start: 0.7741 (t-90) cc_final: 0.7394 (t-90) REVERT: H 199 LEU cc_start: 0.7399 (tp) cc_final: 0.7186 (tp) REVERT: H 211 ILE cc_start: 0.8481 (mm) cc_final: 0.8224 (mt) REVERT: H 215 GLU cc_start: 0.7632 (pt0) cc_final: 0.7282 (pt0) outliers start: 0 outliers final: 4 residues processed: 325 average time/residue: 0.8401 time to fit residues: 288.7557 Evaluate side-chains 270 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 266 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 226 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN C 275 ASN E 98 ASN F 98 ASN G 98 ASN H 98 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.177942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.138896 restraints weight = 53295.919| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 4.84 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12225 Z= 0.127 Angle : 0.548 10.396 16442 Z= 0.282 Chirality : 0.038 0.114 1778 Planarity : 0.005 0.055 2066 Dihedral : 18.866 171.837 2169 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.64 % Allowed : 9.39 % Favored : 88.98 % 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 (0.23), residues: 1422 helix: 2.37 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -1.01 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 46 TYR 0.011 0.001 TYR A 230 PHE 0.009 0.001 PHE B 272 TRP 0.016 0.002 TRP B 240 HIS 0.004 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00238 (12225) covalent geometry : angle 0.54810 (16442) hydrogen bonds : bond 0.05225 ( 878) hydrogen bonds : angle 3.45550 ( 2644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 283 time to evaluate : 0.419 Fit side-chains REVERT: A 109 GLU cc_start: 0.5277 (mt-10) cc_final: 0.5058 (tt0) REVERT: A 123 GLU cc_start: 0.5319 (tt0) cc_final: 0.4875 (tm-30) REVERT: A 163 GLU cc_start: 0.6497 (mt-10) cc_final: 0.6194 (mt-10) REVERT: A 167 LEU cc_start: 0.6955 (mt) cc_final: 0.6567 (tp) REVERT: A 260 GLN cc_start: 0.7206 (pt0) cc_final: 0.6464 (pm20) REVERT: A 271 ARG cc_start: 0.7114 (ttm110) cc_final: 0.6826 (mtm-85) REVERT: A 274 GLU cc_start: 0.7710 (tt0) cc_final: 0.7472 (tt0) REVERT: A 276 ARG cc_start: 0.7411 (mmm-85) cc_final: 0.7140 (mmm160) REVERT: A 279 ASP cc_start: 0.6684 (m-30) cc_final: 0.6378 (m-30) REVERT: B 109 GLU cc_start: 0.5304 (mt-10) cc_final: 0.4842 (tp30) REVERT: B 119 GLU cc_start: 0.5918 (tm-30) cc_final: 0.5642 (tm-30) REVERT: B 123 GLU cc_start: 0.5462 (OUTLIER) cc_final: 0.5070 (tm-30) REVERT: B 163 GLU cc_start: 0.6647 (mm-30) cc_final: 0.6320 (mt-10) REVERT: B 164 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6768 (mt-10) REVERT: B 260 GLN cc_start: 0.7303 (pt0) cc_final: 0.6540 (pm20) REVERT: B 271 ARG cc_start: 0.7180 (ttm110) cc_final: 0.6923 (mtm-85) REVERT: B 274 GLU cc_start: 0.7696 (tt0) cc_final: 0.7487 (tt0) REVERT: B 279 ASP cc_start: 0.6727 (m-30) cc_final: 0.6475 (m-30) REVERT: B 281 MET cc_start: 0.6430 (OUTLIER) cc_final: 0.4470 (mpt) REVERT: C 109 GLU cc_start: 0.5320 (mt-10) cc_final: 0.4869 (tp30) REVERT: C 119 GLU cc_start: 0.5651 (tm-30) cc_final: 0.5397 (tm-30) REVERT: C 123 GLU cc_start: 0.5617 (tt0) cc_final: 0.5155 (tm-30) REVERT: C 162 GLU cc_start: 0.6338 (pt0) cc_final: 0.5985 (pt0) REVERT: C 163 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6658 (mt-10) REVERT: C 164 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6692 (mt-10) REVERT: C 169 GLN cc_start: 0.6347 (mt0) cc_final: 0.5841 (pt0) REVERT: C 177 LYS cc_start: 0.7054 (mtpp) cc_final: 0.6570 (mmtt) REVERT: C 260 GLN cc_start: 0.7162 (pt0) cc_final: 0.6568 (pm20) REVERT: C 271 ARG cc_start: 0.7101 (ttm110) cc_final: 0.6811 (mtm-85) REVERT: C 274 GLU cc_start: 0.7738 (tt0) cc_final: 0.7478 (tt0) REVERT: C 276 ARG cc_start: 0.7410 (mmm-85) cc_final: 0.7206 (mmm160) REVERT: C 281 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.5281 (mpt) REVERT: D 109 GLU cc_start: 0.5239 (mt-10) cc_final: 0.4815 (tp30) REVERT: D 119 GLU cc_start: 0.5640 (tm-30) cc_final: 0.5412 (tm-30) REVERT: D 123 GLU cc_start: 0.5104 (tt0) cc_final: 0.4596 (tm-30) REVERT: D 167 LEU cc_start: 0.6547 (mt) cc_final: 0.6104 (tp) REVERT: D 177 LYS cc_start: 0.7022 (mtpp) cc_final: 0.6524 (mmtt) REVERT: D 260 GLN cc_start: 0.7288 (pt0) cc_final: 0.6536 (pm20) REVERT: D 271 ARG cc_start: 0.7159 (ttm110) cc_final: 0.6802 (mtm-85) REVERT: D 279 ASP cc_start: 0.6632 (m-30) cc_final: 0.6413 (m-30) REVERT: D 281 MET cc_start: 0.6349 (mmp) cc_final: 0.5954 (mmm) REVERT: D 283 MET cc_start: 0.3301 (ttp) cc_final: 0.2885 (ptt) REVERT: E 76 ARG cc_start: 0.7241 (mtt180) cc_final: 0.6320 (mpp-170) REVERT: E 132 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6539 (tt0) REVERT: E 143 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6794 (tt0) REVERT: E 147 HIS cc_start: 0.7467 (t-90) cc_final: 0.7161 (t-170) REVERT: E 180 GLU cc_start: 0.5557 (tp30) cc_final: 0.5197 (tm-30) REVERT: E 215 GLU cc_start: 0.7705 (pt0) cc_final: 0.7296 (pt0) REVERT: F 50 ASP cc_start: 0.7101 (m-30) cc_final: 0.6698 (m-30) REVERT: F 143 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6564 (tt0) REVERT: F 147 HIS cc_start: 0.7340 (t-90) cc_final: 0.7053 (t-170) REVERT: F 215 GLU cc_start: 0.7619 (pt0) cc_final: 0.7366 (pt0) REVERT: G 143 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6757 (tt0) REVERT: G 147 HIS cc_start: 0.7478 (t-90) cc_final: 0.7166 (t-170) REVERT: G 180 GLU cc_start: 0.5715 (tp30) cc_final: 0.5484 (tm-30) REVERT: G 208 ARG cc_start: 0.7326 (mtt-85) cc_final: 0.6988 (mmt90) REVERT: G 215 GLU cc_start: 0.7609 (pt0) cc_final: 0.7356 (pt0) REVERT: H 132 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6562 (tt0) REVERT: H 143 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6655 (tt0) REVERT: H 147 HIS cc_start: 0.7396 (t-90) cc_final: 0.7087 (t-170) REVERT: H 215 GLU cc_start: 0.7660 (pt0) cc_final: 0.7409 (pt0) outliers start: 19 outliers final: 1 residues processed: 285 average time/residue: 0.8651 time to fit residues: 260.7569 Evaluate side-chains 259 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 255 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain F residue 49 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 16 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 50.0000 chunk 112 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 275 ASN B 252 ASN B 260 GLN C 260 GLN C 275 ASN D 169 GLN D 260 GLN E 204 GLN F 98 ASN F 204 GLN G 204 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.178215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.139239 restraints weight = 51048.936| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 4.67 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12225 Z= 0.115 Angle : 0.512 8.676 16442 Z= 0.261 Chirality : 0.037 0.116 1778 Planarity : 0.005 0.054 2066 Dihedral : 17.104 164.755 2161 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.15 % Allowed : 12.83 % Favored : 85.01 % 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: 3.27 (0.23), residues: 1422 helix: 2.83 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -1.04 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 46 TYR 0.009 0.001 TYR G 67 PHE 0.008 0.001 PHE G 174 TRP 0.014 0.001 TRP B 240 HIS 0.004 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00228 (12225) covalent geometry : angle 0.51198 (16442) hydrogen bonds : bond 0.04633 ( 878) hydrogen bonds : angle 3.21327 ( 2644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 252 time to evaluate : 0.447 Fit side-chains REVERT: A 108 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6353 (mt) REVERT: A 123 GLU cc_start: 0.5251 (tt0) cc_final: 0.4874 (tm-30) REVERT: A 163 GLU cc_start: 0.6490 (mt-10) cc_final: 0.6179 (mt-10) REVERT: A 179 ASP cc_start: 0.7309 (p0) cc_final: 0.7052 (p0) REVERT: A 271 ARG cc_start: 0.7138 (ttm110) cc_final: 0.6801 (mtm-85) REVERT: A 276 ARG cc_start: 0.7303 (mmm-85) cc_final: 0.7023 (mmm160) REVERT: A 279 ASP cc_start: 0.6575 (m-30) cc_final: 0.6175 (t70) REVERT: B 108 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6418 (mt) REVERT: B 109 GLU cc_start: 0.5316 (mt-10) cc_final: 0.4821 (tp30) REVERT: B 119 GLU cc_start: 0.5785 (tm-30) cc_final: 0.5451 (tm-30) REVERT: B 123 GLU cc_start: 0.5647 (OUTLIER) cc_final: 0.5244 (tm-30) REVERT: B 164 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6678 (mt-10) REVERT: B 167 LEU cc_start: 0.6680 (tp) cc_final: 0.6477 (tp) REVERT: B 260 GLN cc_start: 0.7249 (pt0) cc_final: 0.7036 (pp30) REVERT: B 271 ARG cc_start: 0.7149 (ttm110) cc_final: 0.6845 (mtm-85) REVERT: B 274 GLU cc_start: 0.7676 (tt0) cc_final: 0.7475 (tt0) REVERT: B 279 ASP cc_start: 0.6675 (m-30) cc_final: 0.6378 (m-30) REVERT: B 281 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.4652 (mpt) REVERT: C 108 LEU cc_start: 0.6754 (mm) cc_final: 0.6415 (mt) REVERT: C 109 GLU cc_start: 0.5354 (mt-10) cc_final: 0.4879 (tp30) REVERT: C 119 GLU cc_start: 0.5590 (tm-30) cc_final: 0.5232 (tm-30) REVERT: C 123 GLU cc_start: 0.5526 (OUTLIER) cc_final: 0.5160 (tm-30) REVERT: C 162 GLU cc_start: 0.6542 (pt0) cc_final: 0.6205 (pt0) REVERT: C 163 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6605 (mt-10) REVERT: C 164 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6685 (mt-10) REVERT: C 177 LYS cc_start: 0.7081 (mtpp) cc_final: 0.6582 (mmtt) REVERT: C 179 ASP cc_start: 0.7321 (p0) cc_final: 0.7066 (p0) REVERT: C 271 ARG cc_start: 0.7119 (ttm110) cc_final: 0.6804 (mtm-85) REVERT: C 274 GLU cc_start: 0.7677 (tt0) cc_final: 0.7451 (tt0) REVERT: C 279 ASP cc_start: 0.6581 (m-30) cc_final: 0.6312 (m-30) REVERT: D 108 LEU cc_start: 0.6808 (mm) cc_final: 0.6408 (mt) REVERT: D 109 GLU cc_start: 0.5268 (mt-10) cc_final: 0.4832 (tp30) REVERT: D 119 GLU cc_start: 0.5610 (tm-30) cc_final: 0.5179 (tm-30) REVERT: D 123 GLU cc_start: 0.5184 (tt0) cc_final: 0.4688 (tm-30) REVERT: D 177 LYS cc_start: 0.7086 (mtpp) cc_final: 0.6607 (mmtt) REVERT: D 179 ASP cc_start: 0.7331 (p0) cc_final: 0.7077 (p0) REVERT: D 271 ARG cc_start: 0.7177 (ttm110) cc_final: 0.6817 (mtm-85) REVERT: D 279 ASP cc_start: 0.6783 (m-30) cc_final: 0.6498 (m-30) REVERT: D 281 MET cc_start: 0.6407 (mmp) cc_final: 0.6168 (mmm) REVERT: D 283 MET cc_start: 0.3500 (ttp) cc_final: 0.2734 (ptt) REVERT: E 143 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6843 (tt0) REVERT: E 147 HIS cc_start: 0.7340 (t-90) cc_final: 0.7094 (t-170) REVERT: E 155 THR cc_start: 0.6713 (m) cc_final: 0.6309 (t) REVERT: E 180 GLU cc_start: 0.5433 (tp30) cc_final: 0.5061 (tm-30) REVERT: F 50 ASP cc_start: 0.7042 (m-30) cc_final: 0.6758 (m-30) REVERT: F 147 HIS cc_start: 0.7189 (t-90) cc_final: 0.6977 (t-170) REVERT: F 215 GLU cc_start: 0.7446 (pt0) cc_final: 0.7094 (pt0) REVERT: G 143 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6914 (tt0) REVERT: G 147 HIS cc_start: 0.7428 (t-90) cc_final: 0.7177 (t-170) REVERT: G 155 THR cc_start: 0.6816 (m) cc_final: 0.6407 (t) REVERT: G 180 GLU cc_start: 0.5599 (tp30) cc_final: 0.5331 (tm-30) REVERT: G 208 ARG cc_start: 0.7272 (mtt-85) cc_final: 0.6946 (mmt90) REVERT: G 215 GLU cc_start: 0.7396 (pt0) cc_final: 0.7075 (pt0) REVERT: H 143 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6754 (tt0) REVERT: H 147 HIS cc_start: 0.7369 (t-90) cc_final: 0.7135 (t-170) REVERT: H 215 GLU cc_start: 0.7411 (pt0) cc_final: 0.7090 (pt0) outliers start: 25 outliers final: 9 residues processed: 256 average time/residue: 0.9092 time to fit residues: 245.8961 Evaluate side-chains 249 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 234 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 260 GLN A 275 ASN C 260 GLN C 275 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.176554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.136748 restraints weight = 51884.690| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 4.68 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12225 Z= 0.120 Angle : 0.517 8.932 16442 Z= 0.265 Chirality : 0.038 0.117 1778 Planarity : 0.004 0.049 2066 Dihedral : 16.691 157.427 2161 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.07 % Allowed : 13.61 % Favored : 84.32 % 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: 3.39 (0.23), residues: 1422 helix: 2.93 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -1.02 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 46 TYR 0.010 0.002 TYR E 67 PHE 0.010 0.001 PHE C 272 TRP 0.014 0.002 TRP C 200 HIS 0.004 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00250 (12225) covalent geometry : angle 0.51748 (16442) hydrogen bonds : bond 0.04585 ( 878) hydrogen bonds : angle 3.24236 ( 2644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 239 time to evaluate : 0.500 Fit side-chains REVERT: A 108 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6238 (mt) REVERT: A 119 GLU cc_start: 0.5620 (tm-30) cc_final: 0.5330 (tm-30) REVERT: A 123 GLU cc_start: 0.5227 (tt0) cc_final: 0.4720 (tm-30) REVERT: A 163 GLU cc_start: 0.6485 (mt-10) cc_final: 0.6211 (mt-10) REVERT: A 179 ASP cc_start: 0.7411 (p0) cc_final: 0.7095 (p0) REVERT: A 260 GLN cc_start: 0.7232 (pt0) cc_final: 0.7006 (pp30) REVERT: A 271 ARG cc_start: 0.7106 (ttm110) cc_final: 0.6745 (mtm-85) REVERT: A 276 ARG cc_start: 0.7278 (mmm-85) cc_final: 0.6901 (mtp85) REVERT: A 279 ASP cc_start: 0.6541 (m-30) cc_final: 0.6100 (t70) REVERT: B 108 LEU cc_start: 0.6750 (mm) cc_final: 0.6411 (mt) REVERT: B 109 GLU cc_start: 0.5395 (mt-10) cc_final: 0.5163 (tt0) REVERT: B 119 GLU cc_start: 0.5574 (tm-30) cc_final: 0.5367 (tm-30) REVERT: B 123 GLU cc_start: 0.5626 (OUTLIER) cc_final: 0.5125 (tm-30) REVERT: B 163 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6511 (mt-10) REVERT: B 169 GLN cc_start: 0.6371 (mt0) cc_final: 0.6049 (pt0) REVERT: B 271 ARG cc_start: 0.7103 (ttm110) cc_final: 0.6851 (mtm-85) REVERT: B 274 GLU cc_start: 0.7720 (tt0) cc_final: 0.7517 (tt0) REVERT: B 279 ASP cc_start: 0.6773 (m-30) cc_final: 0.6463 (m-30) REVERT: B 281 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.4735 (mpt) REVERT: C 108 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6373 (mt) REVERT: C 109 GLU cc_start: 0.5365 (mt-10) cc_final: 0.4913 (tp30) REVERT: C 119 GLU cc_start: 0.5526 (tm-30) cc_final: 0.5272 (tm-30) REVERT: C 123 GLU cc_start: 0.5513 (OUTLIER) cc_final: 0.5088 (tm-30) REVERT: C 162 GLU cc_start: 0.6619 (pt0) cc_final: 0.6283 (pt0) REVERT: C 163 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6422 (mt-10) REVERT: C 164 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6774 (mt-10) REVERT: C 177 LYS cc_start: 0.7043 (mtpp) cc_final: 0.6513 (mmtt) REVERT: C 179 ASP cc_start: 0.7348 (p0) cc_final: 0.7062 (p0) REVERT: C 260 GLN cc_start: 0.7144 (pt0) cc_final: 0.6875 (pp30) REVERT: C 271 ARG cc_start: 0.7103 (ttm110) cc_final: 0.6751 (mtm-85) REVERT: C 274 GLU cc_start: 0.7700 (tt0) cc_final: 0.7446 (tt0) REVERT: C 279 ASP cc_start: 0.6605 (m-30) cc_final: 0.6339 (m-30) REVERT: D 109 GLU cc_start: 0.5220 (mt-10) cc_final: 0.4751 (tp30) REVERT: D 119 GLU cc_start: 0.5433 (tm-30) cc_final: 0.5143 (tm-30) REVERT: D 123 GLU cc_start: 0.5125 (tt0) cc_final: 0.4589 (tm-30) REVERT: D 177 LYS cc_start: 0.7090 (mtpp) cc_final: 0.6598 (mmtt) REVERT: D 179 ASP cc_start: 0.7450 (p0) cc_final: 0.7138 (p0) REVERT: D 271 ARG cc_start: 0.7137 (ttm110) cc_final: 0.6771 (mtm-85) REVERT: D 279 ASP cc_start: 0.6814 (m-30) cc_final: 0.6496 (m-30) REVERT: D 281 MET cc_start: 0.6773 (mmp) cc_final: 0.6544 (mmm) REVERT: E 143 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6906 (tt0) REVERT: E 147 HIS cc_start: 0.7446 (t-90) cc_final: 0.7206 (t-170) REVERT: E 155 THR cc_start: 0.6791 (m) cc_final: 0.6383 (t) REVERT: F 50 ASP cc_start: 0.7065 (m-30) cc_final: 0.6846 (m-30) REVERT: F 143 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6951 (mt-10) REVERT: F 147 HIS cc_start: 0.7397 (t-90) cc_final: 0.7143 (t-170) REVERT: F 215 GLU cc_start: 0.7497 (pt0) cc_final: 0.7105 (pt0) REVERT: G 143 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6947 (tt0) REVERT: G 147 HIS cc_start: 0.7562 (t-90) cc_final: 0.7308 (t-170) REVERT: G 155 THR cc_start: 0.6823 (m) cc_final: 0.6410 (t) REVERT: G 215 GLU cc_start: 0.7469 (pt0) cc_final: 0.7147 (pt0) REVERT: H 143 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6923 (tt0) REVERT: H 147 HIS cc_start: 0.7471 (t-90) cc_final: 0.7239 (t-170) REVERT: H 215 GLU cc_start: 0.7519 (pt0) cc_final: 0.7192 (pt0) outliers start: 23 outliers final: 12 residues processed: 247 average time/residue: 0.8728 time to fit residues: 227.9593 Evaluate side-chains 253 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 234 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 275 ASN C 275 ASN E 148 HIS H 93 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.176162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.136010 restraints weight = 52980.763| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 4.62 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12225 Z= 0.133 Angle : 0.549 8.856 16442 Z= 0.279 Chirality : 0.039 0.138 1778 Planarity : 0.004 0.045 2066 Dihedral : 16.885 152.221 2161 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.67 % Allowed : 13.18 % Favored : 84.15 % 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: 3.27 (0.23), residues: 1422 helix: 2.81 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -0.97 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 159 TYR 0.010 0.002 TYR E 67 PHE 0.009 0.002 PHE C 272 TRP 0.015 0.002 TRP C 200 HIS 0.004 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00285 (12225) covalent geometry : angle 0.54852 (16442) hydrogen bonds : bond 0.04886 ( 878) hydrogen bonds : angle 3.32509 ( 2644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 0.399 Fit side-chains REVERT: A 108 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6201 (mt) REVERT: A 119 GLU cc_start: 0.5680 (tm-30) cc_final: 0.5306 (tm-30) REVERT: A 163 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6202 (mt-10) REVERT: A 172 GLN cc_start: 0.4931 (mt0) cc_final: 0.4549 (mt0) REVERT: A 179 ASP cc_start: 0.7454 (p0) cc_final: 0.7140 (p0) REVERT: A 208 MET cc_start: 0.8084 (mtp) cc_final: 0.7668 (mtp) REVERT: A 271 ARG cc_start: 0.7132 (ttm110) cc_final: 0.6841 (mtm-85) REVERT: A 279 ASP cc_start: 0.6506 (m-30) cc_final: 0.6093 (t70) REVERT: B 108 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6417 (mt) REVERT: B 109 GLU cc_start: 0.5448 (mt-10) cc_final: 0.5218 (tt0) REVERT: B 119 GLU cc_start: 0.5593 (tm-30) cc_final: 0.5319 (tm-30) REVERT: B 123 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.5075 (tm-30) REVERT: B 163 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6396 (mt-10) REVERT: B 167 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6329 (tp) REVERT: B 169 GLN cc_start: 0.6434 (mt0) cc_final: 0.6138 (pt0) REVERT: B 271 ARG cc_start: 0.7108 (ttm110) cc_final: 0.6857 (mtm-85) REVERT: B 274 GLU cc_start: 0.7737 (tt0) cc_final: 0.7537 (tt0) REVERT: B 279 ASP cc_start: 0.6784 (m-30) cc_final: 0.6474 (m-30) REVERT: B 281 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.4432 (mpt) REVERT: B 283 MET cc_start: 0.3432 (mmm) cc_final: 0.2176 (ppp) REVERT: C 108 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6385 (mt) REVERT: C 109 GLU cc_start: 0.5462 (mt-10) cc_final: 0.5015 (tp30) REVERT: C 119 GLU cc_start: 0.5535 (tm-30) cc_final: 0.4578 (tp30) REVERT: C 123 GLU cc_start: 0.5719 (OUTLIER) cc_final: 0.5179 (tm-30) REVERT: C 162 GLU cc_start: 0.6578 (pt0) cc_final: 0.6270 (pt0) REVERT: C 163 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6378 (mt-10) REVERT: C 164 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6784 (mt-10) REVERT: C 177 LYS cc_start: 0.7191 (mtpp) cc_final: 0.6647 (mmtt) REVERT: C 179 ASP cc_start: 0.7405 (p0) cc_final: 0.7119 (p0) REVERT: C 271 ARG cc_start: 0.7109 (ttm110) cc_final: 0.6761 (mtm-85) REVERT: C 274 GLU cc_start: 0.7717 (tt0) cc_final: 0.7440 (tt0) REVERT: C 279 ASP cc_start: 0.6712 (m-30) cc_final: 0.6474 (m-30) REVERT: D 108 LEU cc_start: 0.6734 (mm) cc_final: 0.6341 (mt) REVERT: D 109 GLU cc_start: 0.5242 (mt-10) cc_final: 0.4783 (tp30) REVERT: D 119 GLU cc_start: 0.5460 (tm-30) cc_final: 0.5221 (tm-30) REVERT: D 177 LYS cc_start: 0.7103 (mtpp) cc_final: 0.6592 (mmtt) REVERT: D 179 ASP cc_start: 0.7424 (p0) cc_final: 0.7106 (p0) REVERT: D 271 ARG cc_start: 0.7130 (ttm110) cc_final: 0.6877 (mtm-85) REVERT: D 279 ASP cc_start: 0.6758 (m-30) cc_final: 0.6456 (m-30) REVERT: E 143 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6900 (tt0) REVERT: E 147 HIS cc_start: 0.7551 (t-90) cc_final: 0.7306 (t-170) REVERT: E 155 THR cc_start: 0.6776 (m) cc_final: 0.6372 (t) REVERT: E 208 ARG cc_start: 0.7400 (mtt180) cc_final: 0.7180 (mtt90) REVERT: F 147 HIS cc_start: 0.7479 (t-90) cc_final: 0.7187 (t-170) REVERT: F 215 GLU cc_start: 0.7609 (pt0) cc_final: 0.7232 (pt0) REVERT: G 143 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6954 (mt-10) REVERT: G 147 HIS cc_start: 0.7599 (t-90) cc_final: 0.7323 (t-170) REVERT: G 148 HIS cc_start: 0.7288 (t70) cc_final: 0.7045 (t-170) REVERT: G 155 THR cc_start: 0.6823 (m) cc_final: 0.6396 (t) REVERT: G 215 GLU cc_start: 0.7550 (pt0) cc_final: 0.7224 (pt0) REVERT: H 143 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6882 (tt0) REVERT: H 147 HIS cc_start: 0.7540 (t-90) cc_final: 0.7281 (t-170) REVERT: H 148 HIS cc_start: 0.7231 (t70) cc_final: 0.7028 (t-170) outliers start: 30 outliers final: 12 residues processed: 256 average time/residue: 0.8210 time to fit residues: 222.9104 Evaluate side-chains 258 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 275 ASN B 275 ASN C 275 ASN E 93 HIS E 148 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.176943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136968 restraints weight = 55550.697| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 4.93 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12225 Z= 0.114 Angle : 0.509 8.918 16442 Z= 0.261 Chirality : 0.037 0.115 1778 Planarity : 0.004 0.048 2066 Dihedral : 16.358 141.845 2161 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.33 % Allowed : 14.04 % Favored : 83.63 % 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: 3.47 (0.23), residues: 1422 helix: 2.98 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -1.00 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 159 TYR 0.009 0.001 TYR E 67 PHE 0.015 0.002 PHE D 110 TRP 0.012 0.001 TRP B 240 HIS 0.004 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00235 (12225) covalent geometry : angle 0.50923 (16442) hydrogen bonds : bond 0.04364 ( 878) hydrogen bonds : angle 3.21213 ( 2644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 0.424 Fit side-chains REVERT: A 108 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6126 (mt) REVERT: A 119 GLU cc_start: 0.5490 (tm-30) cc_final: 0.5161 (tm-30) REVERT: A 163 GLU cc_start: 0.6428 (mt-10) cc_final: 0.6153 (mt-10) REVERT: A 172 GLN cc_start: 0.4916 (mt0) cc_final: 0.4429 (mt0) REVERT: A 179 ASP cc_start: 0.7456 (p0) cc_final: 0.7131 (p0) REVERT: A 208 MET cc_start: 0.7942 (mtp) cc_final: 0.7554 (mtp) REVERT: A 271 ARG cc_start: 0.7088 (ttm110) cc_final: 0.6773 (mtm-85) REVERT: A 276 ARG cc_start: 0.7255 (mmm160) cc_final: 0.6861 (mtp85) REVERT: A 279 ASP cc_start: 0.6409 (m-30) cc_final: 0.5996 (t70) REVERT: B 108 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6393 (mt) REVERT: B 109 GLU cc_start: 0.5463 (mt-10) cc_final: 0.5202 (tt0) REVERT: B 119 GLU cc_start: 0.5584 (tm-30) cc_final: 0.4614 (tp30) REVERT: B 123 GLU cc_start: 0.5665 (OUTLIER) cc_final: 0.5118 (tm-30) REVERT: B 163 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6261 (mt-10) REVERT: B 169 GLN cc_start: 0.6396 (mt0) cc_final: 0.6077 (pt0) REVERT: B 271 ARG cc_start: 0.7067 (ttm110) cc_final: 0.6714 (mtm-85) REVERT: B 274 GLU cc_start: 0.7749 (tt0) cc_final: 0.7534 (tt0) REVERT: B 279 ASP cc_start: 0.6736 (m-30) cc_final: 0.6432 (m-30) REVERT: B 281 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.4583 (mpt) REVERT: B 283 MET cc_start: 0.3286 (mmm) cc_final: 0.2126 (ppp) REVERT: C 108 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6374 (mt) REVERT: C 109 GLU cc_start: 0.5447 (mt-10) cc_final: 0.4959 (tp30) REVERT: C 119 GLU cc_start: 0.5431 (tm-30) cc_final: 0.4510 (tp30) REVERT: C 123 GLU cc_start: 0.5627 (OUTLIER) cc_final: 0.5072 (tm-30) REVERT: C 162 GLU cc_start: 0.6574 (pt0) cc_final: 0.6231 (pt0) REVERT: C 163 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6451 (mt-10) REVERT: C 164 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6760 (mt-10) REVERT: C 177 LYS cc_start: 0.7094 (mtpp) cc_final: 0.6566 (mmtt) REVERT: C 179 ASP cc_start: 0.7404 (p0) cc_final: 0.7107 (p0) REVERT: C 271 ARG cc_start: 0.7085 (ttm110) cc_final: 0.6733 (mtm-85) REVERT: C 274 GLU cc_start: 0.7694 (tt0) cc_final: 0.7440 (tt0) REVERT: C 279 ASP cc_start: 0.6675 (m-30) cc_final: 0.6440 (m-30) REVERT: D 109 GLU cc_start: 0.5245 (mt-10) cc_final: 0.4693 (tp30) REVERT: D 119 GLU cc_start: 0.5438 (tm-30) cc_final: 0.5229 (tm-30) REVERT: D 123 GLU cc_start: 0.5389 (tt0) cc_final: 0.4825 (tm-30) REVERT: D 177 LYS cc_start: 0.7083 (mtpp) cc_final: 0.6585 (mmtt) REVERT: D 179 ASP cc_start: 0.7471 (p0) cc_final: 0.7162 (p0) REVERT: D 271 ARG cc_start: 0.7130 (ttm110) cc_final: 0.6862 (mtm-85) REVERT: D 279 ASP cc_start: 0.6724 (m-30) cc_final: 0.6430 (m-30) REVERT: E 143 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6889 (tt0) REVERT: E 147 HIS cc_start: 0.7498 (t-90) cc_final: 0.7258 (t-170) REVERT: E 155 THR cc_start: 0.6495 (m) cc_final: 0.6214 (t) REVERT: E 208 ARG cc_start: 0.7388 (mtt180) cc_final: 0.7176 (mtt90) REVERT: E 215 GLU cc_start: 0.7684 (pt0) cc_final: 0.7260 (pt0) REVERT: F 143 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6869 (mt-10) REVERT: F 147 HIS cc_start: 0.7419 (t-90) cc_final: 0.7135 (t-170) REVERT: F 148 HIS cc_start: 0.7215 (t70) cc_final: 0.6948 (t-170) REVERT: F 155 THR cc_start: 0.6435 (m) cc_final: 0.6023 (t) REVERT: F 215 GLU cc_start: 0.7565 (pt0) cc_final: 0.7201 (pt0) REVERT: G 135 MET cc_start: 0.6890 (mmt) cc_final: 0.6560 (mmm) REVERT: G 143 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6905 (tt0) REVERT: G 147 HIS cc_start: 0.7569 (t-90) cc_final: 0.7292 (t-170) REVERT: G 148 HIS cc_start: 0.7189 (t70) cc_final: 0.6938 (t-170) REVERT: G 155 THR cc_start: 0.6641 (m) cc_final: 0.6340 (t) REVERT: G 215 GLU cc_start: 0.7519 (pt0) cc_final: 0.7178 (pt0) REVERT: H 143 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6863 (tt0) REVERT: H 147 HIS cc_start: 0.7441 (t-90) cc_final: 0.7176 (t-170) REVERT: H 148 HIS cc_start: 0.7178 (t70) cc_final: 0.6943 (t-170) REVERT: H 215 GLU cc_start: 0.7521 (pt0) cc_final: 0.7211 (pt0) outliers start: 26 outliers final: 10 residues processed: 257 average time/residue: 0.8386 time to fit residues: 228.3466 Evaluate side-chains 256 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 238 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 9 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 120 optimal weight: 0.0570 chunk 38 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 overall best weight: 2.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 275 ASN B 252 ASN B 275 ASN C 275 ASN E 148 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.175845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135762 restraints weight = 47808.392| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 4.36 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12225 Z= 0.152 Angle : 0.589 8.864 16442 Z= 0.299 Chirality : 0.040 0.167 1778 Planarity : 0.005 0.042 2066 Dihedral : 16.989 145.272 2161 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.41 % Allowed : 13.78 % Favored : 83.81 % 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: 3.14 (0.23), residues: 1422 helix: 2.70 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -1.00 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 46 TYR 0.011 0.002 TYR G 212 PHE 0.017 0.002 PHE D 110 TRP 0.016 0.002 TRP D 200 HIS 0.005 0.002 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00338 (12225) covalent geometry : angle 0.58872 (16442) hydrogen bonds : bond 0.05192 ( 878) hydrogen bonds : angle 3.43104 ( 2644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 108 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6287 (mt) REVERT: A 119 GLU cc_start: 0.5509 (tm-30) cc_final: 0.5176 (tm-30) REVERT: A 163 GLU cc_start: 0.6544 (mt-10) cc_final: 0.6279 (mt-10) REVERT: A 172 GLN cc_start: 0.4825 (mt0) cc_final: 0.4355 (mt0) REVERT: A 179 ASP cc_start: 0.7450 (p0) cc_final: 0.7134 (p0) REVERT: A 208 MET cc_start: 0.8027 (mtp) cc_final: 0.7650 (mtp) REVERT: A 271 ARG cc_start: 0.7157 (ttm110) cc_final: 0.6879 (mtm-85) REVERT: A 279 ASP cc_start: 0.6417 (m-30) cc_final: 0.6092 (t70) REVERT: B 108 LEU cc_start: 0.6737 (mm) cc_final: 0.6391 (mt) REVERT: B 119 GLU cc_start: 0.5721 (tm-30) cc_final: 0.4802 (tp30) REVERT: B 123 GLU cc_start: 0.5767 (OUTLIER) cc_final: 0.5139 (tm-30) REVERT: B 163 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6365 (mt-10) REVERT: B 169 GLN cc_start: 0.6452 (mt0) cc_final: 0.6176 (pt0) REVERT: B 271 ARG cc_start: 0.7132 (ttm110) cc_final: 0.6876 (mtm-85) REVERT: B 274 GLU cc_start: 0.7729 (tt0) cc_final: 0.7468 (tt0) REVERT: B 279 ASP cc_start: 0.6673 (m-30) cc_final: 0.6276 (t70) REVERT: B 281 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.4274 (mpt) REVERT: B 283 MET cc_start: 0.3402 (mmm) cc_final: 0.2262 (ppp) REVERT: C 109 GLU cc_start: 0.5538 (mt-10) cc_final: 0.5024 (tp30) REVERT: C 119 GLU cc_start: 0.5576 (tm-30) cc_final: 0.4652 (tp30) REVERT: C 123 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.5168 (tm-30) REVERT: C 162 GLU cc_start: 0.6539 (pt0) cc_final: 0.6235 (pt0) REVERT: C 163 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6439 (mt-10) REVERT: C 177 LYS cc_start: 0.7195 (mtpp) cc_final: 0.6666 (mmtt) REVERT: C 179 ASP cc_start: 0.7442 (p0) cc_final: 0.7147 (p0) REVERT: C 208 MET cc_start: 0.8032 (mtp) cc_final: 0.7732 (mtp) REVERT: C 271 ARG cc_start: 0.7121 (ttm110) cc_final: 0.6828 (mtm-85) REVERT: C 274 GLU cc_start: 0.7756 (tt0) cc_final: 0.7475 (tt0) REVERT: C 279 ASP cc_start: 0.6669 (m-30) cc_final: 0.6429 (m-30) REVERT: D 108 LEU cc_start: 0.6640 (mm) cc_final: 0.6277 (mt) REVERT: D 109 GLU cc_start: 0.5381 (mt-10) cc_final: 0.4888 (tp30) REVERT: D 119 GLU cc_start: 0.5515 (tm-30) cc_final: 0.5303 (tm-30) REVERT: D 123 GLU cc_start: 0.5275 (tt0) cc_final: 0.4835 (tm-30) REVERT: D 177 LYS cc_start: 0.7128 (mtpp) cc_final: 0.6631 (mmtt) REVERT: D 179 ASP cc_start: 0.7429 (p0) cc_final: 0.7139 (p0) REVERT: D 208 MET cc_start: 0.7969 (mtp) cc_final: 0.7641 (mtp) REVERT: D 271 ARG cc_start: 0.7153 (ttm110) cc_final: 0.6900 (mtm-85) REVERT: E 143 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6893 (tt0) REVERT: E 147 HIS cc_start: 0.7572 (t-90) cc_final: 0.7312 (t-170) REVERT: E 155 THR cc_start: 0.6587 (m) cc_final: 0.6324 (t) REVERT: F 147 HIS cc_start: 0.7544 (t-90) cc_final: 0.7247 (t-170) REVERT: F 148 HIS cc_start: 0.7240 (t70) cc_final: 0.6974 (t-170) REVERT: F 155 THR cc_start: 0.6580 (m) cc_final: 0.6156 (t) REVERT: F 215 GLU cc_start: 0.7652 (pt0) cc_final: 0.7334 (pt0) REVERT: G 143 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6923 (mt-10) REVERT: G 147 HIS cc_start: 0.7659 (t-90) cc_final: 0.7369 (t-170) REVERT: G 148 HIS cc_start: 0.7214 (t70) cc_final: 0.6999 (t-170) REVERT: G 155 THR cc_start: 0.6676 (m) cc_final: 0.6344 (t) REVERT: H 147 HIS cc_start: 0.7565 (t-90) cc_final: 0.7294 (t-170) outliers start: 27 outliers final: 13 residues processed: 238 average time/residue: 0.8311 time to fit residues: 209.7040 Evaluate side-chains 239 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 79 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 275 ASN B 275 ASN C 275 ASN E 148 HIS H 148 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.177300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.137448 restraints weight = 50769.260| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 4.47 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12225 Z= 0.117 Angle : 0.518 8.871 16442 Z= 0.265 Chirality : 0.037 0.125 1778 Planarity : 0.004 0.048 2066 Dihedral : 16.519 144.270 2161 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.81 % Allowed : 15.07 % Favored : 83.12 % 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: 3.42 (0.23), residues: 1422 helix: 2.94 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -0.99 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 159 TYR 0.009 0.001 TYR G 212 PHE 0.014 0.002 PHE D 110 TRP 0.012 0.001 TRP A 240 HIS 0.004 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00243 (12225) covalent geometry : angle 0.51788 (16442) hydrogen bonds : bond 0.04427 ( 878) hydrogen bonds : angle 3.26685 ( 2644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 237 time to evaluate : 0.469 Fit side-chains REVERT: A 108 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6200 (mt) REVERT: A 119 GLU cc_start: 0.5502 (tm-30) cc_final: 0.5229 (tm-30) REVERT: A 163 GLU cc_start: 0.6462 (mt-10) cc_final: 0.6178 (mt-10) REVERT: A 172 GLN cc_start: 0.5009 (mt0) cc_final: 0.4526 (mt0) REVERT: A 179 ASP cc_start: 0.7456 (p0) cc_final: 0.7138 (p0) REVERT: A 208 MET cc_start: 0.7978 (mtp) cc_final: 0.7603 (mtp) REVERT: A 271 ARG cc_start: 0.7143 (ttm110) cc_final: 0.6859 (mtm-85) REVERT: A 279 ASP cc_start: 0.6418 (m-30) cc_final: 0.6077 (t70) REVERT: B 119 GLU cc_start: 0.5792 (tm-30) cc_final: 0.4900 (tp30) REVERT: B 163 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6346 (mt-10) REVERT: B 169 GLN cc_start: 0.6452 (mt0) cc_final: 0.6160 (pt0) REVERT: B 271 ARG cc_start: 0.7093 (ttm110) cc_final: 0.6782 (mtm-85) REVERT: B 274 GLU cc_start: 0.7731 (tt0) cc_final: 0.7516 (tt0) REVERT: B 279 ASP cc_start: 0.6683 (m-30) cc_final: 0.6447 (m-30) REVERT: B 281 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.4527 (mpt) REVERT: B 283 MET cc_start: 0.3456 (mmm) cc_final: 0.2224 (ppp) REVERT: C 109 GLU cc_start: 0.5297 (mt-10) cc_final: 0.4820 (tp30) REVERT: C 119 GLU cc_start: 0.5576 (tm-30) cc_final: 0.4648 (tp30) REVERT: C 123 GLU cc_start: 0.5642 (OUTLIER) cc_final: 0.5114 (tm-30) REVERT: C 162 GLU cc_start: 0.6577 (pt0) cc_final: 0.6279 (pt0) REVERT: C 163 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6488 (mt-10) REVERT: C 164 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6768 (mt-10) REVERT: C 177 LYS cc_start: 0.7080 (mtpp) cc_final: 0.6583 (mmtt) REVERT: C 179 ASP cc_start: 0.7433 (p0) cc_final: 0.7135 (p0) REVERT: C 271 ARG cc_start: 0.7112 (ttm110) cc_final: 0.6820 (mtm-85) REVERT: C 274 GLU cc_start: 0.7714 (tt0) cc_final: 0.7467 (tt0) REVERT: C 279 ASP cc_start: 0.6613 (m-30) cc_final: 0.6413 (m-30) REVERT: C 281 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.5405 (mpt) REVERT: D 108 LEU cc_start: 0.6680 (mm) cc_final: 0.6316 (mt) REVERT: D 109 GLU cc_start: 0.5346 (mt-10) cc_final: 0.4849 (tp30) REVERT: D 123 GLU cc_start: 0.5292 (tt0) cc_final: 0.4807 (tm-30) REVERT: D 177 LYS cc_start: 0.7157 (mtpp) cc_final: 0.6682 (mmtt) REVERT: D 179 ASP cc_start: 0.7479 (p0) cc_final: 0.7185 (p0) REVERT: D 271 ARG cc_start: 0.7154 (ttm110) cc_final: 0.6780 (mtm-85) REVERT: E 76 ARG cc_start: 0.6898 (mtt180) cc_final: 0.6315 (mpp-170) REVERT: E 143 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6872 (tt0) REVERT: E 147 HIS cc_start: 0.7521 (t-90) cc_final: 0.7276 (t-170) REVERT: E 155 THR cc_start: 0.6474 (m) cc_final: 0.6231 (t) REVERT: E 215 GLU cc_start: 0.7705 (pt0) cc_final: 0.7257 (pt0) REVERT: F 143 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6866 (mt-10) REVERT: F 147 HIS cc_start: 0.7489 (t-90) cc_final: 0.7201 (t-170) REVERT: F 148 HIS cc_start: 0.7223 (t70) cc_final: 0.6991 (t-170) REVERT: F 155 THR cc_start: 0.6527 (m) cc_final: 0.6155 (t) REVERT: G 143 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6890 (tt0) REVERT: G 147 HIS cc_start: 0.7582 (t-90) cc_final: 0.7301 (t-170) REVERT: G 148 HIS cc_start: 0.7177 (t70) cc_final: 0.6920 (t-170) REVERT: G 155 THR cc_start: 0.6593 (m) cc_final: 0.6313 (t) REVERT: G 215 GLU cc_start: 0.7621 (pt0) cc_final: 0.7300 (pt0) REVERT: H 147 HIS cc_start: 0.7491 (t-90) cc_final: 0.7226 (t-170) outliers start: 20 outliers final: 11 residues processed: 246 average time/residue: 0.8744 time to fit residues: 228.1032 Evaluate side-chains 247 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 230 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 26 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 275 ASN B 275 ASN C 275 ASN E 148 HIS H 148 HIS H 204 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.177202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137023 restraints weight = 54030.154| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 4.83 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12225 Z= 0.119 Angle : 0.527 8.874 16442 Z= 0.269 Chirality : 0.037 0.134 1778 Planarity : 0.004 0.048 2066 Dihedral : 16.365 145.211 2161 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.64 % Allowed : 15.50 % Favored : 82.86 % 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: 3.42 (0.23), residues: 1422 helix: 2.93 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -0.98 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 159 TYR 0.010 0.001 TYR E 67 PHE 0.014 0.002 PHE D 110 TRP 0.013 0.002 TRP B 200 HIS 0.004 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00249 (12225) covalent geometry : angle 0.52750 (16442) hydrogen bonds : bond 0.04470 ( 878) hydrogen bonds : angle 3.28352 ( 2644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 234 time to evaluate : 0.454 Fit side-chains REVERT: A 108 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6135 (mt) REVERT: A 119 GLU cc_start: 0.5455 (tm-30) cc_final: 0.5188 (tm-30) REVERT: A 163 GLU cc_start: 0.6448 (mt-10) cc_final: 0.6162 (mt-10) REVERT: A 172 GLN cc_start: 0.5085 (mt0) cc_final: 0.4604 (mt0) REVERT: A 179 ASP cc_start: 0.7481 (p0) cc_final: 0.7162 (p0) REVERT: A 208 MET cc_start: 0.7933 (mtp) cc_final: 0.7527 (mtp) REVERT: A 271 ARG cc_start: 0.7140 (ttm110) cc_final: 0.6847 (mtm-85) REVERT: A 279 ASP cc_start: 0.6391 (m-30) cc_final: 0.6005 (t70) REVERT: B 108 LEU cc_start: 0.6687 (mm) cc_final: 0.6322 (mt) REVERT: B 119 GLU cc_start: 0.5662 (tm-30) cc_final: 0.4770 (tp30) REVERT: B 163 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6253 (mt-10) REVERT: B 169 GLN cc_start: 0.6418 (mt0) cc_final: 0.6110 (pt0) REVERT: B 271 ARG cc_start: 0.7080 (ttm110) cc_final: 0.6771 (mtm-85) REVERT: B 274 GLU cc_start: 0.7726 (tt0) cc_final: 0.7518 (tt0) REVERT: B 281 MET cc_start: 0.6324 (OUTLIER) cc_final: 0.4485 (mpt) REVERT: B 283 MET cc_start: 0.3581 (mmm) cc_final: 0.2364 (ppp) REVERT: C 109 GLU cc_start: 0.5323 (mt-10) cc_final: 0.4800 (tp30) REVERT: C 119 GLU cc_start: 0.5509 (tm-30) cc_final: 0.4590 (tp30) REVERT: C 123 GLU cc_start: 0.5673 (OUTLIER) cc_final: 0.5090 (tm-30) REVERT: C 162 GLU cc_start: 0.6540 (pt0) cc_final: 0.6233 (pt0) REVERT: C 163 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6394 (mt-10) REVERT: C 164 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6751 (mt-10) REVERT: C 177 LYS cc_start: 0.7057 (mtpp) cc_final: 0.6557 (mmtt) REVERT: C 179 ASP cc_start: 0.7425 (p0) cc_final: 0.7127 (p0) REVERT: C 271 ARG cc_start: 0.7105 (ttm110) cc_final: 0.6804 (mtm-85) REVERT: C 274 GLU cc_start: 0.7705 (tt0) cc_final: 0.7444 (tt0) REVERT: C 279 ASP cc_start: 0.6602 (m-30) cc_final: 0.6399 (m-30) REVERT: D 108 LEU cc_start: 0.6616 (mm) cc_final: 0.6234 (mt) REVERT: D 109 GLU cc_start: 0.5355 (mt-10) cc_final: 0.4807 (tp30) REVERT: D 123 GLU cc_start: 0.5325 (tt0) cc_final: 0.4801 (tm-30) REVERT: D 177 LYS cc_start: 0.7087 (mtpp) cc_final: 0.6612 (mmtt) REVERT: D 179 ASP cc_start: 0.7485 (p0) cc_final: 0.7175 (p0) REVERT: D 271 ARG cc_start: 0.7139 (ttm110) cc_final: 0.6756 (mtm-85) REVERT: E 76 ARG cc_start: 0.6925 (mtt180) cc_final: 0.6276 (mpp-170) REVERT: E 143 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6884 (tt0) REVERT: E 147 HIS cc_start: 0.7508 (t-90) cc_final: 0.7264 (t-170) REVERT: E 155 THR cc_start: 0.6575 (m) cc_final: 0.6315 (t) REVERT: E 215 GLU cc_start: 0.7700 (pt0) cc_final: 0.7280 (pt0) REVERT: F 143 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6909 (mt-10) REVERT: F 147 HIS cc_start: 0.7468 (t-90) cc_final: 0.7170 (t-170) REVERT: F 148 HIS cc_start: 0.7194 (t70) cc_final: 0.6957 (t-170) REVERT: F 155 THR cc_start: 0.6448 (m) cc_final: 0.6091 (t) REVERT: G 143 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6946 (mt-10) REVERT: G 147 HIS cc_start: 0.7588 (t-90) cc_final: 0.7310 (t-170) REVERT: G 148 HIS cc_start: 0.7209 (t70) cc_final: 0.6943 (t-170) REVERT: G 155 THR cc_start: 0.6541 (m) cc_final: 0.6263 (t) REVERT: G 215 GLU cc_start: 0.7623 (pt0) cc_final: 0.7316 (pt0) REVERT: H 143 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6855 (mt-10) REVERT: H 147 HIS cc_start: 0.7483 (t-90) cc_final: 0.7225 (t-170) outliers start: 18 outliers final: 11 residues processed: 242 average time/residue: 0.8686 time to fit residues: 222.8778 Evaluate side-chains 247 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 66 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 137 optimal weight: 0.0050 chunk 28 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 3 optimal weight: 0.0010 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 275 ASN B 275 ASN C 275 ASN E 148 HIS H 148 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.178030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139263 restraints weight = 46909.392| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 4.64 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12225 Z= 0.109 Angle : 0.512 9.003 16442 Z= 0.261 Chirality : 0.037 0.123 1778 Planarity : 0.004 0.051 2066 Dihedral : 16.027 146.285 2161 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.29 % Allowed : 15.76 % Favored : 82.95 % 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: 3.54 (0.23), residues: 1422 helix: 3.03 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -1.01 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 159 TYR 0.009 0.001 TYR E 67 PHE 0.013 0.001 PHE D 110 TRP 0.013 0.001 TRP B 240 HIS 0.004 0.001 HIS F 57 Details of bonding type rmsd covalent geometry : bond 0.00224 (12225) covalent geometry : angle 0.51162 (16442) hydrogen bonds : bond 0.04186 ( 878) hydrogen bonds : angle 3.22004 ( 2644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 234 time to evaluate : 0.539 Fit side-chains REVERT: A 119 GLU cc_start: 0.5465 (tm-30) cc_final: 0.5211 (tm-30) REVERT: A 163 GLU cc_start: 0.6437 (mt-10) cc_final: 0.6163 (mt-10) REVERT: A 172 GLN cc_start: 0.5061 (mt0) cc_final: 0.4582 (mt0) REVERT: A 179 ASP cc_start: 0.7473 (p0) cc_final: 0.7146 (p0) REVERT: A 271 ARG cc_start: 0.7105 (ttm110) cc_final: 0.6818 (mtm-85) REVERT: A 279 ASP cc_start: 0.6478 (m-30) cc_final: 0.5975 (t70) REVERT: B 108 LEU cc_start: 0.6633 (mm) cc_final: 0.6265 (mt) REVERT: B 119 GLU cc_start: 0.5679 (tm-30) cc_final: 0.4781 (tp30) REVERT: B 163 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6274 (mt-10) REVERT: B 169 GLN cc_start: 0.6413 (mt0) cc_final: 0.6115 (pt0) REVERT: B 271 ARG cc_start: 0.7045 (ttm110) cc_final: 0.6702 (mtm-85) REVERT: B 281 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.4574 (mpt) REVERT: B 283 MET cc_start: 0.3504 (mmm) cc_final: 0.2470 (ppp) REVERT: C 109 GLU cc_start: 0.5344 (mt-10) cc_final: 0.4768 (tp30) REVERT: C 119 GLU cc_start: 0.5605 (tm-30) cc_final: 0.4760 (tp30) REVERT: C 123 GLU cc_start: 0.5574 (OUTLIER) cc_final: 0.5037 (tm-30) REVERT: C 162 GLU cc_start: 0.6586 (pt0) cc_final: 0.6262 (pt0) REVERT: C 163 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6408 (mt-10) REVERT: C 164 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6705 (mt-10) REVERT: C 177 LYS cc_start: 0.7047 (mtpp) cc_final: 0.6560 (mmtt) REVERT: C 179 ASP cc_start: 0.7406 (p0) cc_final: 0.7105 (p0) REVERT: C 271 ARG cc_start: 0.7084 (ttm110) cc_final: 0.6765 (mtm-85) REVERT: C 274 GLU cc_start: 0.7707 (tt0) cc_final: 0.7444 (tt0) REVERT: C 279 ASP cc_start: 0.6617 (m-30) cc_final: 0.6096 (t70) REVERT: D 108 LEU cc_start: 0.6595 (mm) cc_final: 0.6230 (mt) REVERT: D 109 GLU cc_start: 0.5303 (mt-10) cc_final: 0.4792 (tp30) REVERT: D 123 GLU cc_start: 0.5283 (tt0) cc_final: 0.4765 (tm-30) REVERT: D 177 LYS cc_start: 0.7022 (mtpp) cc_final: 0.6575 (mmtt) REVERT: D 179 ASP cc_start: 0.7512 (p0) cc_final: 0.7208 (p0) REVERT: D 271 ARG cc_start: 0.7147 (ttm110) cc_final: 0.6759 (mtm-85) REVERT: E 76 ARG cc_start: 0.6887 (mtt180) cc_final: 0.6251 (mpp-170) REVERT: E 143 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6833 (tt0) REVERT: E 147 HIS cc_start: 0.7513 (t-90) cc_final: 0.7278 (t-170) REVERT: E 155 THR cc_start: 0.6559 (m) cc_final: 0.6313 (t) REVERT: E 215 GLU cc_start: 0.7680 (pt0) cc_final: 0.7266 (pt0) REVERT: F 143 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6897 (mt-10) REVERT: F 147 HIS cc_start: 0.7399 (t-90) cc_final: 0.7124 (t-170) REVERT: F 148 HIS cc_start: 0.7136 (t70) cc_final: 0.6892 (t-170) REVERT: F 155 THR cc_start: 0.6458 (m) cc_final: 0.6132 (t) REVERT: F 166 GLU cc_start: 0.5667 (mm-30) cc_final: 0.5432 (mt-10) REVERT: G 135 MET cc_start: 0.6891 (mmt) cc_final: 0.6568 (mmm) REVERT: G 143 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6905 (mt-10) REVERT: G 147 HIS cc_start: 0.7568 (t-90) cc_final: 0.7288 (t-170) REVERT: G 148 HIS cc_start: 0.7217 (t70) cc_final: 0.6946 (t-170) REVERT: G 155 THR cc_start: 0.6506 (m) cc_final: 0.6251 (t) REVERT: G 215 GLU cc_start: 0.7519 (pt0) cc_final: 0.7213 (pt0) REVERT: H 135 MET cc_start: 0.6853 (mmt) cc_final: 0.6491 (mmm) REVERT: H 143 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6830 (mt-10) REVERT: H 147 HIS cc_start: 0.7434 (t-90) cc_final: 0.7206 (t-170) outliers start: 14 outliers final: 9 residues processed: 240 average time/residue: 0.8706 time to fit residues: 221.6626 Evaluate side-chains 243 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 230 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 120 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 275 ASN B 275 ASN C 275 ASN E 148 HIS H 148 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.177577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135675 restraints weight = 49120.829| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 4.84 r_work: 0.3079 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12225 Z= 0.115 Angle : 0.525 9.498 16442 Z= 0.267 Chirality : 0.037 0.135 1778 Planarity : 0.004 0.049 2066 Dihedral : 15.922 145.801 2161 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.38 % Allowed : 15.85 % Favored : 82.77 % 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: 3.48 (0.23), residues: 1422 helix: 2.98 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -1.00 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 159 TYR 0.010 0.002 TYR E 67 PHE 0.013 0.002 PHE D 110 TRP 0.013 0.001 TRP B 200 HIS 0.004 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00240 (12225) covalent geometry : angle 0.52453 (16442) hydrogen bonds : bond 0.04379 ( 878) hydrogen bonds : angle 3.26464 ( 2644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5047.16 seconds wall clock time: 86 minutes 26.69 seconds (5186.69 seconds total)